J. Baker

Identification of novel bone-resorption markers by osteoclasts in vitro and in vivo

This study identifies 22 novel bone-resorption markers produced by osteoclasts in vitro and validates 14 in human biofluids, with two fragments elevated in bone metastasis urine.

Intraspecies warfare restricts strain coexistence in human skin microbiomes

The paper shows that intraspecies warfare limits strain coexistence in human skin microbiomes by analyzing interactions between Staphylococcus epidermidis isolates.

Single cell resolution analysis of multi-tissue derived human iNKT cells reveals novel transcriptional paradigms

This study uses single-cell RNA-sequencing to analyze human iNKT cells from multiple tissues, identifying novel transcriptional patterns and subsets not previously described in mice.

Hominin brain size increase has emerged from within-species encephalization

This study shows that hominin brain size increase over 7 million years came from within-species changes, not between-species differences, and that this trend accelerated over time.

Quantized Thermodynamics, Nested Resonant Structures, and the Entropic Stability of Life

The paper develops a model of thermal scaling to explain how biological systems, like muscle, achieve entropic stability through quantum-like phenomena, bridging classical and molecular thermodynamics.

Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species

The paper reveals hidden strain dynamics in skin microbiome species, showing that while strains are transient, some are more stable and may be targets for therapeutic interventions.

Four Phases of a Force Transient Emerge from a Binary Mechanical System

The paper presents a thermodynamic model of muscle contraction showing four phases of force response following a perturbation, validated against experimental data.

The Kinetic and Energetic Pull of Chemical Entropy

The paper explains how irreversible chemical reactions in biological systems are driven by entropy from a binary system of switches, using muscle contraction as a model.

Stochastic Force Generation in an Isometric Binary Mechanical System: A Thermodynamic Model of Muscle Force Generation

This paper introduces a thermodynamic model of muscle contraction that simulates isometric force generation and shows force kinetics are bounded by thermodynamic equations, with periodic force generation emerging from stochastic simulations.

Pan-antiviral effects of a PIKfyve inhibitor on respiratory virus infection in human nasal epithelium and mice

This study shows that PIKfyve inhibitors reduce viral load and inflammation in respiratory virus infections in human epithelium and mice, suggesting their potential as broad-spectrum antivirals.

Taste shaped the use of botanical drugs

This study examines how chemosensory qualities predict the therapeutic use of ancient Graeco-Roman botanical drugs.

Co-evolutionary dynamics of mammalian brain and body size

This study investigates the co-evolution of brain and body size in mammals, finding a curvilinear relationship and variable evolutionary rates, with primates showing significant increases in relative brain size.

Extracellular release of damaged mitochondria induced by pre-hematopoietic stem cell transplant conditioning exacerbates graft-versus-host disease

This study shows that conditioning before hematopoietic stem cell transplant releases damaged mitochondria, which activate host APCs and worsen GVHD.

SARS-CoV-2 Spike Protein Reduces Burst Activities in Neurons Measured by Micro-Electrode Arrays

This study shows that SARS-CoV-2 S1 protein reduces neuronal burst activity in vitro, while S2 does not, and this effect is blocked by an anti-S1 antibody.

Single-cell Transcriptomics Reveal Different Maturation Stages and Sublineages Commitment of Human Thymic Invariant Natural Killer T cells

This study uses single-cell RNA sequencing to identify maturation stages and sublineage commitment in human thymic iNKT cells, revealing two distinct clusters with immature and mature profiles.

Integrated Analysis of T cell Repertoire and Transcriptome Identifies Mechanisms of Regulatory T cell (Treg) Suppression of Acute Graft-versus-Host-Disease

This study identifies how regulatory T cells suppress acute graft-versus-host disease by modulating conventional T cell transcriptomes and metabolism without affecting graft-versus-tumor activity.

Loss of FOXP3 function causes expansion of two pools of autoreactive T cells in patients with IPEX syndrome.

FOXP3 mutations in humans lead to expansion of autoreactive T cells from both effector and regulatory T cells that gain effector function.

Antibodies to ILT3 abrogate myeloid immunosuppression and enable tumor killing

This study shows anti-ILT3 antibodies block myeloid immunosuppression and enhance tumor killing in solid tumors.

Multi-parameter optical imaging of immune cell activity in chimeric antigen receptor T-cell and checkpoint blockade therapies

The paper develops a small molecule for imaging immune cell activity in cancer immunotherapies and demonstrates its utility in predicting treatment outcomes.

Allogeneic CAR-invariant Natural Killer T Cells Exert Potent Antitumor Effects Through Host CD8 T cell Cross-Priming

This study shows allogeneic CAR-iNKT cells effectively combat tumors in mice by directly attacking cancer cells and boosting host CD8 T cell responses, even across major MHC barriers.

150 million years of sustained increase in pterosaur flight efficiency

This study investigates the evolutionary increase in pterosaur flight efficiency over 150 million years, focusing on changes in locomotion energetics.

The Min system disassembles FtsZ foci and inhibits polar peptidoglycan remodeling in Bacillus subtilis

This study quantifies FtsZ dynamics in Bacillus subtilis and shows the Min system disassembles Z-rings and inhibits polar peptidoglycan remodeling.

Cariogenic Streptococcus mutans produces strain-specific antibiotics that impair commensal colonization

This study identifies a biosynthetic pathway in Streptococcus mutans that produces strain-specific antibiotics, which inhibit commensal bacteria and contribute to dental caries.

The Work Performed By Biological Motors

This paper evaluates models of mechanochemical coupling in molecular motors and concludes that Hill's 1930s model best describes their function.

Spatial and Temporal Analysis of the Stomach and Small Intestinal Microbiota in Fasted Healthy Humans

This study analyzes the microbiota composition in the stomach and small intestine of fasted healthy humans over time, finding greater variability in the duodenum and correlations with pH changes.