Yale University

The GndA Microprotein Promotes Cell Growth during Heat Shock in Escherichia coli

Abstract Hundreds of bacterial small open reading frames (sORFs) encoding microproteins of fewer than 50 amino acids have recently been identified. Biological functions have been ascribed to an increasing number of microproteins, some of which play roles in bacterial stress respo...

AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes

Abstract Here we present AmpliconSuite, a toolkit for focal amplification analysis from cancer whole-genome sequencing that identifies extrachromosomal DNA (ecDNA), breakage–fusion–bridges and other amplification modes. Its ecContext module categorizes ecDNA structures to underst...

Modeling the heterogeneity of cognitive dysfunction in Parkinson’s disease using partially ordered set models

Abstract Traditional binary classifications of Parkinson’s disease (PD) cognitive dysfunction fail to capture its inherent heterogeneity. This study introduces the Partially Ordered Set (POSET) model, a Bayesian framework, to analyze cognitive heterogeneity using Parkinson’s Prec...

Neutrophil to Lymphocyte Ratio and Neurological Outcome in Ischemic Stroke at 4.5 to 24 Hours: A Post Hoc Analysis of TRACE-III Trial

Whether neutrophil to lymphocyte ratio (NLR), as a marker of increased inflammatory response, modifies the efficacy and safety of tenecteplase is uncertain in patients 4.5–24 h after stroke onset. We investigated this in the Tenecteplase Reperfusion Therapy in Acute Ischemic Cere...

Conditional diffusion for single-cell Hi-C data imputation and enhancement with scHiC-Diff

Single-cell high-throughput chromosome conformation capture (scHi-C) enables the analysis of cell-to-cell variability in three-dimensional (3D) genome organization, but its utility is severely limited by pervasive technical dropouts, leading to extremely sparse contact maps. Accu...

Harassment and structural violence against abortion providers in Colombia: A national mixed‐methods study

OBJECTIVE: To examine the discrepancy between a single-item harassment screening and a behaviorally anchored stigma scale among Colombian physicians who provide voluntary termination of pregnancy (VTP), and to explore how providers who do not identify as victims describe their ex...

Multiomics Profiling Supports Cathepsin B as a Protective Factor in White Matter Hyperintensities and Cognition

BACKGROUND: White matter hyperintensities (WMH) are a common brain magnetic resonance imaging marker of cerebral small vessel disease and a major risk factor for stroke and dementia, yet the molecular mechanisms governing lesion formation remain incompletely understood. We sought...

Reflect-Guard: Enhancing LLM Safeguards Against Adversarial Prompts via Logical Self-Reflection

LLM safety classifiers such as Llama Guard detect overtly harmful prompts well but remain vulnerable to jailbreaks that disguise intent via role-play, fictional framing, or indirect requests. We present Reflect-Guard: Llama-Guard-3-8B fine-tuned via QLoRA to generate a distilled,...

Schizophrenia research in 2026: report from the annual meeting of the Schizophrenia International Research Society

Abstract SIRS 2026, held under the theme “Schizophrenia Research in the Era of Artificial Intelligence,” brought together researchers, clinicians, and persons with lived experience to take stock of a field whose tools for measuring, predicting, and intervening in psychosis have e...

Associations between methodological quality and representation in clinical trials of systemic lupus erythematosus therapies

Background Randomized clinical trials support drug development and uptake of new therapies for systemic lupus erythematosus (SLE). However, challenges to conducting high-quality clinical trials have been noted, including underrepresentation of minoritized populations. Currently,...

Perverse sheaves and $t$-structures on the thin and thick affine flag varieties

We study the categories \mathrm{Perv}_{\mathrm{thin}} , \mathrm{Perv}_{\mathrm{thick}} of Iwahori-equivariant perverse sheaves on the thin and thick affine flag varieties associated to a split reductive group G . An earlier work of the first author describes \mathrm{Perv}_{\mathr...

Supporting Young People With First-Episode Psychosis: A Qualitative Study of Caregiver Perceptions and Experiences

The diagnosis of a psychotic disorder in youth often leads to high costs, emotional distress, and isolation for caregivers. Yet, caregiving experiences are underexplored in research, resulting in a potentially missed area to enhance care. We aim to explore the experiences, percep...

Associations of food processing and dietary risk factors with colorectal cancer incidence in the NIH-AARP Diet and Health Study: A cohort study

Background Ultra-processed foods (UPF) account for >50% of energy intake by US adults. UPF intake can include dietary components linked to lower colorectal cancer (CRC) risk, such as whole grain and dairy products, and others linked to higher CRC risk, such as processed meats, po...

Single-cell multi-omics in IPF and COPD: from atlas to impact

Single-cell and spatial multi-omics technologies are transforming our understanding of the normal lung cellular repertoire as well the molecular and cellular networks of chronic lung diseases. In this review we focus on idiopathic pulmonary fibrosis (IPF) and chronic obstructive...

Personalized genomic landscape of prostate cancer in African American men reveals novel drivers and therapeutic opportunities

African American (AA) men experience disproportionately high prostate cancer incidence and mortality. Despite this disparity, current genomic repositories are predominantly derived from European populations, and studies using archived tissues are often limited by stromal contamin...

Laparoscopic and Robotic Device Malfunction: A Scoping Review

Laparoscopic and robotic surgeries have become the gold standard for many operations. Device malfunctions during these procedures represent a preventable source of patient harm; however, the trends in malfunction reporting and their implications for surveillance systems, surgical...

Accuracy of commercial pollen forecasts in the United States

Approximately 80 million Americans suffer from seasonal pollen allergies, and many rely on commercial pollen forecasts to guide exposure reduction and medication timing. However, these forecasts are proprietary, and their accuracy has never been comprehensively evaluated. Here, w...

Near-Flatband Resonances in Bilayer Moire Superlattices for Visible-to-Infrared Meta-Optics

Abstract Flat photonic bands enable extreme light confinement, slow-light effects, and angle-robust resonances that are valuable for meta-optics and integrated photonics. Here we report the design, fabrication, and experimental characterization of 1D Moiré superlattices formed b...

Screening strategies for the early detection of non-cardia gastric cancer in low- to moderate-prevalence regions: Asia-Pacific gastroesophageal cancer congress consensus 2026

Abstract Background Gastric cancer (GC) remains a major global health burden, and early detection is essential for improving patient outcomes. Although GC screening has been widely implemented in East Asian countries with a high disease burden, the optimal screening strategy for...

High-performance parallel implementation of spin-free high-order coupled-cluster theories

High-order coupled-cluster theories with iterative triples (CCSDT), perturbative quadruples [CCSDT(Q)], and iterative quadruples (CCSDTQ) provide benchmark-quality correlation energies, but their steep computational scalings, O(N8), O(N9), and O(N10), together with the large memo...