J. Lai

A generative reference grammar of healthy TCR repertoires reveals cancer-associated immune remodeling

CRAFT, a transformer model, learns a generative grammar of healthy TCR repertoires to detect cancer-associated immune remodeling through structured deviations in sequence space.

Transcriptomic responses of gecarcinid land crabs to acute and prolonged desiccation stress

This study examines transcriptomic responses to desiccation stress in three gecarcinid land crab species, identifying differentially expressed osmoregulatory genes and their evolutionary implications.

rarestR: An R package using rarefaction metrics to estimate α-diversity (species richness) and β-diversity (species shared) for incomplete samples

rarestR estimates α- and β-diversity for incomplete samples using rarefaction metrics and parametric extrapolations, offering visualization tools for curve fitting.

Unveiling the Intricate Sinking behavior of Large Diatoms: Insights from Time-Frequency Analysis of Palmerina hardmaniana Sinking under Silicate-Depleted Conditions

This study uses wavelet analysis to examine how silicate depletion affects the sinking behavior of Palmerina hardmaniana, revealing intermittent regulation with similar frequency ranges in control and stressed conditions.

Cognate Antigen Engagement Induces HIV-1 Expression In CD4+ T Cells From People On Long-Term ART

The paper shows that cognate antigen engagement in CD4+ T cells on long-term ART increases HIV-1 transcription through T cell activation, suggesting a role in viral rebound.

Islands of genomic stability in the face of genetically unstable metastatic cancer

The paper identifies genomically stable regions in metastatic pancreatic cancer that can be targeted by CRISPR-Cas9 due to preserved PAM sites, suggesting a potential gene therapy approach.

Multivalent DNA-encoded lectins on phage enable detecting compositional glycocalyx differences

This paper develops a phage-based liquid lectin array to detect subtle glycocalyx differences by displaying multivalent lectins on DNA-barcoded M13 phage.

The microbial community of rust layer biofilm was driven by seawater microbial community

The paper analyzes microbial communities in rust layer biofilm and seawater, identifying dominant taxa and their interactions, and provides insights into microbial corrosion mechanisms in marine environments.

Targeted photodynamic neutralization of SARS-CoV-2 mediated by singlet oxygen

This paper develops a targeted photodynamic approach to neutralize SARS-CoV-2 by enhancing antibody efficacy through singlet oxygen generation.

Talaromyces marneffei suppresses human macrophages inflammatory by producing the truncated protein NCOR2-013 via TUT1-regulated alternative splicing

This study identifies TUT1-regulated alternative splicing of NCOR2 producing NCOR2-013 as a mechanism by which Talaromyces marneffei suppresses macrophage inflammation.

HSP90.6 is involved in grain filling via carbon and nitrogen metabolism in maize.

HSP90.6 regulates maize grain filling by affecting 26S proteasome-mediated nitrogen recycling and GF14-6-mediated carbon metabolism.

Outsourced hearing in an orb-weaving spider that uses its web as an auditory sensor

This paper demonstrates that the orb-weaving spider uses its web as an acoustic sensor to detect and localize airborne sounds, surpassing the efficiency of known eardrums.

Computational design of highly signaling active membrane receptors through de novo solvent-mediated allosteric networks

This paper designs novel membrane receptors with enhanced activity and stability through engineered allosteric networks involving solvent-mediated interactions.

Tuft cell-produced cysteinyl leukotrienes and IL-25 synergistically initiate lung type 2 inflammation

The paper shows that tuft cell-produced cysteinyl leukotrienes and IL-25 synergistically drive lung type 2 inflammation in response to aeroallergens.

Maxent modeling for predicting the potential distribution of global talaromycosis

This paper uses Maxent modeling to predict the global distribution of talaromycosis, identifying key environmental and epidemiological drivers.

rdacca.hp: an R package for generalizing hierarchical and variation partitioning in multiple regression and canonical analysis

The paper introduces an R package for generalizing hierarchical and variation partitioning in canonical analysis to improve model interpretation with multiple response variables.

The immunophilin protein FKBPL and its peptide derivatives are novel regulators of vascular integrity and inflammation via NF-kappaB signaling

This paper identifies FKBPL and its peptides as regulators of vascular integrity and inflammation via NF-kappaB signaling, showing therapeutic potential in inflammatory diseases.

Talaromyces marneffei promotes M2 polarization of human macrophages by downregulating SOCS3 expression and activating TLR9 pathway

This study shows Talaromyces marneffei induces M2 macrophage polarization by downregulating SOCS3 and activating TLR9, enhancing fungal survival.

Antigen-driven clonal selection shapes the persistence of HIV-1 infected CD4+ T cells in vivo

This study links antigen responsiveness, proviral sequences, integration sites, and TCRβ sequences to show antigen-driven clonal selection maintains HIV-1 persistence in CD4+ T cells.

Transcriptome Profiling of different types of human respiratory tract cells infected by SARS-CoV-2 Highlight an unique Role for Inflammatory and Interferon Response

This study identifies 36 upregulated genes across SARS-CoV-2-infected respiratory tract cells, highlighting inflammatory and interferon response pathways linked to cytokine storms in severe COVID-19.

Selective Optogenetic Stimulation of Glutamatergic, but not GABAergic, Vestibular Nuclei Neurons Induces Immediate and Reversible Postural Imbalance in Mice

This paper uses optogenetics to show that glutamatergic vestibular nuclei neurons, but not GABAergic ones, cause immediate postural imbalance in mice.

Characterization and establishment of a novel EBV strain simultaneously associated with nasopharyngeal carcinoma and B-cell lymphoma

The paper characterizes a novel EBV strain, Yu103, associated with both nasopharyngeal carcinoma and B-cell lymphoma, showing its dual tropism and unique genomic features.

Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage

This study identifies colibactin-645 as a genotoxic metabolite that induces DNA double-strand breaks via a copper-mediated oxidative mechanism, revealing its role in colorectal cancer progression.

Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size

This study assesses the precision and repeatability of HIV-1 latent reservoir size measurements using QVOA across labs and storage conditions, finding assay variability and supporting frozen storage.