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Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers

Year 2018 😗


State-of-the-art software tools for neuronal network simulations scale to the largest computing systems available today and enable investigations of large-scale networks of up to 10% of the human cortex at a resolution of individual neurons and synapses. Due to an upper limit on the number of incoming connections of a single neuron, network connectivity becomes extremely sparse at this scale. To manage computational costs, simulation software ultimately targeting the brain scale needs to fully exploit this sparsity. Here we present a two-tier connection infrastructure and a framework for directed communication among compute nodes accounting for the sparsity of brain-scale networks. We demonstrate the feasibility of this approach by implementing the technology in the NEST simulation code and we investigate its performance in different scaling scenarios of typical network simulations. Our results show that the new data structures and communication scheme prepare the simulation kernel for post-petascale high-performance computing facilities without sacrificing performance in smaller systems.

Modern neuroscience has established numerical simulation as a third pillar supporting the investigation of the dynamics and function of neuronal networks, next to experimental and theoretical approaches. Simulation software reflects the diversity of modern neuroscientific research with tools ranging from the molecular scale to investigate processes at individual synapses (Wils and De Schutter, 2009) to whole-brain simulations at the population level that can be directly related to clinical measures (Sanz Leon et al., 2013). Most neuronal network simulation software, however, is based on the hypothesis that the main processes of brain function can be captured at the level of individual nerve cells and their interactions through electrical pulses. Since these pulses show little variation in shape, it is generally believed that they convey information only through their timing or rate of occurrence.

I got a chip implanted in a biohacking garage

In the underground movement known as, people are taking their health into their own hands. Biohacking ranges from people making simple lifestyle changes to extreme body modifications.

One popular form of focuses on nutrigenomics, where biohackers study how the foods they eat affect their genes over time. They believe they can map and track the way their diet affects genetic function. They use dietary restrictions and blood tests, while tracking their moods, energy levels, behaviors, and cognitive abilities.

Then there are grinders, a subculture of A grinder believes there’s a hack for every part of the body. Rather than attempting to modify our existing biology, grinders seek to enhance it with implanted technology.

Unmasking BACE1 in aging and age-related diseases

The BACE1 enzyme has a rate-limiting role in the amyloidogenic pathway (see Glossary) and has been extensively studied for its neuronal functions[1]. Since 2000, intensive efforts have focused on developing small-molecule BACE1 inhibitors to reduce amyloid ÎČ (AÎČ) production in Alzheimer’s disease (AD) brains. However, human clinical trials involving most BACE1 inhibitors were stopped at Phase 2/3 due to limited therapeutic benefits[2]. BACE1 inhibitors act by reducing AÎČ-related pathologies in AD brains, that is, they are used to treat the symptoms rather than the underlying disease.

CRISPR technology improves Huntington’s disease symptoms in models

Huntington’s disease (HD) is a neurological disorder that causes progressive loss of movement, coordination and cognitive function. It is caused by a mutation in a single gene called huntingtin (HTT). More than 200,000 people worldwide live with the genetic condition, approximately 30,000 in the United States. More than a quarter of a million Americans are at risk of inheriting HD from an affected parent. There is no cure.

But in a new study, published December 12, 2022 in Nature Neuroscience, researchers at University of California San Diego School of Medicine, with colleagues elsewhere, describe using RNA-targeting CRISPR/Cas13D technology to develop a new therapeutic strategy that specifically eliminates toxic RNA that causes HD.

CRISPR is known as a genome-editing tool that allows scientists to add, remove or alter genetic material at specific locations in the genome. It is based on a naturally occurring immune defense system used by bacteria. However, current strategies run the risk of off-target edits at unintended sites that may cause permanent and inheritable chromosomal insertions or genome alterations. Because of this, significant efforts have focused on identifying CRISPR systems that target RNA directly without altering the genome.

CAR-T-cell shows promise in patients with lymphoma of the brain and spinal cord in early trial

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A CAR-T-cell therapy known as axicabtagene ciloleucel (axi-cel) is safe and shows encouraging signs of efficacy in a small pilot trial involving patients with lymphoma of the brain and/or spinal cord, Dana-Farber Cancer Institute investigators report at the 64th American Society of Hematology (ASH) Annual Meeting.

The research features an in-depth, molecular study of individual CAR-T cells isolated from patients’ blood and cerebrospinal fluid (CSF), which surrounds the brain and spinal cord. This unprecedented analysis, conducted in collaboration with the Cellular Therapeutics and Systems Immunology Lab (CTSI), directed by Leslie Kean, MD, PhD, at Dana-Farber and Boston Children’s Hospital, reveals a surprising difference between the two CAR-T-cell populations: the cells in the CSF display a molecular signature that indicates activation of the interferon pathway, an important step in rallying the immune system. These studies are reported in two oral abstracts at ASH. “For many patients with lymphoma of the central nervous system, there aren’t great treatment options,” said Dana-Farber’s Caron Jacobson, MD, MMSc, who led the trial and will present the findings at ASH. “Our early results suggest that expanding the applicability of CAR-T cells to this indication could improve patient outcomes.”

Lymphomas can begin within the brain or spinal cord, or the tumors can spread to those sites (known collectively as the central nervous system or CNS) after they originate in other parts of the body. While the underlying biology of these primary and secondary CNS lymphomas can be quite different, these cancers are often difficult to treat, especially once the tumors evade standard treatments. In that case, patients typically do not live more than 2 years.

Bees may feel pain

We swat bees to avoid painful stings, but do they feel the pain we inflict? A new study suggests they do, a possible clue that they and other insects have sentience—the ability to be aware of their feelings.

“It’s an impressive piece of work” with important implications, says Jonathan Birch, a philosopher and expert on animal sentience at the London School of Economics who was not involved with the paper. If the study holds up, he says, “the world contains far more sentient beings than we ever realized.”

Previous research has shown honey bees and bumble bees are intelligent, innovative, creatures. They understand the concept of zero, can do simple math, and distinguish among human faces (and probably bee faces, too). They’re usually optimistic when successfully foraging, but can become depressed if momentarily trapped by a predatory spider. Even when a bee escapes a spider, “her demeanor changes; for days after, she’s scared of every flower,” says Lars Chittka, a cognitive scientist at Queen Mary University of London whose lab carried out that study as well as the new research. “They were experiencing an emotional state.”

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