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Category: biotech/medical – Page 56

An interesting paper where Schuette et al. develop a generative diffusion-based AI model for predicting the 3D structure of chromatin. Their model takes chromatin accessibility sequence data as input and outputs a statistical distribution of predicted 3D chromatin structures. Remarkably, their model generalizes across cell types, making it broadly useful! #computationalbiology #ai #generativeai

Computational approaches for predicting chromatin conformations de novo using only sequencing data remain scarce. Compared to existing polymer simulation–based prediction approaches, ChromoGen maintains unique advantages. The generative nature of ChromoGen enables efficient production of statistically independent samples, thus avoiding the inefficient navigation of state space that polymer simulations require to produce a diverse set of conformations. Moreover, ChromoGen’s transformer-based front end provides additional advantages, extracting features from sequencing data and placing the information in low-dimensional embeddings that the diffusion model handles efficiently. This powerful design markedly reduces the computational cost of each diffusion step, providing a practical means to achieve cell type–specific de novo predictions with the full benefit of DNA sequence and chromatin accessibility data. In contrast, incorporating DNA sequence information into polymer models has long been a challenging task that is often indirectly addressed by incorporating various histone marks.

In its current form, ChromoGen can be immediately applied to any cell type with available DNAse-seq data, enabling a vast number of studies into the heterogeneity of genome organization both within and between cell types to proceed. However, several improvements could enhance its utility. Notably, the current model exclusively predicts chromatin conformations in 1.28-Mb regions at 20-kb resolution, the latter restriction primarily stemming from our decision to maximize resolution within the constraints imposed by the available Dip-C data. However, higher-resolution single-cell datasets are becoming available, such as those at 5-kb resolution (50), and we anticipate that ChromoGen will require no modifications to perform well after training on these improved datasets. Similarly, we anticipate that ChromoGen can be directly applied to longer genomic regions if using a lower resolution, e.g.

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Published in the Journal of the American Chemical Society, the research by scientists at King’s College London and their collaborators suggests that chromatin—the complex of DNA

DNA, or deoxyribonucleic acid, is a molecule composed of two long strands of nucleotides that coil around each other to form a double helix. It is the hereditary material in humans and almost all other organisms that carries genetic instructions for development, functioning, growth, and reproduction. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).

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Dairy cattle in Nevada have been infected with a new type of bird flu that’s different from the version that has spread in U.S. herds since last year, Agriculture Department officials said Wednesday.

The detection indicates that distinct forms of the virus known as Type A H5N1 have spilled over from wild birds into cattle at least twice. Experts said it raises new questions about wider spread and the difficulty of controlling infections in animals and the people who work closely with them.

“I always thought one bird-to-cow transmission was a very rare event. Seems that may not be the case,” said Richard Webby, an influenza expert at St. Jude Children’s Research Hospital.

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Clinical trials are underway for a drug that could potentially prevent Alzheimer’s long before it kicks in. Researchers from Washington University School of Medicine are studying the effects of an experimental antibody called remternetug.

The drug was developed by pharmaceutical giant Eli Lilly. It is designed for genetically predisposed people to develop Alzheimer’s and its study focuses on young people aged 18 and up.

Remternetug targets amyloid beta, a protein that forms plaque in the brain. The presence of plaque is one of the key hallmarks of Alzheimer’s disease. Other recently approved drugs, like donanemab, also target amyloid plaque, since that seems to be what you attack if you want to chip away at Alzheimer’s.

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A 2020 assessment of IKN by the National Planning and Development Agency highlighted the risks, citing data including the abundance of disease-carrying mosquitoes. At least two construction workers caught malaria in 2022 while at the site, according to the Ministry of Health. Last year, 54 cases were reported there, but the ministry claimed the patients were infected elsewhere. Although the construction authority has taken some control measures, such as handing out mosquito nets to workers, it’s not well-equipped for the job, says Mirza Buana, a legal scholar at Lambung Mangkurat University in South Kalimantan: “It has all the authorities but no capabilities.” The agency has shifted most of the tasks—such as vector control and screening workers entering or leaving IKN—to district health officials, who have struggled to keep up.

Surendra is particularly worried about the potential spread of P. knowlesi, a parasite first discovered in the 1930s. It emerged as a public health threat in the early 2000s, in areas in the Malaysian part of Borneo where forests were cleared for oil palm plantations. It has since been identified in many Southeast Asian countries.

