Detecting abnormal cell behaviors from dry mass time series

The prediction of pathological changes on single cell behaviour is a challenging task for deep learning models. Indeed, in self-supervised learning methods, no prior labels are used for the training and all of the information for event predictions are extracted from the data themselves. We present here a novel self-supervised learning model for the detection of anomalies in a given cell population, StArDusTS. Cells are monitored over time, and analysed to extract time-series of dry mass values. We assessed its performances on different cell lines, showing a precision of 96% in the automatic detection of anomalies. Additionally, anomaly detection was also associated with cell measurement errors inherent to the acquisition or analysis pipelines, leading to an improvement of the upstream methods for feature extraction. Our results pave the way to novel architectures for the continuous monitoring of cell cultures in applied research or bioproduction applications, and for the prediction of pathological cellular changes.

Approximation of modal wavenumbers and group speeds in an oceanic waveguide using a neural network

Underwater acoustic propagation is influenced not only by the property of the water column, but also by the seabed property. Modeling this propagation using normal mode simulation can be computationally intensive, especially for wideband signals. To address this challenge, a Deep Neural Network is used to predict modal horizontal wavenumbers and group velocities. Predicted wavenumbers are then used to compute modal depth functions and transmission losses, reducing computational cost without significant loss in accuracy. This is illustrated on a simulated Shallow Water 2006 inversion scenario.

Shells of the bivalve Astarte moerchi give new evidence of a strong pelagic-benthic coupling shift occurring since the late 1970s in the North Water polynya

Climate changes in the Arctic may weaken the currently tight pelagic-benthic coupling. In response to decreasing sea ice cover, arctic marine systems are expected to shift from a 'sea-ice algae-benthos' to a 'phytoplankton-zooplankton' dominance. We used mollusc shells as bioarchives and fatty acid trophic markers to estimate the effects of the reduction of sea ice cover on the food exported to the seafloor. Bathyal bivalve Astarte moerchi living at 600 m depth in northern Baffin Bay reveals a clear shift in growth variations and Ba/Ca ratios since the late 1970s, which we relate to a change in food availability. Tissue fatty acid compositions show that this species feeds mainly on microalgae exported from the euphotic zone to the seabed. We, therefore, suggest that changes in pelagic-benthic coupling are likely due either to local changes in sea ice dynamics, mediated through bottom-up regulation exerted by sea ice on phytoplankton production, or to a mismatch between phytoplankton bloom and zooplankton grazing due to phenological change. Both possibilities allow a more regular and increased transfer of food to the seabed. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Target detection and localization in shallow water: an experimental demonstration of the acoustic barrier problem at the laboratory scale

This study demonstrates experimentally at the laboratory scale the detection and localization of a wavelength-sized target in a shallow ultrasonic waveguide between two source-receiver arrays at 3 MHz. In the framework of the acoustic barrier problem, at the 1/1000 scale, the waveguide represents a 1.1-km-long, 52-m-deep ocean acoustic channel in the kilohertz frequency range. The two coplanar arrays record in the time-domain the transfer matrix of the waveguide between each pair of source-receiver transducers. Invoking the reciprocity principle, a time-domain double-beamforming algorithm is simultaneously performed on the source and receiver arrays. This array processing projects the multireverberated acoustic echoes into an equivalent set of eigenrays, which are defined by their launch and arrival angles. Comparison is made between the intensity of each eigenray without and with a target for detection in the waveguide. Localization is performed through tomography inversion of the acoustic impedance of the target, using all of the eigenrays extracted from double beamforming. The use of the diffraction-based sensitivity kernel for each eigenray provides both the localization and the signature of the target. Experimental results are shown in the presence of surface waves, and methodological issues are discussed for detection and localization.

Epidemiological study of bovine respiratory syncytial virus infections in calves: influence of maternal antibodies on the outcome of disease

A prospective epidemiological survey on bovine respiratory syncytial virus (BRSV) infections in calves was carried out on 21 dairy farms during one BRSV epidemic season. Special attention was paid to the role of maternal antibodies. On 15 farms the spread of the virus was demonstrated during the investigation period and on eight farms this was accompanied by an outbreak of acute respiratory disease. Disease seldom occurred in calves younger than two weeks old and the most severe disease was observed in calves from one to three months old. Although maternal antibodies did not effectively prevent the disease, both the incidence and severity of disease were inversely related to the level of specific maternal antibodies. Two serodiagnostic techniques were compared. In calves older than three months from herds with disease outbreaks associated with bovine respiratory syncytial virus the diagnosis was established in 80 per cent of the animals by an increase in IgG titre against BRSV and in 77 per cent by the detection of BRSV specific IgM. In comparison, only 10 per cent of the calves younger than three months were positive by IgG serodiagnosis, and 51 per cent by IgM serodiagnosis. On farms where the spread of the virus was accompanied by an outbreak of clinical disease more calves were present, a higher proportion of the calves was younger than three months, and calves of all ages were more often housed together.