Using Artificial Intelligence to Predict Life-Threatening Bacterial Disease in Dogs

UC Davis Veterinarians Develop AI Model for Accurate, Early Detection of Leptospirosis Infections

Peer-Reviewed Publication

UNIVERSITY OF CALIFORNIA - DAVIS

 

IMAGE: THE BACTERIAL DISEASE LEPTOSPIROSIS, IF NOT CAUGHT EARLY, CAN CAUSE KIDNEY FAILURE IN DOGS AMONG OTHER LIFE-THREATENING SYMPTOMS. view more 

CREDIT: UC VETERINARY MEDICAL CENTER - SAN DIEGO

Leptospirosis, a disease that dogs can get from drinking water contaminated with Leptospira bacteria, can cause kidney failure, liver disease and severe bleeding into the lungs. Early detection of the disease is crucial and may mean the difference between life and death.

Veterinarians and researchers at the University of California, Davis, School of Veterinary Medicine have discovered a technique to predict leptospirosis in dogs through the use of artificial intelligence. After many months of testing various models, the team has developed one that outperformed traditional testing methods and provided accurate early detection of the disease. The groundbreaking discovery was published in Journal of Veterinary Diagnostic Investigation.

“Traditional testing for Leptospira lacks sensitivity early in the disease process,” said lead author Krystle Reagan, a board-certified internal medicine specialist and assistant professor focusing on infectious diseases. “Detection also can take more than two weeks because of the need to demonstrate a rise in the level of antibodies in a blood sample. Our AI model eliminates those two roadblocks to a swift and accurate diagnosis.”

The research involved historical data of patients at the UC Davis Veterinary Medical Teaching Hospital that had been tested for leptospirosis. Routinely collected blood work from these 413 dogs was used to train an AI prediction model. Over the next year, the hospital treated an additional 53 dogs with suspected leptospirosis. The model correctly identified all nine dogs that were positive for leptospirosis (100% sensitivity). The model also correctly identified approximately 90% of the 44 dogs that were ultimately leptospirosis negative.

The goal for the model is for it to become an online resource for veterinarians to enter patient data and receive a timely prediction.

“AI-based, clinical decision making is going to be the future for many aspects of veterinary medicine,” said School of Veterinary Medicine Dean Mark Stetter. “I am thrilled to see UC Davis veterinarians and scientists leading that charge. We are committed to putting resources behind AI ventures and look forward to partnering with researchers, philanthropists, and industry to advance this science.”  

Detection model may help people

Leptospirosis is a life-threatening zoonotic disease, meaning it can transfer from animals to humans. As the disease is also difficult to diagnose in people, Reagan hopes the technology behind this groundbreaking detection model has translational ability into human medicine.

“My hope is this technology will be able to recognize cases of leptospirosis in near real time, giving clinicians and owners important information about the disease process and prognosis,” said Reagan. “As we move forward, we hope to apply AI methods to improve our ability to quickly diagnose other types of infections.”

Reagan is a founding member of the school’s Artificial Intelligence in Veterinary Medicine Interest Group comprising veterinarians promoting the use of AI in the profession. This research was done in collaboration with members of UC Davis’ Center for Data Science and Artificial Intelligence Research, led by professor of mathematics Thomas Strohmer. He and his students were involved in the algorithm building. The center strives to bring together world-renowned experts from many fields of study with top data science and AI researchers to advance data science foundations, methods, and applications.

Reagan’s group is actively pursuing AI for prediction of outcome for other types of infections, including a prediction model for antimicrobial resistant infections, which is a growing problem in veterinary and human medicine. Previously, the group developed an AI algorithm to predict Addison’s disease with an accuracy rate greater than 99%.

Other authors include Shaofeng Deng, Junda Sheng, Jamie Sebastian, Zhe Wang, Sara N. Huebner, Louise A. Wenke, Sarah R. Michalak and Jane E. Sykes. Funding support comes from the National Science Foundation.

