Machine learning discriminates a movement disorder in a zebrafish model of Parkinson's disease

Animal models of human disease provide an in vivo system that can reveal molecular mechanisms by which mutations cause pathology, and, moreover, have the potential to provide a valuable tool for drug development. Here, we have developed a zebrafish model of Parkinson's disease (PD) together with a novel method to screen for movement disorders in adult fish, pioneering a more efficient drug-testing route. Mutation of the PARK7 gene (which encodes DJ-1) is known to cause monogenic autosomal recessive PD in humans, and, using CRISPR/Cas9 gene editing, we generated a Dj-1 loss-of-function zebrafish with molecular hallmarks of PD. To establish whether there is a human-relevant parkinsonian phenotype in our model, we adapted proven tools used to diagnose PD in clinics and developed a novel and unbiased computational method to classify movement disorders in adult zebrafish. Using high-resolution video capture and machine learning, we extracted novel features of movement from continuous data streams and used an evolutionary algorithm to classify parkinsonian fish. This method will be widely applicable for assessing zebrafish models of human motor diseases and provide a valuable asset for the therapeutics pipeline. In addition, interrogation of RNA-seq data indicate metabolic reprogramming of brains in the absence of Dj-1, adding to growing evidence that disruption of bioenergetics is a key feature of neurodegeneration.This article has an associated First Person interview with the first author of the paper.

Characterization and classification of adherent cells in monolayer culture using automated tracking and evolutionary algorithms

This paper presents a novel method for tracking and characterizing adherent cells in monolayer culture. A system of cell tracking employing computer vision techniques was applied to time-lapse videos of replicate normal human uro-epithelial cell cultures exposed to different concentrations of adenosine triphosphate (ATP) and a selective purinergic P2X antagonist (PPADS), acquired over a 24 h period. Subsequent analysis following feature extraction demonstrated the ability of the technique to successfully separate the modulated classes of cell using evolutionary algorithms. Specifically, a Cartesian Genetic Program (CGP) network was evolved that identified average migration speed, in-contact angular velocity, cohesivity and average cell clump size as the principal features contributing to the separation. Our approach not only provides non-biased and parsimonious insight into modulated class behaviours, but can be extracted as mathematical formulae for the parameterization of computational models.

Computational approaches for understanding the diagnosis and treatment of Parkinson's disease

This study describes how the application of evolutionary algorithms (EAs) can be used to study motor function in humans with Parkinson's disease (PD) and in animal models of PD. Human data is obtained using commercially available sensors via a range of non-invasive procedures that follow conventional clinical practice. EAs can then be used to classify human data for a range of uses, including diagnosis and disease monitoring. New results are presented that demonstrate how EAs can also be used to classify fruit flies with and without genetic mutations that cause Parkinson's by using measurements of the proboscis extension reflex. The case is made for a computational approach that can be applied across human and animal studies of PD and lays the way for evaluation of existing and new drug therapies in a truly objective way.

Intrathecal therapy for cancer and nonmalignant pain: patient selection and patient management

Intrathecal drug delivery improves pain relief, reduces suffering, and enhances quality of life in the small proportion of patients who do not respond well to oral analgesics, including oral morphine. Although morphine is the "gold standard," and the only drug approved for intrathecal pain therapy in the United States, off-label use of alternative agents appears promising, particularly in patients with neuropathic pain. Careful patient selection and management are significant determinants of successful treatment outcomes. Patient selection criteria for cancer and nonmalignant pain are similar; however, a more comprehensive psychological and social assessment is required for patients with nonmalignant pain. In addition, all patients (those with cancer or nonmalignant pain) must exhibit a positive response to an epidural or intrathecal screening test. A multidisciplinary team approach, involving psychologists, nurses, physical therapists, social workers, and spiritual leaders should be used to manage patients. Current practices for patient selection and management, screening tests, and dosing guidelines for intrathecal drug delivery systems are discussed.

Pseudomonas aeruginosa colonisation in an intensive therapy unit: role of cross infection and host factors

Despite the sparsity of Pseudomonas aeruginosa in the environment colonisation and infection with this organism was found at several sites by selective culture in 20 out of 46 patients in an intensive therapy unit. Three patients developed Ps aeruginosa pneumonia. Serial serogrouping and phage typing identified multiple strains in the unit and in the same patient. Rectal carriage occurred in 16 patients but rectal strains did not subsequently appear in tracheal aspirates; strains varied in their affinity for the upper respiratory tract. Colonisation was not directly related to length of stay and was detected in 16 of those colonised within 24 hours of admission. In intubated patients, who were colonised more frequently than those not intubated, upper respiratory tract colonisation correlated strongly with low initial arterial pH values. Personnel were probably responsible for cross infection among patients when the unit was busy. Strain differences and the susceptibility of patients also influenced colonisation and infection. Elimination of major reservoirs of Ps aeruginosa and compliance with procedures to control cross infection remain essential if patients in hospital are to escape colonisation by the organism.