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Study: Gene circuits reshape DNA folding and affect how genes are expressed

When a gene is turned on in a cell, it creates a ripple effect along the DNA strand, changing the physical structure of the strand. A new study by MIT researchers shows that these ripples can stimulate or suppress neighboring genes.

These effects, which result from the winding or unwinding of neighboring DNA, are determined by the order of genes along a strand of DNA. Genes upstream of the active gene are usually turned up, while those downstream are inhibited.

The new findings offer guidance that could make it easier to control the output of synthetic gene circuits. By altering the relative ordering and arrangement of genes, or “gene syntax,” researchers could create circuits that synergize to maximize their output, or that alternate the output of two different genes.

Zuckerberg Trying to Simulate Human Biology at the Cellular Level

Mark Zuckerberg is following a path paved by fellow billionaires Bill Gates and Warren Buffet: laundering his untold billions through a health research prestige project.

Called the Chan Zuckerberg Biohub — his wife Priscilla Chan, a pediatrician, is also involved — the foundation’s stated long-term mission is to “cure and prevent all disease through AI-powered biology, frontier research, and state-of-the-art technology.”

True to those enormous goals, the Biohub recently announced a $500 million investment into AI models of human cells, specifically, in order to “accelerate the cure and prevention of all diseases,” Euronews reported.

ALS and Huntington Disease: Unraveling the Connections between TDP-43 and Huntingtin

Amyotrophic lateral sclerosis (ALS) and Huntington disease (HD) are lethal neurodegenerative diseases affecting motor function. Though their etiology and pathology are distinct, recent evidence suggests commonalities between TAR DNA-binding protein (TDP-43), which is associated with 97% of ALS cases, and huntingtin (HTT), the causative protein of HD. ALS is a heterogeneous, lethal neurodegenerative disease characterized by the progressive loss of upper and lower motor neurons, as well as brainstem and spinal cord degeneration. The causes of ALS are complex, variable, and, in some cases, unknown, but most cases involve mislocalization of the protein TDP-43. In contrast, HD is a monogenic, autosomal dominant, lethal neurodegenerative disease caused by polyglutamine expansion in HTT protein and characterized by the progressive loss of neurons in the brain, particularly in the striatum, which results in motor, cognitive, and behavioral changes. Although HD is not typically associated with motor neuron loss, recent evidence suggests a link between HTT and TDP-43 within the context of both ALS and HD, as well as links to related neurodegenerative diseases, such as frontotemporal dementia (FTD) and spinocerebellar ataxia type 2 (SCA2). Herein, we discuss confirmed cases of concurrent ALS and HD and the overlap of underlying disease mechanisms that potentially contribute to the onset and progression of these two devastating neurodegenerative diseases, with a focus on commonalities between TDP-43 and HTT. We propose that elucidating these commonalities will aid in the identification of broad-spectrum disease risk factors and potential overlapping treatment targets.

Copenhagen interpretation

Other articles where Copenhagen interpretation is discussed: Solvay Conferences: …be known as the “Copenhagen interpretation” of quantum mechanics, which postulated that the indeterminacy in the theory (i.e., that only the probability of a result could be predicted) was fundamental and should be accepted by scientists. There was no underlying deterministic order to be found. Some physicists, most notably…

Temporal superposition and feature geometry of RNNs under memory demands

Abstract: Understanding how populations of neurons represent information is a central challenge across machine learning and neuroscience. Recent work in both fields has begun to characterize the representational geometry and functionality underlying complex distributed activity. For example, artificial neural networks trained on data with more features than neurons compress data by representing features non-orthogonally in so-called *superposition*. However, the effect of time (or memory), an additional capacity-constraining pressure, on underlying representational geometry in recurrent models is not well understood. Here, we study how memory demands affect representational geometry in recurrent neural networks (RNNs), introducing the concept of temporal superposition. We develop a theoretical framework in RNNs with linear recurrence trained on a delayed serial recall task to better understand how properties of the data, task demands, and network dimensionality lead to different representational strategies, and show that these insights generalize to nonlinear RNNs. Through this, we identify an effectively linear, dense regime and a sparse regime where RNNs utilize an interference-free space, characterized by a phase transition in the angular distribution of features and decrease in spectral radius. Finally, we analyze the interaction of spatial and temporal superposition to observe how RNNs mediate different representational tradeoffs. Overall, our work offers a mechanistic, geometric explanation of representational strategies RNNs learn, how they depend on capacity and task demands, and why.

Supplementary Material: zip

Primary Area: interpretability and explainable AI.

SpaceX files for $55 billion semiconductor fab in rural Texas for Musk’s Terafab — total chipmaking fab investment could reach $119 billion

SpaceX has filed a property tax abatement application in Grimes County, Texas, for a semiconductor fab that would cost $55 billion in its initial phases and up to $119 billion if all planned expansions are completed.

The filing, posted on the county government’s website ahead of a public hearing scheduled for June 3, describes the project as a “multi-phase, next-generation, vertically integrated semiconductor manufacturing and advanced computing fabrication facility” to be built at the Gibbons Creek Reservoir site, roughly 90 miles northeast of Austin.

The capital figures in this filing far exceed what was disclosed when Elon Musk announced Terafab in March, where the project carried a $20 billion price tag. Musk later confirmed during Tesla’s earnings call that SpaceX would handle high-volume chip manufacturing while Tesla operates a smaller R&D pilot line at its Austin campus. The Grimes County filing appears to be SpaceX’s first formal step toward securing a site for that production facility.

Movement Triggers a Hidden ‘Brain Cleaning’ Mechanism, Study Shows

We already know that moving your body is important for brain health, but a new study reveals a possible reason why: It could be triggering a kind of hydraulic pump that flushes out fluid in the brain.

By studying mice and conducting simulations, researchers at the Pennsylvania State University (Penn State) have found that movements in the abdominal muscles can ripple all the way up to the brain, potentially cleaning out waste materials that build up during the day.

It’s tangible evidence that what goes on in our brains and our bodies isn’t so separate after all, and a good reminder to get that body moving, in whatever way works for you, throughout the day.

Artificial intelligence accelerates discovery of next-generation disinfectants

Chemists and computer scientists tapped AI to find new disinfectants to combat the growing threat of dangerous “superbugs.”

The Journal of Chemical Information and Modeling published their computational-experimental framework for developing quaternary ammonium compounds, or QACs, to kill bacteria.

The method yielded 11 new QACs that show activity against antimicrobial-resistant bacteria.

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