Biology subjects

Kirkpatrick, L.

Publications and source records attributed to Kirkpatrick, L..

8 recordsLinked to original sources

bioRxiv2025

Validating the Nordic Thingy:53 as an Accessible Tool for Equine Behavioural Analysis using Edge AI

Understanding animal movement and behaviour is integral to ensuring welfare needs are met, a central goal within the scientific community. Among domesticated animals, equids are unique; they serve as both companion and production animals, with estimates showing around 112 million working equids supporting 600 million people worldwide. Furthermore, the horse sport industry is a global multi-billion-dollar sector. However, these roles inevitably expose horses to potential physical and psychological harm. Consequently, being able to monitor behaviour accurately is critical to meeting their welfare needs. Here, we describe the design and evaluation of machine learning models capable of recognizing equine gaits and (semi-)natural behaviours using the Edge AI platform, Edge Impulse. Accelerometer motion data were collected using the Nordic Thingy:53 prototyping platform located on the chest of the horse. Both gaits and behaviours were detected with high mean training and testing accuracies (>95.00%), including idle, walk, trot, canter, fly-twitch, eating hay, head down or up, grazing, and rolling. While transformation types (Fast Fourier Transform (FFT) vs. Wavelet transform) were compared, they were not found to have a drastic effect on model performance. Instead, model accuracy and sensitivity were most impacted by the volume of training data included. This suggests that while transformations may refine model selection, sufficient training data is the single most important factor in defining effective Edge AI models. This study extends the evidence detailing the utility of accelerometers for equine movement and demonstrates that the accessible Nordic Thingy:53 platform can be used to develop highly accurate models for behavioural analysis. This is an important first step towards building effective monitoring methods that can recognise subtle behavioural changes that indicate alterations to emotional or physical states in equines.

animal behavior and cognition↗

bioRxiv2025

Microparasite prevalence in Southern giant pouched rats (Cricetomys ansorgei) in Morogoro, Tanzania.

Rodents play a critical role in the transmission of zoonotic pathogens, with environmental changes and increasing human-wildlife interactions further amplifying disease spillover risks. Cricetomys spp., commonly found in both human dwellings and agricultural fields, are frequently hunted for consumption, potentially facilitating pathogen transmission. However, their roles in pathogen transmission and disease ecology remain poorly understood. This study investigated the prevalence of three microparasite genera, i.e., Bartonella, Hepatozoon, and Anaplasma, in Cricetomys spp. from Morogoro, Tanzania. We observed a prevalence of 71.9% for Bartonella, 17.5% for Hepatozoon, and 1.8% for Anaplasma. To our knowledge, this is the first study to investigate Bartonella, Hepatozoon, and Anaplasma in Cricetomys spp. in Tanzania. Furthermore, preliminary results indicate that Bartonella infection prevalence is influenced by habitat type, with a significantly higher prevalence observed in rural areas compared to urban areas. This study underscores the potential role of Cricetomys spp. as important reservoirs of infectious diseases.

ecology↗

bioRxiv2024

First report of astroviruses in Tanzanian bats

Emerging and re-emerging infectious diseases have posed significant global health threats, with many attributed to zoonotic RNA viruses. These pathogens can, under some conditions, cross species barriers, facilitating transmission from animal hosts to humans. Bats, characterised by unique physiological and ecological features, and remarkable species diversity, are recognized to host numerous viruses with cross-species transmission potential. This study aimed to investigate the presence of RNA viruses from a broad diversity of Tanzanian bats while valorising archived biological samples. RNA was extracted from 125 samples (28 faeces and 97 oral swabs) of 17 bat species, followed by PCR amplification targeting five distinct viral genera (Filovirus, Coronavirus, Hantavirus, Paramyxovirus and Astrovirus). Overall, 1.6 % (3/125) of the samples from two bat species (Scotophilus dinganii and Miniopterus fraterculus) tested positive for astrovirus, with the coinfection of one bat with two AstV strains. No samples tested positive for Filovirus, Coronavirus, Hantavirus and Paramyxovirus. Phylogenetic analysis based on RNA-dependent RNA polymerase sequences revealed these sequences are respectively clustering with astroviruses detected in other bat species from the genus Scotophilus from East Asia and with astroviruses detected in Miniopterus bats from Africa and Asia. Altogether, these results are the first report of astroviruses in Tanzanian bats.