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JOURNAL

Journal of Veterinary Diagnostic Investigation

DOI

10.1177/10406387221096781 

METHOD OF RESEARCH

Computational simulation/modeling

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Use of machine-learning algorithms to aid in the early detection of leptospirosis in dogs

ARTICLE PUBLICATION DATE

21-May-2022

COI STATEMENT

The authors declared no potential conflicts of interests with respect to the research, authorship, and/or publication of this article.

DeepSqueak tool identifies marine mammal calls #ASA182

User-friendly deep learning model analyzes bioacoustics signals from whales, dolphins

Reports and Proceedings

ACOUSTICAL SOCIETY OF AMERICA

 

IMAGE: AT THE 182ND ASA MEETING, ELIZABETH FERGUSON, FROM OCEAN SCIENCE ANALYTICS, WILL DESCRIBE HOW DEEPSQUEAK, A DEEP LEARNING TOOL, CAN CLASSIFY UNDERWATER ACOUSTIC SIGNALS. view more 

CREDIT: FERGUSON

DENVER, May 23, 2022 – Lurking beneath the ocean's surface, marine mammals use sound for navigation, prey detection, and a wide range of natural behaviors. Passive acoustic data from underwater environments can provide valuable information on these animals, such as their presence or absence within an area, their density and abundance, and their vocal response to anthropogenic noise sources.

As the size and number of acoustic datasets increase, accurately and quickly matching the bioacoustics signals to their corresponding sources becomes more challenging and important. This is especially difficult in noisy, natural acoustic environments.

Elizabeth Ferguson, from Ocean Science Analytics, will describe how DeepSqueak, a deep learning tool, can classify underwater acoustic signals at the 182nd Meeting of the Acoustical Society of America during her presentation, "Development of deep neural networks for marine mammal call detection using an open-source, user friendly tool." The session will take place May 23 at 11:25 a.m. Eastern U.S. as part of the conference at the Sheraton Denver Downtown Hotel.

Spectrograms show how acoustic signals of different frequencies vary with time. They look like heat maps, with brighter regions indicating higher sound intensity at that frequency and time. DeepSqueak uses deep neural network image recognition and classification methods to determine the important features within spectrograms, then match those features to specific sources.

"Although we used DeepSqueak to detect underwater sounds, this user-friendly, open source tool would be useful for a variety of terrestrial species," said Ferguson. "The capabilities of call detection extend to frequencies below the ultrasonic sounds it was originally intended for. Due to this and the capability of DeepSqueak to detect variable call types, development of neural networks is possible for many species of interest."

DeepSqueak was originally developed to classify ultrasound signals from rodents, but its neural network framework allows the technique to adapt to detect sounds at other frequencies. Ferguson and her team used the method and data from hydrophones on the Ocean Observatories Initiative's Coastal Endurance Array to detect humpback whales, delphinids, and fin whales, which have highly variable calls with a wide range of frequencies.

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ABOUT THE ACOUSTICAL SOCIETY OF AMERICA

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The case for speaking politely to animals

Peer-Reviewed Publication

UNIVERSITY OF COPENHAGEN - FACULTY OF SCIENCE

 

IMAGE: ELODIE BRIEFER view more 

CREDIT: KRISTIAN BJØRN-HANSEN, COPENHAGEN UNIVERSITY

How we speak matters to animals. Horses, pigs and wild horses can distinguish between negative and positive sounds from their fellow species and near relatives, as well as from human speech. This, according to new research in behavioral biology at the University of Copenhagen. The study provides insight into the history of emotional development and opens up interesting perspectives with regards to animal welfare.

The idea of horse whisperers – those with a talent for communicating with horses – may bring a chuckle to many. But according to new research from the University of Copenhagen and ETH Zurich, there may be something about their whispering skills. In an international collaboration, along with researchers Anne-Laure Maigrot and Edna Hillmann, behavioral biologist Elodie Briefer of the University of Copenhagen’s Department of Biology investigated whether a range of animals can distinguish between positively and negatively charged sounds.

"The results showed that domesticated pigs and horses, as well as Asian wild horses, can tell the difference, both when the sounds come from their own species and near relatives, as well as from human voices," explains Elodie Briefer.
Pigs were studied along with boar, their wild relatives. Just as in the case of the two related horse species, the pigs clearly reacted to how the sounds of their counterparts were emotionally charged. In fact, to the same extent as when it came to sounds of their own kind.

