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GDFold2: A fast and parallelizable protein folding environment with freely defined objective functions.
Protein Sci
February 2025
MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.
An important step of mainstream protein structure prediction is to model the 3D protein structure based on the predicted 2D inter-residue geometric information. This folding step has been integrated into a unified neural network to allow end-to-end training in state-of-the-art methods like AlphaFold2, but is separately implemented using the Rosetta folding environment in some traditional methods like trRosetta. Despite the inferiority in prediction accuracy, the conventional approach allows for the sampling of various protein conformations compatible with the predicted geometric constraints, partially capturing the dynamic information.
View Article and Find Full Text PDFEnhancement of titanium surfaces using different acid solutions at room temperature to improve bone cell responses.
J Dent Sci
January 2025
School of Dental Technology, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.
Background/purpose: Early osseointegration of titanium (Ti) dental implants relies on the surface topography. Surface modification of Ti seeks to enhance bone regeneration around implants. Acid etching is the simple, less technique sensitive and cost-effective technique for surface treatment.
View Article and Find Full Text PDFNon-invasive Assessment of Human Epidermal Growth Factor Receptor 2 Expression in Gastric Cancer Based on Deep Learning: A Computed Tomography-based Multicenter Study.
Acad Radiol
January 2025
Department of Radiology, Xinhua Hospital, Shanghai Jiaotong University Medical School, Shanghai 200092, China (Z.H.W., Y.Q.M., X.Y.W., N.X.Y., X.Y.W., G.R.). Electronic address:
Rationale And Objectives: The expression of human epidermal growth factor receptor 2 (HER2) in gastric cancer is closely associated with its treatment outcomes and prognosis. This study aims to develop and validate a HER2 prediction model based on computed tomography (CT). Additionally, the study evaluates the robustness of the proposed model.
View Article and Find Full Text PDFAn efficient heuristic for geometric analysis of cell deformations.
Comput Biol Med
January 2025
SCOPIA Research Group, University of the Balearic Islands, Dpt. of Mathematics and Computer Science, Crta. Valldemossa, Km 7.5, Palma, E-07122, Spain; Health Research Institute of the Balearic Islands (IdISBa), Palma, E-07122, Spain; Laboratory for Artificial Intelligence Applications at UIB (LAIA@UIB), Palma, E-07122, Spain; Artificial Intelligence Research Institute of the Balearic Islands (IAIB), Palma, E-07122, Spain. Electronic address:
Sickle cell disease causes erythrocytes to become sickle-shaped, affecting their movement in the bloodstream and reducing oxygen delivery. It has a high global prevalence and places a significant burden on healthcare systems, especially in resource-limited regions. Automated classification of sickle cells in blood images is crucial, allowing the specialist to reduce the effort required and avoid errors when quantifying the deformed cells and assessing the severity of a crisis.
View Article and Find Full Text PDFListening to the Formation of Polymorphs in a Ball Mill.
Anal Chem
January 2025
ICGM, Univ. Montpellier, CNRS, ENSCM, 34000 Montpellier, France.
In this contribution, we apply our newly developed ball-milling platform, which combines Raman spectroscopy and thermal (IR) imaging, as well as acoustic and high-speed optical video recordings, to the synthesis and transformation of citric acid-isonicotinamide (1:2) cocrystal polymorphs in transparent PMMA jars. Particularly, we demonstrate how Raman, temperature, acoustic, and video data are complementary and enable detection and connection of chemical and physical events happening during ball-milling in a time-resolved manner. Importantly, we show that the formation of the three cocrystal polymorphs can be detected through acoustic analyses solely.
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