molecular biology↗

bioRxiv2023

The pGinger family of expression plasmids

The pGinger suite of expression plasmids comprises 43 plasmids that will enable precise constitutive and inducible gene expression in a wide range of gram-negative bacterial species. Constitutive vectors are composed of 16 synthetic constitutive promoters upstream of RFP, with a broad host range BBR1 origin and a kanamycin resistance marker. The family also has seven inducible systems (Jungle Express, Psal/NahR, Pm/XylS, Prha/RhaS, LacO1/LacI, LacUV5/LacI, and Ptet/TetR) controlling RFP expression on BBR1/kanamycin plasmid backbones. For four of these inducible systems (Jungle Express, Psal/NahR, LacO1/LacI, and Ptet/TetR), we created variants that utilize the RK2 origin and spectinomycin or gentamicin selection. Relevant RFP expression and growth data have been collected in the model bacterium Escherichia coli as well as Pseudomonas putida. All pGinger vectors are available via the Joint BioEnergy Institute (JBEI) Public Registry.

synthetic biology↗

bioRxiv2022

Incorporating space in hierarchical capture mark recapture models: can we better capture variance?

Capture mark recapture (CMR) models allow the estimation of various components of animal populations, such as survival and recapture probabilities. In recent years, incorporating the spatial distribution of the devices used to detect an animals presence has become possible. By incorporating spatial information, we explicitly acknowledge the fact that there will be spatial structuring in the ecological processes which give rise to the capture data. Individual detection probability is not heterogeneous for a range of different reasons, for example the location of traps within an individuals home range, the environmental context around the trap or the individual characteristics of an animal such as its age. Spatial capture recapture models incorporate this heterogeneity by including the spatial coordinates of traps, data which is often already collected in standard CMR approaches. Here, we compared how the inclusion of spatial data changed estimations of survival, detection probability, and to some extent the probability of seroconversion to a common arenavirus, using the multimammate mouse as our model system. We used a Bayesian framework to develop non spatial, partially spatial and fully spatial models alongside multievent CMR models. First, we used simulations to test whether certain parameters were sensitive to starting parameters, and whether models were able to return the expected values. Then we applied the non-spatial, partially spatial and fully spatial models to a real dataset. We found that bias and precision were similar for the three different model types, with simulations always returning estimates within the 95% credible intervals. When applying our models to the real data set, we found that the non-spatial model predicted a lower survival of individuals exposed to Morogoro virus (MORV) compared to unexposed individuals, yet in the spatial model survival between exposed and non-exposed individuals was the same. This suggests that the non-spatial model underestimated the survival of seropositive individuals, most likely due to an age effect. We suggest that spatial coordinates of traps should always be recorded when carrying out CMR and spatially explicit methods of analysis should be used whenever possible, particularly as incorporating spatial variation may more easily capture ecological processes without the need for additional data collection that can be challenging to acquire with wild animals.

ecology↗

bioRxiv2021

ProxLogs: Miniaturised proximity loggers for monitoring association behaviour in small mammals

