Treat

Cover of Critical Care Medicine

Development of a Core Critical Care Data Dictionary With Common Data Elements to Characterize Critical Illness and Injuries Using a Modified Delphi Method

OBJECTIVES: To develop the first core Critical Care Data Dictionary (C2D2) with common data elements (CDEs) to characterize critical illness and injuries. DESIGN: Group consensus process using modified Delphi approach. SETTING: Electronic surveys and in-person meetings. SUBJECTS: A multidisciplinary workgroup of clinicians and researchers with expertise in the care of the critically ill and injured….

Workflow diagram of offline modeling and online planning for blood flow.

Real-time virtual intervention for simple and serial coronary artery disease using the HarVI framework

Virtual planning tools that provide intuitive user interaction and immediate hemodynamic feedback are crucial for cardiologists to effectively treat coronary artery disease. Current FDA-approved tools for coronary intervention planning require days of preliminary processing and rely on conventional 2D displays for hemodynamic evaluation. Immersion offered by extended reality (XR) has been found to benefit intervention…

Primitives of PTM-Mamba

PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks

Proteins serve as the workhorses of living organisms, orchestrating a wide array of vital functions. Post-translational modifications (PTMs) of their amino acids greatly influence the structural and functional diversity of different protein types and uphold proteostasis, allowing cells to swiftly respond to environmental changes and intricately regulate complex biological processes. To this point, efforts to…

Origin of fusion oncoproteins

FusOn-pLM: a fusion oncoprotein-specific language model via adjusted rate masking

Fusion oncoproteins, a class of chimeric proteins arising from chromosomal translocations, are major drivers of various pediatric cancers. These proteins are intrinsically disordered and lack druggable pockets, making them highly challenging therapeutic targets for both small molecule-based and structure-based approaches. Protein language models (pLMs) have recently emerged as powerful tools for capturing physicochemical and functional…

PepPrCLIP model training and evaluation

De novo design of peptide binders to conformationally diverse targets with contrastive language modeling

Designing binders to target undruggable proteins presents a formidable challenge in drug discovery. In this work, we provide an algorithmic framework to design short, target-binding linear peptides, requiring only the amino acid sequence of the target protein. To do this, we propose a process to generate naturalistic peptide candidates through Gaussian perturbation of the peptidic…

Comparison of SaLT&PepPr protein structure predictions with PPBS dataset models

SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders

Protein-protein interactions (PPIs) are critical for biological processes and predicting the sites of these interactions is useful for both computational and experimental applications. We present a Structure-agnostic Language Transformer and Peptide Prioritization (SaLT&PepPr) pipeline to predict interaction interfaces from a protein sequence alone for the subsequent generation of peptidic binding motifs. Our model fine-tunes the ESM-2 protein language model (pLM)…