Cornell University

Modeling the interferon response to avian influenza

Highly pathogenic avian influenza viruses, such as H5N1, cause severe disease in humans and pose a persistent pandemic threat, yet the mechanism by which the type I interferon response shapes their within-host dynamics remains unclear. Here we fit three ordinary differential equa...

MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics

Since the original publication of Model-based Analysis for ChIP-Seq (MACS), the software has been widely used to identify enriched genomic regions in ChIP-seq, ATAC-seq, CUT&RUN, DNase-seq, and related regulatory genomics assays. Over the years, MACS has evolved substantially, wi...

Toward scalable organ-level 3D plant segmentation: A systematic and quantitative review through the lens of the data-algorithm-computing triangle

The precise characterization of plant morphology provides valuable insights into plant-environment interactions and genetic evolution. A key technology for extracting this information is 3D segmentation, which delineates individual plant organs from complex point clouds. Despite...

Narrative 2 Numbers (N2N): Leveraging a Hackathon Approach to Generate Ideas and Approaches for Using Mixed Methods to Strengthen Public Health Preparedness and Response

ABSTRACT: Public health emergencies require rapid decision making using incomplete and evolving information, yet tools to quickly integrate actionable qualitative and quantitative data remain limited. To address this gap, we describe a replicable hackathon model that enabled the...

Carbon finance as climate adaptation depends on smallholder livelihood contexts in Uganda

Nature-based solutions in voluntary carbon markets have become increasingly important instruments for financing climate adaptation and mitigation, yet limited evidence exists on whether and how these mechanisms enable smallholder adaptation. This research examines smallholder par...

Pre-Diagnostic Plasma Endogenous Steroids and the Risk of Exfoliation Glaucoma

Purpose: Exfoliation glaucoma (XFG) is the most common secondary glaucoma. Prior studies suggest a higher incidence in women and links to reproductive history, implying estrogen-related pathways. Metabolomic data also indicated inverse associations with steroid-related plasma met...

Signal-integrated control of immune and reparative programs establishes blood-derived fibrocytes reprogrammable toward induced pluripotency

Fibrocytes represent a distinct somatic cell type derived from peripheral blood leukocytes, first described as spindle-shaped adherent cells with dual hematopoietic and mesenchymal features. Although fibrocytes were identified in early descriptive studies across several mammalian...

Allele-specific expression reveals complex regulatory divergence underlying fruit phenotypic differences between cultivated and wild tomato species

Abstract Background Tomato ( Solanum lycopersicum ) is one of the most important agricultural crops and serves as a model system for fleshy fruit biology. However, domestication bottlenecks have led to limited genetic diversity for further crop improvement. Wild relatives represe...

Superconducting Weak Links at Substrate Steps in Bilayer Nickelate Films

Abstract Ambient-pressure superconductivity above 40 K has been realized in bilayer nickelate thin films on SrLaAlO4 (001), yet resistive measurements often exhibit incomplete zero-resistance states and/or two-step superconducting transitions of unresolved origin. We show that th...

Partisans misperceive and are influenced by dynamic norms

Abstract Perceptions of social norms, and how those norms change over time, play a central role in shaping how people understand and respond to political divides. We developed and iteratively refined dynamic‐norm messages about bipartisan attitude change to reduce divisive outpar...

Markers of microvascular instability predict severity and survival in idiopathic pulmonary fibrosis

Introduction Most research on idiopathic pulmonary fibrosis (IPF) has focused on the interplay among fibroblasts, the immune system and epithelial cells. There is growing evidence that microvascular dysfunction also plays a role in disease progression, but large human translation...

Dispersion Polymerization in an Elastomeric Solvent

Abstract Polymerization-induced phase separation (PIPS) provides a powerful route to generate structured polymeric materials by coupling chemical conversion with thermodynamic demixing. PIPS in liquid-state systems underlies dispersion polymerization, serving as a cornerstone tec...

Cellulose-Binding Module-Mediated Immobilization of l -Arabinose Isomerase for Reusable d -Tagatose Production

Abstract The development of stable and recyclable biocatalysts is vital for sustainable bioprocessing. In this study, we demonstrated fusion of l-arabinose isomerase from Thermotoga neapolitana (TnAI) with a cellulose-binding module (CBM) to facilitate direct, noncovalent immobil...

Detecting Meiotic Crossing-Overs in Maize Using Chromatin Immunoprecipitation-Sequencing (ChIP-seq)

During meiosis, homologous chromosomes engage in reciprocal exchanges of segments in a process known as crossing over (CO). About 85% of CO events in maize are products of the class I pathway. Class I COs are interference-sensitive, meaning that the formation of one CO reduces th...

Directionality of transcriptional regulatory elements

Divergent transcription is a critical marker of active transcriptional regulatory elements (TREs), including enhancers and promoters, in mammals. However, distal elements with unidirectional transcriptional patterns are often overlooked, leaving their identity and function poorly...

Site-Specific Measurement of Meiotic Crossing-Over Rate with Droplet Digital PCR

Understanding the frequency and distribution of meiotic crossovers (COs) is critical for both fundamental studies on meiosis and for practical applications in plant breeding, where controlling recombination can accelerate crop improvement. Determining CO rates at specific genomic...

Configurational diversity of metabotropic glutamate receptor complexes with beta-arrestins

Beta-arrestins (β-arrs) are cytosolic proteins which mediate G protein-coupled receptor (GPCR) desensitization, endocytosis, and signaling. Despite the widespread physiological roles of β-arr coupling, the molecular basis of GPCR/β-arr interaction has been studied primarily in mo...

The plausible relationship between deep long-period earthquakes and volatiles: a case study of the Alaska-Aleutian arc

Abstract Deep long-period (DLP) earthquakes are observed beneath volcanoes in various tectonic settings during background activity, unrest, and eruption. The exact processes generating DLPs have been subject to ongoing debate, as they may provide insight into deep magmatic plumbi...

AnExplainable AI Engineering Framework for Claims-Only First-Stage Provider Audit Triage Using SHAP-Guided Hybrid Retrieval-Augmented Generation

This study proposes an explainable artificial intelligence (XAI) engineering workflow for provider-level healthcare claim audit prioritization using SHAP-guided hybrid retrieval-augmented generation (RAG). The framework integrates provider-level claim aggregation, tree-based risk...

Self-reported cannabis use following cash transfer: Estimating the short-term impacts of the Alaska Permanent Fund Dividend

Aims Researchers have hypothesized that cash transfers affect substance use through two competing pathways: relieving financial strain which could reduce use, or expanding spendable income, which could increase use. We tested whether payments from the Permanent Fund Dividend (PFD...