O_LIThe ability to monitor associations between wild animals is essential for understanding the processes governing gene transfer, information transfer, competition, predation and disease transmission. C_LIO_LIUntil recently, such insights have been confined to large, visible or captive animals. However, the rapid development of miniature sensors for consumer electronics is allowing ecologists to monitor the natural world in ways previously considered impossible. C_LIO_LIHere we describe miniature (<1g) proximity loggers we have developed that use Bluetooth Low Energy transmission to register contacts between individuals. Our loggers are open source, low cost, rechargeable, able to store up to 2000 contacts, can be programmed in situ and can download data remotely or through a mobile phone application, increasing their utility in remote areas or with species which are challenging to recapture. C_LIO_LIWe successfully trialled our loggers in a range of field realistic conditions, demonstrating that Bluetooth Low Energy is capable of logging associations in structurally complex habitats, and that changes in received signal strength can be equated to short range changes in distance between loggers. Furthermore, we tested the system on starlings (Sturnidae vulgaris). C_LIO_LIThe ability to include other sensors is retained in our prototypes, allowing for the potential integration of physiological and behavioural inference into social networks derived from our approach. Due to its open source nature, small size, flexibility of use and the active research currently being undertaken with Bluetooth Low Energy, we believe that our approach is a valuable addition to the biologging toolkit. C_LI

animal behavior and cognition↗

bioRxiv2020

Evaluation of nafamostat mesylate safety and inhibition of SARS-CoV-2 replication using a 3-dimensional human airway epithelia model

In the current COVID-19 pandemic context, Ensysce and its subsidiary Covistat have been working to repurpose nafamostat mesylate as an effective oral and inhalation treatment against SARS-CoV-2 infection. Prior reports used cell lines to demonstrate the antiviral potential of nafamostat against coronaviral infections and determined its mechanism of action through inhibition of transmembrane protease serine 2 (TMPRSS2). We selected a biologically relevant pre-clinical experimental model of SARS-CoV-2 lung infection using a 3D human reconstituted airway epithelial model of nasal origin to characterize the effects of nafamostat on tissue-level cellular ultrastructure and viral infection kinetics. Our results confirm the not only the relevance of this model for the preclinical evaluation of safety and efficacy of antiviral candidates, but also the highly potent nature of nafamostat SARS-CoV-2 antiviral activity. The studies described herein provided evidence demonstrating the therapeutic potential of nafamostat against COVID-19, as well as its safety upon exposure to lung airway cellular. One Sentence SummaryUsing a human airway model, study demonstrates the powerful inhibitory effect of nafamostat on SARS-CoV-2 genome copy detection when applied apically.

cell biology↗

bioRxiv2018

Patterns of recurrence after curative-intent surgery for pancreas cancer reinforce the importance of locoregional control and adjuvant chemotherapy.

IntroductionThe pattern of recurrence after surgical excision of pancreas cancer may guide alternative pre-operative strategies to either detect occult disease or need for chemotherapy. This study investigated patterns of recurrence after pancreatic surgery.\n\nMethodsRecurrence patterns were described in a series of resected pancreas cancers over a 2-year period and recurrence risk expressed as odds ratio (OR) with 95% confidence interval (C.I.). Survival was displayed by Kaplan-Meier curves.\n\nResultsOf 107 pancreas resections, 69 (65%) had pancreatic cancer. R0 resection was achieved in 21 of 69 (30.4%). Analysis was based on 66 patients who survived 30 days after surgery with median follow up 21 months. Recurrence developed in 41 (62.1%) patients with median time to first recurrence of 13.3 months (interquartile range 6.9, 20.8 months). Recurrence site was most frequently locoregional (n=28, 42%), followed by liver (n=23, 35%), lymph nodes (n=21, 32%), and lungs (n=13, 19%). In patients with recurrence, 9 of 41 had single site recurrence; the remaining 32 patients had more than one site of recurrence. Locoregional recurrence was associated with R+ resection (53% vs 25% for R+ vs R0, respectively; OR 3.5, 95% C.I. 1.1-11.2; P=0.034). Venous invasion was associated with overall recurrence risk (OR 3.3, 95% C.I. 1.1-9.4; P=0.025). In multivariable analysis, R-stage and adjuvant chemotherapy predicted longer survival.\n\nDiscussionThe predominant locoregional recurrence pattern, multiple sites of recurrence and a high R+ resection rate reflect the difficulty in achieving initial local disease control.

pathology↗