The animals even showed the ability to distinguish between positively or negatively charged human voices. While their reactions were more subdued, all but wild boars reacted differently when exposed to human speech that was either charged with positive or negative emotion.

Human gibberish

The researchers played recordings of animal sounds and human voices from hidden speakers.

To avoid having the domesticated animals react to specific words, positive and negative human speech was performed by a professional voice actor in a kind of gibberish without any meaningful phrases.

The animals' behavioral reactions were recorded in a number of categories used in previous studies – everything from their ear position to their movement or lack thereof.

On this basis, the researchers concluded that: How we speak matters to animals.

"Our results show that these animals are affected by the emotions we charge our voices with when we speak to or are around them. They react more strongly – generally faster - when they are met with a negatively charged voice, compared to having a positively charged voice played to them first. In certain situations, they even seem to mirror the emotion to which they are exposed" says Elodie Briefer.

Do animals have an emotional life?

Part of the aim of the study, was to investigate the possibility of "emotional contagion" in animals – a kind of mirroring of emotion. Situations where one expressed emotion is assumed by another. In behavioral biology, this type of reaction is seen as the first step in the empathy category.

"Should future research projects clearly demonstrate that these animals mirror emotions, as this study suggests, it will be very interesting in relation to the history of the development of emotions and the extent to which animals have an emotional life and level of consciousness," says Elodie Briefer.

The study was unable to detect clear observations of "emotional contagion", but an interesting result was in the order by which the sounds where delivered. Sequences in which the negative sound was played first triggered stronger reactions in all but the wild boars. This included human speech.

According to Elodie Briefer, this suggests that the way we talk around animals and the way we talk to animals may have an impact on their well-being.

"It means that our voices have a direct impact on the emotional state of animals, which is very interesting from an animal welfare perspective," she says.

This knowledge doesn’t just raise ethical questions about how we perceive animals – and vice versa, it can also be used as a concrete means of improving animals’ daily lives, if those who work with them are familiar with it.

"When the animals reacted strongly to hearing negatively charged speech first, the same is also true in the reverse. That is, if animals are initially spoken to in a more positive, friendly voice, when met by people, they should react less. They may become calmer and more relaxed," explains Elodie Briefer.

Next step for the Copenhagen University researcher is the switchover. She and her colleagues, are now looking into how well we humans are able to understand animal sounds of emotion.

 

  

CAPTION

Elodie Briefer and her collaborators used emotionally charged animal sounds to investigate the behavioral reactions of pigs, horses, wild horses and wild boar

CREDIT

Kristian Bjørn-Hansen, Copenhagen University

Contact:
Associate professor, Elodie Floriane Mandel-Briefer
Institute of Biology

Copenhagen University
Elodie.Briefer@bio.ku.dk

[Fact box] Axis of emotions

One of the ways that researchers study the emotional lives of animals is to divide them on an axis.

                                 High arousal

Negative valence              +                   Positive valence

                                 Low arousal

In this study, the focus is on emotional valence – a distinction between positive and negative emotions.

 

 

[Fact box] How the researchers did it

• The animals in the experiment were either privately owned (horses), from a research station (pigs) or living in zoos in Switzerland and France (wild Przewalski’s horses and wild boars).
• The researchers used animal sounds with a previously established emotion valence.
• The animal sounds and human voices were played to the animals from hidden speakers.
• Doing so required high sound quality to ensure for the natural frequencies heard best by animals.
• The sounds were played in sequences with either a positive or negatively charged sound first, then a pause, - and then sounds with reverse valence, i.e. the reverse emotion.
• The reactions were recorded on video, which the researchers could subsequently use to observe and record the animals' reactions.

 

[Fact box] Three theses can explain the animal reactions

The researchers worked with three theories about which conditions they expected to influence the animals' reactions in the experiment:

Phylogeny

• According to this theory, depending on the evolution of species, i.e., the history of evolution, animals with a common ancestry may be able to perceive and interpret each other's sounds by virtue of their common biology.

