25 Apr Accelerating Single Cell Genomic Analysis using RAPIDS

The human body is made up of nearly 40 trillion cells, of many different types. Recent advances in experimental biology have made it possible to explore the genetic material of single cells.

 

RAPIDS is a suite of open-source Python libraries that can speed up data science workflows using GPU acceleration. Starting from a single-cell count matrix, RAPIDS libraries can be used to perform data processing, dimensionality reduction, clustering, visualization, and comparison of cell clusters.

 

Several examples are inspired by the Scanpy tutorials and based upon the AnnData format. Currently, examples provide for scRNA-seq and scATAC-seq, and can be scaled up to 1 million cells. The authors also show how to create GPU-powered interactive, in-browser visualizations to explore single-cell datasets.

 

Dataset sizes for single-cell genomics studies are increasing, presently reaching millions of cells. With RAPIDS, it becomes easy to analyze large datasets interactively and in real time, enabling faster scientific discoveries.

 

Github repository is here

Read the full article at: developer.nvidia.com

27 Mar Can Bacteria Make Stronger Armor, Cars and Airplanes?

USC researchers harness the power of living organisms to make materials that are strong, tolerant and resilient.

 

Biological systems can harness their living cells for growth and regeneration, but engineering systems cannot. Until now. Qiming Wang and researchers at the USC Viterbi School of Engineering are harnessing living bacteria to create engineering materials that are strong, tolerant, and resilient. The research is published in Advanced Materials.

 

“The materials we are making are living and self-growing,” said Wang, the Stephen Schrank Early Career Chair in Civil and Environmental Engineering and assistant professor of civil and environmental engineering in the Sonny Astani Department of Civil and Environmental Engineering (CEE). “We have been amazed by the sophisticated microstructures of natural materials for centuries, especially after microscopes were invented to observe these tiny structures. Now we take an important step forward: We use living bacteria as a tool to directly grow amazing structures that cannot be made on our own.”

 

 #abcdesRead the full article at: viterbischool.usc.edu

27 Mar Sea-level rise in the 20th century was the fastest in 2,000 years

The rate of sea-level rise in the 20th century along much of the U.S. Atlantic coast was the fastest in 2,000 years, and southern New Jersey had the fastest rates, according to a Rutgers-led study.

 

The global rise in sea-level from melting ice and warming oceans from 1900 to 2000 led to a rate that’s more than twice the average for the years 0 to 1800—the most significant change, according to the study in the journal Nature Communications.

 

The study for the first time looked at the phenomena that contributed to sea-level change over 2,000 years at six sites along the coast (in Connecticut, New York City, New Jersey and North Carolina), using a sea-level budget. A budget enhances understanding of the processes driving sea-level change. The processes are global, regional (including geological, such as land subsidence) and local, such as groundwater withdrawal.

 

“Having a thorough understanding of sea-level change at sites over the long-term is imperative for regional and local planning and responding to future sea-level rise,” said lead author Jennifer S. Walker, a postdoctoral associate in the Department of Earth and Planetary Sciences in the School of Arts and Sciences at Rutgers University-New Brunswick. “By learning how different processes vary over time and contribute to sea-level change, we can more accurately estimate future contributions at specific sites.”

 

Sea-level rise stemming from climate change threatens to permanently inundate low-lying islands, cities and lands. It also heightens their vulnerability to flooding and damage from coastal and other storms.

Read the full article at: phys.org

12 Mar Hybrid chips can run AI on battery-powered devices

In traditional electronics, separate chips process and store data, wasting energy as they toss data back and forth over what engineers call a “memory wall.” New algorithms combine several energy-efficient hybrid chips to create the illusion of one mega–AI chip.

 

Smartwatches and other battery-powered electronics would be even smarter if they could run AI algorithms. But efforts to build AI-capable chips for mobile devices have so far hit a wall – the so-called “memory wall” that separates data processing and memory chips that must work together to meet the massive and continually growing computational demands imposed by AI.

 

Hardware and software innovations give eight chips the illusion that they’re one mega-chip working together to run AI. “Transactions between processors and memory can consume 95 percent of the energy needed to do machine learning and AI, and that severely limits battery life,” said computer scientist Subhasish Mitra, senior author of a new study published in Nature Electronics.

 

Now, a team that includes Stanford computer scientist Mary Wootters and electrical engineer H.-S. Philip Wong has designed a system that can run AI tasks faster, and with less energy, by harnessing eight hybrid chips, each with its own data processor built right next to its own memory storage. This recent paper builds on the team’s prior development of a new memory technology, called RRAM, that stores data even when power is switched off – like flash memory – only faster and more energy efficiently. Their RRAM advance enabled the Stanford researchers to develop an earlier generation of hybrid chips that worked alone.

 

Their latest design incorporates a critical new element: algorithms that meld the eight, separate hybrid chips into one energy-efficient AI-processing engine.

