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Molecular Simulation and Artificial Intelligence for the Circular Economy of Bioenergy and Bioproducts

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Susan Gregurick @sgregurick.bsky.social · Sep 7

www.cell.com/biophysj/abs.... 🧪 nice work from Jeremey smith at ORNL discuss the role of MD and ML/AI to overcome lignocellulose recalcitrance by designing pretreatment methods to efficiently produce solubilized cellulose/lignin/hemicellulose, and improve energy-intensive manufacturing challenges.

The concept of the circular bioeconomy is a carbon neutral, sustainable system with zero waste. One vision for such an economy is based upon lignocellulosic biomass. This lignocellulosic circular bioe...

www.cell.com

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Susan Gregurick @sgregurick.bsky.social · Sep 7

www.nature.com/articles/s41...
🧪. this study provides evidence indicating S. mutans can colonize the gut and affect PD pathology via microbial UrdA and its metabolite, imidazole propionate.

Gut microbial production of imidazole propionate drives Parkinson’s pathologies - Nature Communications

Here, the authors show that the oral microbe Streptococcus mutans, elevated in the gut microbiome of Parkinson’s patients, produces imidazole propionate via UrdA that in mice reaches the brain and tri...

https://doi.org/10.1001/jamaneurol.2025.2218

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Reposted by Susan Gregurick

Shicheng Guo @shihcheng.bsky.social · Sep 5

Study reveals 90%^+ agreement between real-world amyloid-PET visual reads and quantification, aiding cognitive impairment diagnosis! 🧠 PMID:40720133, JAMA Neurol 2025, @JAMANeuro https://doi.org/10.1001/jamaneurol.2025.2218 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

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doi.org

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Susan Gregurick @sgregurick.bsky.social · Sep 5

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Susan Gregurick @sgregurick.bsky.social · Sep 5

link.springer.com/article/10.1...
Neat study finds that cholesterol metabolism was clearly altered in the TDP-43 proteinopathies of effected brains, pointing towards an accumulation of cholesterol esters and triglycerides in the form of lipid droplets

TDP-43 dysregulation impairs cholesterol metabolism linked with myelination defects - Acta Neuropathologica

TDP-43 is a nuclear protein encoded by the TARDBP gene, which forms pathological aggregates in various neurodegenerative diseases, collectively known as TDP-43 proteinopathies, including amyotrophic l...

TDP-43 dysregulation impairs cholesterol metabolism linked with myelination defects - Acta Neuropathologica

Reposted by Susan Gregurick

Susan Gregurick @sgregurick.bsky.social · Sep 5

link.springer.com/article/10.1...
Neat study finds that cholesterol metabolism was clearly altered in the TDP-43 proteinopathies of effected brains, pointing towards an accumulation of cholesterol esters and triglycerides in the form of lipid droplets

TDP-43 is a nuclear protein encoded by the TARDBP gene, which forms pathological aggregates in various neurodegenerative diseases, collectively known as TDP-43 proteinopathies, including amyotrophic l...

TDP-43 dysregulation impairs cholesterol metabolism linked with myelination defects - Acta Neuropathologica

Susan Gregurick @sgregurick.bsky.social · Sep 5

link.springer.com/article/10.1...
Neat study finds that cholesterol metabolism was clearly altered in the TDP-43 proteinopathies of effected brains, pointing towards an accumulation of cholesterol esters and triglycerides in the form of lipid droplets

TDP-43 is a nuclear protein encoded by the TARDBP gene, which forms pathological aggregates in various neurodegenerative diseases, collectively known as TDP-43 proteinopathies, including amyotrophic l...