Domestication

• Close contact with humans, over a long period of time, may have increased the ability to interpret human emotions.
• Animals that are good at picking up human emotions might have been preferred for breeding.

Familiarity

• Based on learning. The specific animals in the study may have learned a greater understanding of humans and fellow species, who they were in close contact with where they were housed.

The conclusion is as follows. Among the horse species, the phylogeny thesis best explained their behavior. In contrast, the behavior of the pig species best fit the domestication hypothesis.

 

[Fact box] About the Study:

• The study was initiated at ETH Zürich and funded by the Swiss National Science Foundation
• The researchers behind the study are:

• Anne-Laure Maigrot, based at the Swiss National Stud Farm of Agroscope
• Edna Hillmann, based at Humboldt-Universität zu Berlin
• Elodie Floriane Mandel-Briefer, Institute of Biology, at University of Copenhagen

• The actors voices were provided by the GEMEP Corpus - a collection of audio and video recordings featuring 10 actors portraying 18 affective states, with different verbal contents and different modes of expression for use in scientific research. https://www.unige.ch/cisa/gemep,
• The pigs were tested at  Agroscope Tänikon Research Station

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JOURNAL

BMC Biology

DOI

10.1186/s12915-022-01311-5 

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Cross-species discrimination of vocal expression of emotional valence by Equidae and Suidae

ARTICLE PUBLICATION DATE

24-May-2022

DEMOCRACY IS LOUD & NOISY

'Democracy' governs mass jackdaw take-offs

Peer-Reviewed Publication

UNIVERSITY OF EXETER

 

IMAGE: JACKDAWS ROOSTING view more 

CREDIT: ALEX THORNTON

Jackdaws use a "democratic" process to decide when to leave their roosts en masse, new research shows.

In winter, jackdaws roost in groups of hundreds or even thousands, and it is common for most or all of the birds to take flight in a sudden mass departure around sunrise.

In the new study, a team led by the University of Exeter recorded the rising racket of jackdaw calls that happens before mass departures at various roosts in Cornwall.

By combining this with tests in which pre-recorded jackdaw calls were played at a colony, the team found evidence that the birds' calls are used in a form of "consensus decision-making".

"After roosting in a large group at night, each jackdaw will have a slightly different preference about when they want to leave, based on factors like their size and hunger," said Alex Dibnah, who led the study as part of a Masters by Research at Exeter's Penryn Campus in Cornwall.

"However, it's useful to reach a consensus. Leaving the roost together has various benefits, including safety from predators and access to information such as where to find food.

"Our study shows that by calling out jackdaws effectively ‘cast a vote’ and, when calling reaches a sufficient level, a mass departure takes place."

The research team – which included the University of Cambridge and Barcelona's Centre for Ecological Research and Forestry Applications – also found:

• Mass departures happened almost instantly, with all departing birds in the air within less than five seconds on average.
• These departures took place in the period from 45 minutes before sunrise to 15 minutes afterwards. Rain and heavy cloud tended to delay departures.
• When the intensity of calling rose more steeply, birds departed earlier.
• Playing recordings of roosting calls brought forward the time of the first mass departure by an average of more than six minutes.
• Recordings of wind noise did not lead to earlier mass departures, suggesting that the birds respond specifically to calls of their fellow birds (not to noise in general).

Jackdaws did not always leave their roost in mass departures. If the level of calling did not rise sufficiently, roost members failed to reach a consensus and instead left in a stream of small groups.

Commenting on the wider significance of the research, Professor Alex Thornton – of Exeter's Centre for Ecology and Conservation – said: "It helps us to understand how really large groups of animals can coordinate their actions – something that has rarely been tested in detail before.

"Also, our findings provide further evidence that vocalisations are really fundamental in allowing some species to reach group decisions – so we need to investigate what happens when we as humans create noise pollution that might influence how information spreads through these social groups.

"The next stage of our research will look into this."

The research was funded by the Human Frontier Science Program.

The paper, published in the journal Current Biology, is entitled: "Vocally-mediated consensus decisions govern mass departures from jackdaw roosts."