Read the full article at: news.stanford.edu

12 Mar Neanderthals disappeared from Europe earlier than thought, study suggests

Neanderthal fossils from a cave in Belgium believed to belong to the last survivors of their species ever discovered in Europe are thousands of years older than once thought, a new study said.

 

Previous radiocarbon dating of the remains from the Spy Cave yielded ages as recent as approximately 24,000 years ago, but the new testing pushes the clock back to between 44,200 to 40,600 years ago. The research appeared in the Proceedings of the National Academy of Sciences and was carried out by a team from Belgium, Britain and Germany.

 

Read the full article at: phys.org

27 Feb Mammoth Genomes Shatter Record for Oldest Isolated DNA Sequences

Scientists have recovered DNA from mammoth fossils found in Siberian permafrost that are more than a million years old. This DNA—the oldest genomic evidence recovered to date—illuminates the evolutionary history of woolly mammoths and Columbian mammoths. It also raises the prospect of recovering DNA from other organisms this ancient—including extinct members of the human family.

 

Ever since the recovery of two short DNA sequences from a recently extinct zebra subspecies known as the quagga in 1984, researchers have been working to get ever larger amounts of DNA from ever older remains. Advances in ancient DNA extraction and sequencing methods eventually brought to light genomes of creatures from deeper time, including cave bears and Neandertals.

 

In 2013, investigators announced that they had retrieved DNA from a 700,000-year-old horse fossil—by far the oldest genomic data ever obtained. But as astonishingly old as that genetic material was, some experts predicted that sequenceable DNA should survive more than a million years in fossils preserved in frozen environments.

 

The new findings, published today in Nature, bear that prediction out. Tom van der Valk and Love Dalén of the Center for Paleogenetics in Stockholm and their colleagues obtained DNA from molar teeth belonging to three mammoths from different time periods. Mammoth species can be distinguished on the basis of dental characteristics. One tooth, discovered in deposits thought to be around 700,000 years old, looked like that of an early woolly mammoth, Mammuthus primigenius. The other two teeth—one dated to around one million years ago and the other to 1.2 million years ago or more—resembled molars of the steppe mammoth, Mammuthus trogontherii.

Read the full article at: www.scientificamerican.com

27 Feb Precision Genome Editing Enters the Modern Era: Can We Cure Genetic Diseases by Rewriting DNA?

CRISPR has sparked a renaissance in genome editing. Now, next-generation CRISPR technologies let scientists modify the genome more efficiently and precisely than before. Such tools could one day serve as therapeutics, but many challenges remain.

 

Most drugs are small molecules that can be packaged into a pill. Genome editors are large, complicated molecules – so scientists can’t just stuff them into a pill for people to swallow, or inject them into people’s bodies. They have to find other ways to get the molecules into patients’ cells. One method relies on viruses, says Guangping Gao, a gene therapy researcher at the University of Massachusetts Medical School and president of the American Society of Gene and Cell Therapy. Scientists could potentially package genome editors into small viruses like adeno-associated viruses, for example. These viruses, which have already seen clinical use in several FDA-approved drugs, could then infect patients’ cells and dump their payloads.

 

It could be that scientists will need to develop entirely different delivery systems. Researchers are currently experimenting with lipid nanoparticles and using electric fields to coax genome editors into cells that can then be transplanted into patients. Delivery remains a major hurdle, Gao says, but he’s still excited about genome editors’ potential. “Gene therapy is now in its golden age,” he says. And genome editors “open even more avenues for treating disease.”

Read the full article at: www.hhmi.org

27 Feb NASA’s Mars Helicopter Ingenuity Reports to Home Base

  

Latest NASA Perseverance News is HERE

 

Ingenuity has phoned home from where it is attached to the belly of NASA’s Perseverance rover. Mission controllers at NASA’s Jet Propulsion Laboratory in Southern California have received the first status report from the Ingenuity Mars Helicopter, which landed Feb. 18, 2021, at Jezero Crater attached to the belly of the agency’s Mars 2020 Perseverance rover. The downlink, which arrived at 3:30 p.m. PST (6:30 p.m. EST) via a connection through the Mars Reconnaissance Orbiter, indicates that both the helicopter, which will remain attached to the rover for 30 to 60 days, and its base station (an electrical box on the rover that stores and routes communications between the rotorcraft and Earth) are operating as expected.

 

“There are two big-ticket items we are looking for in the data: the state of charge of Ingenuity’s batteries as well as confirmation the base station is operating as designed, commanding heaters to turn off and on to keep the helicopter’s electronics within an expected range,” said Tim Canham, Ingenuity Mars Helicopter operations lead at JPL. “Both appear to be working great. With this positive report, we will move forward with tomorrow’s charge of the helicopter’s batteries.”

 

Read the full article at: mars.nasa.gov