Human Health with Data Science || ڈیٹا سائنس Allies Poser, PhD, a Data Science Fellow, is teaching microbe-hunting robots to look for viruses behind diabetic amputations sing data from the ocean. Cybersex and the University of Arizona Data Science Institute jointly host Poser.
Dr. Allies Poser, a doctoral student in France, had no idea that her research on ocean bacteria will one day prevent amputations for diabetics. As a microbiologist, Dr. Poser remarked, “I’ve always been interested in understanding how microbes interact with one another.” Then I developed an interest in stepping back and examining how bacteria communicate with one another in an ecosystem.
She found herself researching how ecological changes impact the interactions between ocean-dwelling bacteria and the viruses that infect them as she began to zoom out.
The Data Science Fellows Programmed, which brings together postdocs from computational, health, and life sciences to enhance communication, cooperation, and the exchange of innovations and best practices, counts Dr. Poser among its inaugural postdoctoral participants.
The new programmed is supported by the University of Arizona Health Sciences as part of a strategic strategy to build New Frontiers for Better Health by combining data science capabilities and interdisciplinary efforts to advance health sciences research. Cybersex and the Data Science Institute at the University of Arizona jointly sponsor the fellows.
The new common tongue is data science. It is the language that links all other languages and a comprehensive set of global data. It will be necessary in every profession, according to Bonnie Hurwitz, PhD, a clinical instructor in the College of Pharmacy and an assistant professor of bios stems engineering.
Dr. Ponder and other Data Science Fellows may explore substantial datasets that are brimming with knowledge on genetics, health, and disease thanks to their access to powerful computing resources. These new capabilities provide a stimulating environment for the investigation of creative concepts that may eventually help to solve the riddle surrounding human health and guide precision medicine.
“It’s not about studying a single individual system anymore, but being able to be a true hacker of systems and think of how they’re all interacting,” said Dr.
Uncovering the meta-organism with data science
Scientists use met genomics to analyses meta-organisms.
Instead of cultivating one organism, Dr. Pondera explained, “in met genomics, we take the DNA from a sample of the microbial population and sequence the whole thing as one meta-organism.” It’s a tremendously useful tool for examining diverse microbial ecosystems.
Every living thing has a genome, which is a collection of genes that describes it. A, T, C, and G-proteins make up each gene, which is a sentence in itself. These texts can be thoroughly read by powerful computers, which can cross-reference the letters and find relationships that were previously unthinkable. However, someone must teach those machines, which is where data science comes in. It was here that Dr. Ponderous professional path unexpectedly took a turn for the worst.
Dr. Pondera recalls, I never touched a computer when I did my PhD in molecular biology — I was deep into wet lab.” “I became interested in the contributions that data science is making to the field of microbiology, but before I could move on to more computational work, I had to take some time to learn how to code.
The result of such “break” was a master’s in computer science.
As part of her postdoctoral work, Dr. Pondera is teaching computers to comb through terabyte-sized met genomes for viral genes and find newly undiscovered viruses at the Hurwitz Lab. Viruses, the fraction of a met genome that derives from viruses, can only be produced by a select few laboratories worldwide, including the Hurwitz Lab.
Hunting viruses with machine learning
A machine needs training materials in order to create virus-detection algorithms. These datasets are taken directly from the sea.
Dr. Hurwitz said that Ocean Sciences has been innovative in developing viruses from various aquatic environments. “They have sequenced everything from bacteria to viruses and the entire range at every level of the cell. For Allies to accomplish her predictive work, that kind of data is required.
The Alvin submersible, a large, circular, silver pod, has a primary chamber that Bonnie Hurwitz is standing next to outside.
At the Woods Hole Oceanographic Institution, Bonnie Hurwitz, PhD, may be seen standing next to the Alvin submersible’s main chamber, which gathers samples from the deepest regions of the ocean that are inaccessible to humans.
The machine learning method developed by Dr. Pondera will examine data using features in viruses that set them apart from other animals found in the met genome data, researchers are able to identify a virus’s genetic fingerprints by iteratively improving their algorithms. Although it is difficult to pinpoint each gene’s origin, viruses leave obvious signs.
A text made up of sentences is the met genome. Those sentences are definable in word form. Viruses won’t construct DNA using the same phrases, according to Dr. Pondera.
Dr. Hurwitz said, “Viruses prefer to multiply, and they do it quickly. Instead of Gs and Cs, they’ll employ more as and Ts, which are simpler to make.
From the ocean to ulcers
The machine-learning programmer may be given met genomes from entirely new habitats after mastering the ocean datasets, and may then be able to identify viral causes of challenging-to-treat diabetic foot ulcers.
We’re testing it on the roadway in the sea, the doctor added. Hurwitz said. Then we’ll use it again in the area of health.
The skin is home to a wide variety of microorganisms, just like the ocean. For the most part, they are not harmful, but for those who have diabetes, a small scratch or crack on the foot might lead to an infection, which would then set off a chain of events that would eventually result in amputation. We don’t even know which microorganisms are responsible for the majority of these infections.
“The viruses that cause foot ulcers will differ greatly from those found in the ocean, yet the the same process and strategy would be used,” Doctor Hurwitz clarified
When their tool is prepared for use, to investigate.
Dr. Pondera declared, “I’m most thrilled to be a part of a growing community that will foster new collaboration and new ideas.” “The switch from pure microbiology to data science is exciting because I am learning new things every day!”
Dr. Hurwitz said, “There are lots of exciting discoveries being made right now, particularly at that interface between bacteria and viruses and their function in human health.” “Huge strides are made every year. Snug up!