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JOURNAL

Current Biology

DOI

10.1016/j.cub.2022.04.032 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Vocally-mediated consensus decisions govern mass departures from jackdaw roosts

ARTICLE PUBLICATION DATE

23-May-2022

JACKDAWS ARE CORVIDS, THIS APPPLIES TO RAVENS, CROWS & MAGPIES ALSO TALKING/SQUAKING CORVIDS

 

Noisy jackdaw birds reach “consensus” before taking off

Peer-Reviewed Publication

CELL PRESS

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VIDEO: OVER A THOUSAND JACKDAWS PERFORMING A SUDDEN AND FAST MASS DEPARTURE THAT LASTS ONLY SECONDS, WITH BIRDS TRAVELLING IN ONE COHESIVE FLOCK IN THE SAME DIRECTION. view more 

CREDIT: DIBNAH ET AL./CURRENT BIOLOGY

On cold, dark winter mornings, small black crows known as jackdaws can be heard calling loudly to one another from their winter roosting spots in the U.K. before taking off simultaneously right around sunrise. Now, researchers who’ve studied their daily activities in unprecedented detail report evidence that these groups of hundreds of individuals rely on a “democratic” decision-making process to coordinate with one another and take to the skies all at once. The findings are reported in the journal Current Biology on May 23.

“Like humans, large animal groups can use decision-making processes to overcome their individual differences and reach a kind of ‘democratic’ consensus,” says Alex Thornton (@CornishJackdaws) of the University of Exeter.

Previous studies had investigated consensus decision-making in animal groups that were relatively small or made up of family members, he explained. What struck them about the jackdaw roosts was their sheer size. Not only are their groups large, they also include individuals of different ages, sexes, family groups, and colonies all spread across the treetops.

It’s not likely that all those different individuals would just naturally prefer to take off at precisely the same moment. And, yet, sticking together has advantages, such as reducing the risk of predation and giving individuals information from their peers about where to find food. The researchers wanted to explore how the birds decide when it is time to go.

To look more closely, Thornton and colleagues, including first author Alex Dibnah (@alexdibnah01), recorded hours and hours of audio and video of six different jackdaw roosts in Cornwall, U.K. over the course of the winter months. The size of the roosts varied from 160 to almost 1,500 individuals. They quantified the intensity of the birds’ calls leading up to and right after they took off in flight.

The evidence shows that the timing of departure is tightly linked to calling intensity within the roost. While on some mornings, the birds left in a stream of small groups over about 20 minutes, most of the time they set out in mass departures, with hundreds of birds taking off within about 4 seconds of each other.

On most mornings, they found that calling intensity increased over the hour before the biggest group departure. It sometimes got delayed by rain or heavy cloud cover. They concluded that changes in calling intensity could serve as a reliable source of information, enabling the birds to synchronize their daily takeoffs.

To confirm cause and effect, the researchers played the sounds of conspecifics calling to them to see if they could get the birds to take off earlier than they otherwise would have. And they found that they could. By adding calls into the mix, the birds took flight an average of about 6.5 minutes earlier.

“Through their calls, jackdaws appear to effectively signal their willingness to leave, providing large groups with a means of achieving consensus to perform cohesive, collective departures from the roost,” the researchers write.

They say the observational data indicate that consensus is achieved as the intensity of calls build to a point that triggers them to act. The playback experiments help to show a causal link between calling intensity and takeoff. Together, they offer new insight into the ways that animals make decisions about mass movements in nature.

It is also notable that, on the few occasions when the intensity of calling did not build up sufficiently, the birds apparently failed to reach consensus. As a result, they took off in “dribs and drabs” instead of all at once.

In future studies, researchers hope to learn more about how human activities may affect these dynamics.

“As human impacts on wildlife grow, we are very interested in understanding to understand whether and how human disturbance—for instance, from light and noise pollution—may affect animal groups’ abilities to communicate and reach consensus decisions,” Thornton says.

CAPTION

Jackdaws roosting in a tree

CREDIT

Jolle Jolles

This research was supported by the Swedish Research Council, the Human Frontier Science Program, the Whitten Lectureship in Marine Biology, the Royal Society Dorothy Hodgkin Research Fellowship, and a Severo Ochoa Postdoctoral grant through the Spanish Program for Centres of Excellence.

