Cleaning cosmic microwave background data to measure gravitational lensing

NERSC facilitates development of new analysis filter to better map the invisible universe

A set of cosmic microwave background 2D images with no lensing effects (top row) and with exaggerated cosmic microwave background gravitational lensing effects (bottom row). Image: Wayne Hu and Takemi Okamoto/University of Chicago

Cosmic microwave background (CMB) radiation is everywhere in the universe, but its frigid (-460° F), low-energy microwaves are invisible to the human eye. So cosmologists use specialized telescopes to map out the temperature spectrum of this relic radiation — left over from the Big Bang — to learn about the origin and structure of galaxy clusters and dark matter.

Gravity from distant galaxies cause tiny distortions in the CMB temperature maps, a process called gravitational lensing, which are detected by data analysis software run on supercomputers like the Cori system at Lawrence Berkeley National Laboratory’s (Berkeley Lab’s) National Energy Research Scientific Computing (NERSC) facility. Unfortunately, this temperature data is often corrupted by “foreground emissions” from extragalactic dust, gas, and other noise sources that are challenging to model.

“CMB images get distorted by gravitational lensing. This distortion is not a nuisance, it’s the signal we’re trying to measure,” said Emmanuel Schaan, a postdoctoral researcher in the Physics Division at Berkeley Lab. “However, various foreground emissions always contaminate CMB maps. These foregrounds are nuisances because they can mimic the effect of lensing and bias our lensing measurements. So we developed a new method for analyzing CMB data that is largely immune to the foreground noise effects.”

Schaan collaborated with Simone Ferraro, a Divisional Fellow in Berkeley Lab’s Physics Division, to develop their new statistical method, which is described in a paper published May 8, 2019 in Physical Review Letters.

“Our paper is mostly theoretical, but we also demonstrated that the method works on realistic simulations of the microwave sky previously generated by Neelima Sehgal and her collaborators,” Schaan said.

These publicly available simulations were originally generated using computing resources at the National Science Foundation’s TeraGrid project and Princeton University’s TIGRESS file system. Sehgal’s team ran N-body three-dimensional simulations of the gravitational evolution of dark matter in the universe, which they then converted into two-dimensional (2D) simulated maps of various components of the microwave sky at different frequencies — including 2D temperature maps of foreground emissions.

These 2D images show different types of foreground emissions that can interfere with CMB lensing measurements, as simulated by Neelima Sehgal and collaborators. From left to right: The cosmic infrared background, composed of intergalactic dust; radio point sources, or radio emission from other galaxies; the kinematic Sunyaev-Zel’dovich effect, a product of gas in other galaxies; and the thermal Sunyaev-Zel’dovich effect, which also relates to gas in other galaxies. Image: Emmanuel Schaan and Simone Ferraro/Berkeley Lab

Testing Theory On Simulated Data

NERSC provided resources that weren’t otherwise available to the team. Schaan and Ferraro applied their new analysis method on the existing 2D CMB temperature maps using NERSC. They wrote their analysis code in Python and used a library called pathos to run across multiple nodes in parallel. The final run that generated all the published results were run on  NERSC’s Cori supercomputer.

“As we progressively improved our analysis, we had to test the improved methods,” Schaan said. “Having access to NERSC was very useful for us.”

The Berkeley Lab researchers did many preliminary runs on NERSC’s Edison supercomputer before it was decommissioned because the wait time for the Edison queue was much shorter than the Cori queues. Schaan said they haven’t yet optimized the code for the Cori many-core energy-efficient KNL nodes, but they need to do that soon.

It might be time to speed up that code given their future research plans. Schaan and Ferraro are still perfecting their analysis, so they may need to run an improved method on the same 2D CMB simulations using NERSC. They also hope to begin working with real CMB data.

“In the future, we want to apply our method to CMB data from Simons Observatory and CMB S4, two upcoming CMB experiments that will have data in a few years. For that data, the processing will very likely be done on NERSC,” Schaan said.

NERSC is a U.S. Department of Energy Office of Science User Facility.

For more information, see this Berkeley Lab news release: A New Filter to Better Map the Dark Universe.

This is a reposting of my news feature orginally published by Berkeley Lab’s Computing Sciences.


Space, the new surgical frontier? A Q&A

Photo by WikiImages

Many medical treatments — in their current form — would be unfeasible on deep space missions, such as a journey to Mars.

How will we diagnose and treat the ailments of future space travelers? And what medical issues will they likely encounter? I posed these questions to Sandip Panesar, MD, a postdoctoral research fellow at Stanford who wrote a recent article about surgery in space in the British Journal of Surgery.

What inspired you to research surgery in space?

“From a young age, I’ve always been interested in space travel. I also have a background in surgery, trauma and emergency medicine. So it just clicked one day when I was reading about SpaceX. I realized they may actually send people to Mars, so we need to consider the medical implications of that. Specifically, how would you perform surgery?

The need for surgical care in space in the near future will likely revolve around emergency situations — such as crushes, impacts, falls and burns — since the possibility of trauma occurring during exploratory missions can never be ruled out. In cases of severe trauma, significant internal bleeding may necessitate invasive surgical procedures.”

What adverse conditions do space travelers face?

“People are exposed to a few key physical conditions in space — solar particle radiation, temperature extremes and a lack of gravity. Solar particle radiation is a lot different than the particles people are exposed to on Earth. It has a higher chance of causing DNA damage, leading to an increased risk of high-grade cancers prone to metastasize. However, a lack of gravity causes a whole host of even more critical changes in the human body.”

How does this extraterrestrial environment impact human physiology?

“One of the biggest changes is the redistribution of bodily fluids. On Earth, gravity and walking upright pulls most of our fluids down to our legs. In space, these fluids distribute evenly throughout the body. This affects heart rate and blood pressure, increases intracranial pressure and causes face swelling. And it decreases leg size, a phenomenon called ‘chicken legs.’

An absence of gravity also causes the bones and muscles to atrophy.

In addition, the makeup of white blood cells changes in space. Plus, the body produces more stress hormones, called glucocorticoids, which further weaken the immune system. This may negatively affect wound healing, which is critical to surgical recovery.

Microbes are also known to be more pathological in space, making the risk of a serious infection after surgery even higher.”

How can surgery be adapted for space?

“One idea is to include a trauma pod, an enclosed medical suite, in the space station or vessel — a concept that originated in military medicine.

We’ve also proposed minimally-invasive keyhole surgery, but it has limited use in trauma situations and a pretty large learning curve. So open surgery is likely but challenging in space. For instance, the bowel is free-floating within the abdominal cavity,  so it can float out when you open the stomach if there’s no gravity. This carries a risk of infection, contamination and perforation. One potential solution is to use a hermetically sealed enclosure — placing a clear plastic box over the wound and working essentially in a glove box with a pressure differential.”

Could surgical robots or other equipment help?

“Mars is 48 million miles away and the radio signal delay is 20 minutes, so using robots controlled by surgeons on Earth isn’t feasible. Instead, researchers are developing robots that can perform surgery by themselves or with really minimal human assistance. There have already been trials of robots that can suture together pig bowels with minimal assistance.

Finally, the size and weight of the payload is a huge barrier and surgical specialties all use different tools. A feasible solution is to bring a 3D printer that can print bandages, casts, surgical tools and even maybe pharmaceuticals. Also, you could diagnosis with an ultrasound scanner and a compact CT scanner like the ones used in ambulances in the UK.”

Would you want to be an on-board surgeon?

“Not just yet. I still have a lot of things I want to do on Earth.”

This is a reposting of my Scope blog story, courtesy of Stanford School of Medicine.