Exploring the uncharted role of cell senescence in rare diseases - Orphanet Journal of Rare Diseases

Reposted by Susan Gregurick

PLOS Biology @plosbiology.org · Sep 3

What causes viral transmission bottlenecks? This study uses barcoded virions to show that in the case of #influenza A #virus, early within-host replication dynamics (rather than a reduced inoculum population) drive loss of diversity during transmission @plosbiology.org 🧪 plos.io/4ngicDK

Population diversity declines between inoculated and exposed guinea pigs. Viral titers in nasal lavage samples are indicated by the overall height of the bar. Red lines show LOD (50 PFU/mL). Colors within the bars represent unique barcodes, and the height of each color indicates barcode frequency within the sample. Plots for individual animals are paired with those of their cage mate. Representative pairs for direct contact (top half) and aerosol (bottom half) exposure are shown from three experimental replicates. Guinea pig ID numbers are shown in the upper right corner of each plot.

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Susan Gregurick @sgregurick.bsky.social · Sep 3

ojrd.biomedcentral.com/articles/10..... A good read. 🧪

Background Cellular senescence is a biological process in which the cell cycle is arrested in response to DNA damage caused by different endogenous and exogenous stimuli. In senescent cells, activatio...

ojrd.biomedcentral.com

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Susan Gregurick @sgregurick.bsky.social · Aug 29

movementecologyjournal.biomedcentral.com/articles/10....
Neat article on tiger adaptation and movement.

Rest to roam: behavioural adaptations of tigers in anthropogenically altered landscapes - Movement Ecology

Background Large carnivores in human-dominated landscapes face significant risks from increased anthropogenic pressure, making it crucial to understand their movement behaviour for conservation strate...

movementecologyjournal.biomedcentral.com

Susan Gregurick @sgregurick.bsky.social · Aug 29

Cardiovascular and kidney outcomes of GLP‐1 receptor agonists in adults with obesity: A target trial emulation study - Tang - Diabetes, Obesity and Metabolism - Wiley Online Library dom-pubs.pericles-prod.literatumonline.com/doi/10.1111/...
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dom-pubs.pericles-prod.literatumonline.com

Susan Gregurick @sgregurick.bsky.social · Aug 26

www.nature.com/articles/s43...
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Interesting article on deep active optimization for low data problems. The back propagation out of local minima and benchmarks on finding tricky global minima using DNN is cool. The discussion on tradeoffs between Bayesian optimization and active optimization is cool

Deep active optimization for complex systems - Nature Computational Science

This study introduces a deep active optimization pipeline that effectively tackles high-dimensional, complex problems with limited data. The approach minimizes sample size and surpasses existing metho...

Machine learning to predict bacteriuria in the emergency department - Scientific Reports

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Susan Gregurick @sgregurick.bsky.social · Aug 25

www.nature.com/articles/s41... 🧪

Scientific Reports - Machine learning to predict bacteriuria in the emergency department

Image-based honey bee larval viral and bacterial diagnosis using machine learning - Scientific Reports

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Susan Gregurick @sgregurick.bsky.social · Aug 22

www.nature.com/articles/s41... what a nice article highlighting deep learning methods to detect brood disease in honeybees

Scientific Reports - Image-based honey bee larval viral and bacterial diagnosis using machine learning

Advances in Ischemic Stroke Treatment: Current and Future Therapies - Neurology and Therapy

Susan Gregurick @sgregurick.bsky.social · Aug 14

link.springer.com/article/10.1...
🧪. Really interesting in particular the section on blood pressure control post thrombectomy

This review summarizes current concepts in our understanding of stroke anatomy, pathophysiology of cerebral hypoperfusion, and collateral circulation. It also provides an evidence-based update in stro...

Widespread, perception-related information in the human brain scales with levels of consciousness

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Susan Gregurick @sgregurick.bsky.social · Aug 13

direct.mit.edu/imag/article...
🧪. Researchers illustrate that the presence of information is far more distributed across the brain than previously thought and that information is fairly accessible

Abstract. How does the human brain generate coherent, subjective perceptions—transforming yellow and oblong visual sensory information into the perception of an edible banana? This is a hard problem. ...

direct.mit.edu

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Susan Gregurick @sgregurick.bsky.social · Aug 12

open-research-europe.ec.europa.eu/articles/5-1... 🧪 unexpected and really fun read. I enjoyed the discussion on developing the ontology and use of Protégé. Makes me want to travel and try this out.

open-research-europe.ec.europa.eu