#ScienceNews

[cbirt]

Large-scale gene expression data is used by Geneformer and scGPT models to build fundamental single-cell biology models. These models implicitly learn gene and cellular activities from millions of cell expression profiles, necessitating labor-intensive training and considerable data curation. Here, researchers from Stanford University use gene embeddings from the literature leveraging ChatGPT to investigate a much easier solution. In order to create gene embeddings, GenePT uses the GPT-3.5 and the NCBI text descriptions of specific genes. 

GenePT is an effective technique for creating single-cell embeddings by averaging gene embeddings according to the expression level of each gene. It performs on par with or better than Geneformer and other models, and it is user-friendly and efficient. GenePT generates sentence embeddings for every cell by sorting gene names according to expression level. It shows that a straightforward and efficient route for biological foundation models is the large language model embedding of literature.

The foundation models Geneformer and scGPT  are made to learn gene and cell embeddings for further investigations. Using a deep learning architecture, these models link input genes and cells to a high-dimensional embedding vector and collect large datasets of single-cell gene expression for pretraining. A small amount of task-specific data can be used to refine the model and improve its predictive power for downstream tasks.

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[amoebadiscovery]

Pelomyxa is a genus of large amoebae with distinctive biological features that make them significant in the study of protists. These organisms possess multiple nuclei that exist at various stages throughout their life cycle, allowing them to adapt to specific environmental conditions.

Although their surface is covered by numerous flagella, these structures are not functional for movement, as they have undergone evolutionary reduction and lost their role in locomotion. Rather than utilizing flagella for locomotion, Pelomyxa employs a slow crawling mechanism along the bottom of lakes and ponds, moving at a gradual pace.

Pelomyxa is specialized for life in low-oxygen zones found in the bottom sediments of freshwater environments. These amoebae are typically located in the sediment-covered bottoms of ponds and small lakes, where the soil is rich in decaying organic matter, especially decomposed plant material such as broken-down leaves. These conditions provide an ideal environment for Pelomyxa to develop in relative isolation, hidden from most other aquatic organisms.

Currently, 14 species of Pelomyxa are recognized, while historical records mention about 20 additional species that have not been observed since their initial descriptions. Some of these species may have gone extinct, while others may still exist in unexplored habitats, awaiting rediscovery.

An interesting example is Amoeba quarta, first described in 1884 by the researcher August Gruber. After its initial observation, this species seemingly disappeared from scientific knowledge until 2024, when researchers from St. Petersburg rediscovered it during a study of the sediments of Lake Osinovskoe in northwest Russia. Subsequent investigations revealed that this organism belonged to the genus Pelomyxa, and the species was renamed Pelomyxa quarta.

These rediscoveries emphasize the importance of studying ecosystems that often remain overlooked but may conceal organisms critical for understanding biodiversity. The slow-moving, inconspicuous Pelomyxa offers valuable insights into ecological processes in the depths of freshwater ecosystems, which are frequently underexplored. This also serves as a reminder that many unknown species may still be waiting to be discovered and included in contemporary biological research.

For the curious and the scientifically minded, you can read more in the full research paper here: https://doi.org/10.21685/1680-0826-2024-18-3-5

[manifestisnow]

Anything is possible in the Quantum field Using Affirmations can help you get in flow with it.

Love and Light Manifestisnow.

[whatshappeningintheworlds-blog]

Officials confirmed on Monday that the metal item that crashed from the sky, tearing through the roof of a Naples, Florida, home last month and lodged in a family's wall, was part of the debris from a trash pallet NASA launched into space three years prior.

[sassylightcycle]

read Full article click

[neosciencehub]

Babies develop Food Preferences in the Womb, Study Reveals

Babies develop Food Preferences in the Womb, Study Reveals @neosciencehub #Babies #Womb #Study #NewResearch #Pregnancy #Sciencenews #neosciencehub

Babies may begin developing food preferences while still in the womb, according to new research conducted by Durham University, UK. Scientists found that newborns positively responded to the smells of foods their mothers had consumed during pregnancy. The findings open doors to understanding how early flavour exposure might influence long-term eating habits and provide a pathway to encourage…

[biopractify]

"How to stay updated with the latest research in bioinformatics?

Bioinformatics is evolving rapidly, with new discoveries, algorithms, and datasets emerging every day. Whether you're a student, researcher, or professional, staying updated is crucial for growth in this interdisciplinary field. But with the overwhelming amount of information out there, how can you keep track of the latest research?

Here’s a step-by-step guide to staying informed about bioinformatics advancements:

📚 1. Follow Peer-Reviewed Journals

Leading journals publish cutting-edge bioinformatics research. Consider subscribing to:

Bioinformatics (Oxford Journals)

BMC Bioinformatics

Nucleic Acids Research (NAR)

Genome Biology

PLoS Computational Biology

Nature Biotechnology

📝 Pro Tip: Set up Google Scholar alerts for specific keywords like "machine learning in bioinformatics" or "single-cell RNA sequencing" to receive relevant papers directly in your inbox.