P. knowlesi primarily infects long-tailed macaques, highly adaptable monkeys that thrive at the forest edge, and is spread by forest-dwelling Anopheles mosquitoes that occasionally bite humans as well. People working in or near the forest, including hunters and loggers, are at the highest risk. Because it has an animal reservoir, the disease is impossible to eliminate completely. Mosquitoes don’t transmit P. knowlesi between people—or very poorly—but some scientists worry that could change.

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Synthetic biologists from Yale were able to re-write the genetic code of an organism—a novel genomically recoded organism (GRO) with one stop codon—using a cellular platform that they developed enabling the production of new classes of synthetic proteins. These synthetic proteins, researchers say, offer the promise of innumerable medical and industrial applications that can benefit society and human health.

The creation of the landmark GRO, known as “Ochre”—which fully compresses redundant, or “degenerate” codons, into a single codon—is described in a new study published in the journal Nature. A codon is a sequence of three nucleotides in DNA or RNA that codes for a specific amino acid, which serves as the biochemical building blocks for proteins.

“This research allows us to ask fundamental questions about the malleability of genetic codes,” said Farren Isaacs, professor of molecular, cellular and at Yale School of Medicine and of biomedical engineering at Yale’s Faculty of Arts and Sciences, who is co-senior author of the paper. “It also demonstrates the ability to engineer the genetic code to endow multi-functionality into proteins and usher in a new era of programmable biotherapeutics and biomaterials.”

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Every cell in the body normally has its fixed place as part of a tissue structure. Except for a few cell types, such as blood or immune cells. But cancer cells also cross established boundaries, grow into the surrounding tissue and multiply. And they can detach from the cell structure and spread via the blood or lymphatic vessels to other areas of the body, where they attach to new cells and form metastases.

The changes that undergo to metastasize are not yet fully understood. Rho (Ras-homologous) GTPases apparently play an important role. These proteins process signals within cells and regulate, among other things, growth, differentiation into the genetically predetermined cell type and cell migration.

Rho GTPases are molecular switches that switch between an active and an inactive state by binding to the phosphate compounds GTP and GDP. GTP corresponds to the ‘on’ position of the switch and starts the molecular biological processes, while GDP corresponds to the ‘off’ position and stops them.

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In this video, Dr. Ben Goertzel, CEO of SingularityNET, TrueAGI and the Artificial Superintelligence Alliance (ASI Alliance), analyzes DeepSeek LLM as an efficiency advancement rather than an AGI breakthrough. The model’s open-source implementation and technical architecture (mixture of experts and multi-token training) improve accessibility while maintaining performance. This development demonstrates the continued democratization of AI capabilities and may redirect industry focus toward alternative computing architectures and decentralized systems.

0:00 Intro.
00:33 Initial Thoughts on DeepSeek.
01:25 Efficiency Gains and Their Implications.
02:58 Technological Singularity and Rapid Advances.
04:07 DeepSeek’s Underlying Technology.
07:27 Open Source Approach and Its Benefits.
09:58 China’s Role in AI and Open Source.
12:20 Broader Implications for AI and AGI
15:42 Conclusion: The Path to Technological Singularity.

#AGI #Deepseek #AI
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SingularityNET was founded by Dr. Ben Goertzel with the mission of creating a decentralized, democratic, inclusive, and beneficial Artificial General Intelligence (AGI). An AGI is not dependent on any central entity, is open to anyone, and is not restricted to the narrow goals of a single corporation or even a single country.

The SingularityNET team includes seasoned engineers, scientists, researchers, entrepreneurs, and marketers. Our core platform and AI teams are further complemented by specialized teams devoted to application areas such as finance, robotics, biomedical AI, media, arts, and entertainment.

Website: https://singularitynet.io.

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Vincent Danen is the Vice President of Product Security at Red Hat.

Cyber threats are an everyday reality. Attackers exploit the unwitting, stealing confidential and sensitive information through online scam campaigns. Data breach prevention is only as strong as the weakest link, and, in most cases, that link is human. As I mentioned in a previous article, it is reported that 74% of data breaches are caused by human error.

According to a 2020 FBI report, there was a 400% spike in cyberattacks during the Covid-19 pandemic. The human element is a significant vulnerability in cybersecurity, often overlooked in favor of technological solutions. Many organizations focus on addressing software vulnerabilities when employees remain the weakest link in the organization’s security program. Even the most secure software, with all vendor security patches applied, is in danger if the human aspect of risk management is neglected.

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