Current Biology, Dibnah et al. “Vocally mediated consensus decisions govern mass departures from jackdaw roosts” https://www.cell.com/current-biology/fulltext/S0960-9822(22)00601-7

Current Biology (@CurrentBiology), published by Cell Press, is a bimonthly journal that features papers across all areas of biology. Current Biology strives to foster communication across fields of biology, both by publishing important findings of general interest and through highly accessible front matter for non-specialists. Visit http://www.cell.com/current-biology. To receive Cell Press media alerts, contact press@cell.com.

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J 

CAPTION

Jackdaws roosting in a tree

CREDIT

Jolle JollesOURNAL

Current Biology

DOI

10.1016/j.cub.2022.04.032 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Vocally mediated consensus decisions govern mass departures from jackdaw roosts

ARTICLE PUBLICATION DATE

23-May-2022

Disclaimer: AAAS and 

UH OH
Alberta confirms 5 cases of avian flu spreading to mammals

Alberta now has five confirmed cases of avian flu that have spread from birds to mammals.

© Carolyn Kury de Castillo/Global News

This red fox at the Medicine River Wildlife Centre is recovering from an illness believed to be avian influenza, although that hasn't been confirmed by labs just yet.

Five skunks from central Alberta have been lab-confirmed as having avian influenza.

"We had an unusually large number of calls about skunks that were acting strange or being found dead and it was all within the area where we had confirmed that the avian influenza virus was present in the snow geese," Dr. Margo Pybus, a provincial wildlife disease specialist with Fish and Wildlife Alberta Environment and Parks, said.

"We believe that the skunks are feeding on the dead geese and they are getting enough virus that it's actually affecting the skunks."

Read more:

Avian flu found in 3 more Alberta communities: CFIA

Pybus said it's uncommon to see avian flu cause sickness in mammals, and added it's uncertain at this point which species are more at risk.

"(It's) very uncommon, but everything is uncommon this year. This is all new to North America. We are learning about this as we go," Pybus said.

She added that avian influenza is a naturally occurring virus in birds, particularly in waterfowl.

"As we learned with COVID, viruses constantly change and avian influenza virus definitely changes very, very often."

Bird flu outbreak on Canadian farms

Staff and volunteers at the Medicine River Wildlife Centre west of Innisfail, Alta., have been dealing with five sick foxes that were brought in recently.

All five had the same symptoms -- blindness, seizures and cloudy eyes, according to executive director Carol Kelly. She said three of them died and two have recovered.

She said Avian influenza wasn't even on the radar as a cause until staff started talking with two other wildlife centres.

"We realized that we were all dealing with a total of around 15 foxes, all with identical symptoms," Kelly said.

"By the time we got the third fox in, we thought this is something very strange. We got an email from an Edmonton rehab centre to say they had just learned that a fox can get this (avian flu) by eating dead birds. It was at that point that we connected this," Kelly said.

"We are learning on the fly because it’s so new."

Read more:

Urban hen owners take precautions amid unprecedented spread of avian flu

The fox cases haven't been confirmed yet by any Alberta labs, which are currently swamped dealing with poultry infections.

However, one dead fox from the Edmonton area is being tested now.

"The labs are entirely focused on trying to provide results that help control that disease in poultry so it doesn’t spread any further," Pybus said. "Alberta is one of the hardest-hit provinces for the poultry industry with this virus and so our labs are just overwhelmed with poultry samples right now."

The foxes that survived at the Medicine River Wildlife Centre have been nursed back to health. They were treated with plenty of hydration and eye drops and are expected to be released this week.

Sick birds have not been as lucky.

Around 20 birds have died from avian flu at the wildlife centre.

According to Pybus, Alberta's outbreak is believed to be on the decline due to the natural migration of geese.

"We do believe that the outbreak is on the downside. We have far fewer calls about dead birds or dead skunks last week than the previous weeks, and that would be consistent with most of the virus now having moved out of the province," Pybus said.