📰 2. Leverage Preprint Servers

Not all groundbreaking research is published in journals immediately. Many researchers upload their work to preprint servers:

bioRxiv (Preprints in biology and bioinformatics)

arXiv (Computational biology & AI in bioinformatics)

🧠 Why use preprints? They help you access fresh research before peer review, giving you a competitive edge.

💻 3. Follow Top Bioinformatics Blogs & Websites

Several platforms curate the latest developments in bioinformatics:

OMGenomics (Personal insights from bioinformatics professionals)

Bits of DNA (Exploring genomics and computational biology)

Biostars (Community-driven discussions on bioinformatics challenges)

SEQC Blog (Sequencing and bioinformatics trends)

🎙️ 4. Listen to Bioinformatics Podcasts

If you prefer learning on the go, podcasts are a great way to absorb new knowledge: 🎧 Best Bioinformatics Podcasts:

The Bioinformatics Chat

Genomics in 5 Minutes

The OmicsCast

🧑‍🤝‍🧑 5. Engage with the Bioinformatics Community

Joining discussions and interacting with experts helps you stay informed: 🔹 Reddit: r/bioinformatics, r/genomics 🔹 Twitter/X: Follow researchers and hashtags like #Bioinformatics, #ComputationalBiology 🔹 LinkedIn Groups: Bioinformatics Discussion Forum, AI in Bioinformatics 🔹 Slack & Discord: Join bioinformatics-specific communities for direct interaction

🎓 6. Take Online Courses & Webinars

Platforms like Coursera, edX, and BioPractify frequently update their courses to reflect the latest techniques in bioinformatics. Also, keep an eye out for:

Workshops by EMBL-EBI

Online tutorials from Galaxy Project & Bioconductor

📅 Tip: Many universities and conferences offer free webinars. Sign up for event notifications!

🔬 7. Attend Conferences & Hackathons

Networking at events helps you learn from researchers and industry leaders. Some key conferences include:

ISMB (Intelligent Systems for Molecular Biology)

RECOMB (Research in Computational Molecular Biology)

Genome Informatics Conference

BioHackathons (Hands-on experience with the latest tools)

🌍 Virtual & Hybrid Options: Many conferences now offer remote participation—take advantage of them!

🚀 8. Stay Hands-On with Open-Source Projects

Following GitHub repositories for bioinformatics tools and frameworks keeps you engaged with real-world applications. Some trending repositories:

Bioconductor (for R-based bioinformatics analysis)

Nextflow (for scalable data analysis workflows)

DeepVariant (AI-powered genome sequencing analysis by Google)

💡 Bonus: Contributing to open-source projects is a great way to learn while building your portfolio.

🔎 Final Thoughts

Bioinformatics is a dynamic field that blends biology, data science, and AI. Staying updated requires a multi-pronged approach—reading journals, engaging in online discussions, participating in hackathons, and continuously learning. By following these strategies, you’ll remain ahead in this ever-evolving domain.

📢 What’s your go-to method for staying updated in bioinformatics? Share your insights below! ⬇️✨

[newspro4706]

Middle East

South Korea’s impeached president detained over martial law gambit

[jameswebb-discoveries]

James Webb Space Telescope Uncovers New Mysteries of the Crab Nebula

NASA’s James Webb Space Telescope has unveiled groundbreaking details about the Crab Nebula! This iconic supernova remnant, observed in unprecedented detail, challenges previous theories about its origins. JWST’s advanced instruments revealed intricate structures and compositions, offering fresh insights into the enigmatic nebula. Dive into the mysteries of space with this latest discovery!

🔭🚀 Read more: https://www.jameswebbdiscovery.com/discoveries/james-webb-space-telescope-uncovers-new-mysteries-of-the-crab-nebula

#NASA #JamesWebb #CrabNebula #SpaceDiscovery #Astronomy #Supernova #SpaceExploration #Astrophysics #ScienceNews

[cbirt]

AlphaFold is a database of protein structures and predictions. It contains predictions for ~214 million proteins. AlphaFold2, developed by DeepMind, has dramatically scaled our capability to predict protein structures in silico. The extent of this data is overwhelming, and there are challenges regarding protein annotation, which practically applies to the information. Hence, researchers from the University of Trieste, SISSA (International School for Advanced Studies), ICTP (International Centre for Theoretical Physics), and IRCCS San Raffaele Institute introduced DPCstruct, an unsupervised clustering algorithm in the classification of protein domains using structural predictions informed by AlphaFold2. They discussed what DPCstruct means and what that might mean for the future of proteomics.

As mentioned above, the AlphaFold database is a paranormal resource with structural predictions for almost 214 million proteins across a large diversity of species. We can explore protein structures as sequence data, too. This correctness in structural predictions could be very productively used in a large number of processes such as drug discovery, variant effect prediction, and understanding evolution at the level of the proteins. While great possibilities can indeed be achieved using AlphaFoldDB, the lack of proper descriptions of full proteins greatly reduces their usability and demands some advanced tools for the classification and annotation of such structures.

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[outer-space-youtube]

Near Future of AI Agents?

AGI is not an AI Agent; AGI is a humanoid robot that can do the job as reliably as a human who is needed to do the job today. That humanoid will need assistance from AI Agents, but it will already be on the light speed neural network do use the Agents instantaneously. These two videos help you not to fear AGI, but to be prepared to use AI Agents, so we don’t need AGI Robots to take our jobs…?

[mpsay]

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A post shared by Mp Say (@mp__say)

🚨 ब्रेकिंग न्यूज़ 🚨 रूस ने बनाई कैंसर की वैक्सीन! 💉🧪

रूस के वैज्ञानिकों ने कैंसर के खिलाफ एक नई वैक्सीन विकसित की है, जो कैंसर कोशिकाओं को नष्ट करने में मददगार साबित हो सकती है। इस वैक्सीन का फिलहाल ट्र���यल चल रहा है, लेकिन शुरुआती नतीजे बेहद उत्साहजनक हैं। विशेषज्ञों का मानना है कि यह वैक्सीन कई प्रकार के कैंसर में कारगर हो सकती है।

इस खोज से कैंसर से जूझ रहे करोड़ों मरीजों के लिए उम्मीद की एक नई किरण जगी है। 🌟🙏

स्वास्थ्य जगत में यह एक बड़ी सफलता मानी जा रही है। जल्द ही इसके और भी अपडेट आपको मिलते रहेंगे! 🗞️ . .

[amoebadiscovery]

Adapting to environments with limited or no oxygen is one of the most remarkable evolutionary achievements, particularly when observed in single-celled organisms such as metamonads. These organisms are especially intriguing due to their extensive biological modifications: many metamonads either possess modified mitochondria or lack them altogether, distinguishing them from most other eukaryotes. Instead of relying on oxygen-dependent energy production, these organisms have evolved alternative metabolic pathways, enabling them to survive in some of the most extreme environments on Earth.

In November 2024, scientists introduced a novel genus of metamonads, Skoliomonas, which provides fresh insights into life in oxygen-deprived habitats. Skoliomonads are characterized by asymmetric morphology, with a rounded anterior and a sharply pointed posterior that extends into a long spike, often nearly as long as the organism's entire body. This distinctive tail is a prominent feature, and the organism’s dorsal surface rises into a pronounced hump, while the ventral side is flattened and features a groove along its right edge. At the terminus of this groove lies a scythe-shaped cytopharynx, a specialized feeding structure essential for nutrient acquisition.

As skoliomonads move through environment, they utilize the cytopharynx to capture bacteria, which are subsequently digested in vacuoles located along the dorsal side of the cell. These vacuoles enlarge and round out as digestion progresses, providing clear evidence of the organism’s feeding process. For locomotion, skoliomonads rely on two flagella; one flagellum sweeps in a large arc, generating a powerful yet fluid movement.

The feeding mechanism of skoliomonads is highly specialized and adapted to their environment. The ventral groove plays a crucial role in capturing and processing food. Although skoliomonads have not been observed filtering water currents under experimental conditions, they are capable of anchoring themselves to surfaces using their sharp posterior spike before detaching and resuming locomotion.

Under unfavorable conditions, skoliomonads can form cysts that provide structural protection and enhance the organism's survival in extreme environments. These cysts have a double wall and a protruding plug. Within the cyst, the nucleus is positioned near the anterior, and the nucleolus—particularly prominent in certain isolates—is eccentrically located. On the left side of the cell, digestive vacuoles distort the organism's shape as they extend across the dorsal side during feeding.

The discovery of skoliomonads significantly deepens our understanding of how life adapts to extreme, oxygen-deprived environments. Although these organisms possess a relatively simple structure, they reveal a complex realm of biological specialization. Their distinctive morphology, feeding mechanisms, and capacity to form protective cysts underscore the extraordinary adaptability of life, even in some of Earth's most inhospitable ecosystems.

For the curious and the scientifically minded, you can read more in the full research paper here: https://doi.org/10.1111/jeu.13048

[newsepick]

The Fibonacci Series: Nature's Math Magic

Discover the fascinating world of the Fibonacci sequence and learn how this mathematical pattern appears in various aspects of life including nature, art, and science, etc.Did you know? Today is the day, we celebrate the Fibonacci Sequence, a mathematical marvel where each number is the sum of the two preceding ones: 0, 1, 1, 2, 3, 5, 8, 13... and so on. This sequence forms the foundation of countless phenomena in mathematics and beyond, bridging the abstract with the tangible. At the heart of its significance lies its connection to the “Golden Ratio” (φ ≈ 1.618), a mathematical constant that emerges when you take the ratio of successive Fibonacci numbers as they approach infinity. The Golden Ratio manifests in nature 🌿—from the arrangement of leaves (phyllotaxis) 🌻 to the spirals of shells 🐚 and galaxies 🌌. It's also a cornerstone of art and architecture, shaping masterpieces like the Parthenon and influencing modern design. Engineers, physicists, and biologists find echoes of φ in wave dynamics, crystal structures, and even DNA's double helix. The Fibonacci sequence also underpins fractals and self-similar patterns, offering insights into chaos theory and recursive algorithms. For more such amazing news stories don’t forget to checkout Newsepick: https://app.newsepick.com/