T-Switch: A specificity-based engineering platform for developing safe and effective T cell therapeutics.

Many promising targets for adoptive T cell therapy (ACT) are self-antigens, but self-reactive T cells are generally eliminated during thymic selection or diverted to regulatory phenotypes. To bypass T cell tolerance and obtain potent and safe T cell therapeutics, we developed T-Switch, an in vitro T cell receptor (TCR) engineering platform for the creation, modification, and comprehensive profiling of TCRs that can target self-antigens. T-Switch first expands T cells that recognize a "foreign" peptide closely related to a self-antigen.

Widespread Neuroanatomical Integration and Distinct Electrophysiological Properties of Glioma-Innervating Neurons.

Unlabelled: Gliomas are the most common malignant primary brain tumors and are often associated with severe neurological deficits and mortality. Unlike many cancers, gliomas rarely metastasize outside the brain, indicating a possible dependency on unique features of brain microenvironment. Synapses between neurons and glioma cells exist, suggesting that glioma cells rely on neuronal inputs and synaptic signaling for proliferation.

High-throughput discovery of MHC class I- and II-restricted T cell epitopes using synthetic cellular circuits.

Antigen discovery technologies have largely focused on major histocompatibility complex (MHC) class I-restricted human T cell receptors (TCRs), leaving methods for MHC class II-restricted and mouse TCR reactivities relatively undeveloped. Here we present TCR mapping of antigenic peptides (TCR-MAP), an antigen discovery method that uses a synthetic TCR-stimulated circuit in immortalized T cells to activate sortase-mediated tagging of engineered antigen-presenting cells (APCs) expressing processed peptides on MHCs. Live, tagged APCs can be directly purified for deconvolution by sequencing, enabling TCRs with unknown specificity to be queried against barcoded peptide libraries in a pooled screening context.

Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn.

We investigate a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To cover large antigenic spaces, we develop Dolphyn, a method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn compresses the size of a peptide library by 78% compared to traditional tiling, increasing the antibody-reactive peptides from 10% to 31%.

The magmatic system under Hunga volcano before and after the 15 January 2022 eruption.

One of the largest explosive eruptions instrumentally recorded occurred at Hunga volcano on 15 January 2022. The magma plumbing system under this volcano is unexplored because of inherent difficulties caused by its submarine setting. We use marine gravity data derived from satellite altimetry combined with multibeam bathymetry to model the architecture and dynamics of the magmatic system before and after the January 2022 eruption.

Volcaniclastic density currents explain widespread and diverse seafloor impacts of the 2022 Hunga Volcano eruption.

The impacts of large terrestrial volcanic eruptions are apparent from satellite monitoring and direct observations. However, more than three quarters of all volcanic outputs worldwide lie submerged beneath the ocean, and the risks they pose to people, infrastructure, and benthic ecosystems remain poorly understood due to inaccessibility and a lack of detailed observations before and after eruptions. Here, comparing data acquired between 2015 - 2017 and 3 months after the January 2022 eruption of Hunga Volcano, we document the far-reaching and diverse impacts of one of the most explosive volcanic eruptions ever recorded.

TScan-II: A genome-scale platform for the de novo identification of CD4 T cell epitopes.

CD4 T cells play fundamental roles in orchestrating immune responses and tissue homeostasis. However, our inability to associate peptide human leukocyte antigen class-II (HLA-II) complexes with their cognate T cell receptors (TCRs) in an unbiased manner has hampered our understanding of CD4 T cell function and role in pathologies. Here, we introduce TScan-II, a highly sensitive genome-scale CD4 antigen discovery platform.

Fast and destructive density currents created by ocean-entering volcanic eruptions.

Volcanic eruptions on land create hot and fast pyroclastic density currents, triggering tsunamis or surges that travel over water where they reach the ocean. However, no field study has documented what happens when large volumes of erupted volcanic material are instead delivered directly into the ocean. We show how the rapid emplacement of large volumes of erupted material onto steep submerged slopes triggered extremely fast (122 kilometers per hour) and long-runout (>100 kilometers) seafloor currents.

Atmosphere injection of sea salts during large explosive submarine volcanic eruptions.

The 15 January 2022 submarine eruption at Hunga volcano was the most explosive volcanic eruption in 140 years. It involved exceptional magma and seawater interaction throughout the entire submarine caldera collapse. The submarine volcanic jet breached the sea surface and formed a subaerial eruptive plume that transported volcanic ash, gas, sea salts and seawater up to ~ 57 km, reaching into the mesosphere.

Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn.

We investigated a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To enhance this approach, we developed Dolphyn, a novel method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn improves the fraction of gut phage library peptides bound by antibodies from 10% to 31% in healthy individuals, while also reducing the number of synthesized peptides by 78%.

Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses.

Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 immunodominant "public epitopes" at high resolution and characterizing several of their cognate antibodies, we concluded that germline-encoded sequences in antibodies drive recurrent recognition.

Spontaneous behaviour is structured by reinforcement without explicit reward.

Spontaneous animal behaviour is built from action modules that are concatenated by the brain into sequences. However, the neural mechanisms that guide the composition of naturalistic, self-motivated behaviour remain unknown. Here we show that dopamine systematically fluctuates in the dorsolateral striatum (DLS) as mice spontaneously express sub-second behavioural modules, despite the absence of task structure, sensory cues or exogenous reward.

Tsunami Runup and Inundation in Tonga from the January 2022 Eruption of Hunga Volcano.

Unlabelled: On January 15th, 2022, at approximately 4:47 pm local time (0347 UTC), several weeks of heightened activity at the Hunga volcano 65 km northwest of Tongatapu, culminated in an 11-h long violent eruption which generated a significant near-field tsunami. Although the Kingdom of Tonga lies astride a large and tsunamigenic subduction zone, it has relatively few records of significant tsunami. Assessment activities took place both remotely and locally.

Stability Loss Analysis for Thin-Walled Shells with Elliptical Cross-Sectional Area.

The aim of the scientific contribution is to point out the possibility of applicability of cylindrical shells with a constant elliptical cross-sectional shape for stability loss analysis. The solution to the problem consists of two approaches. The first approach is the experimental measurement of critical force levels, where the work also describes the method of production of the sample and jigs that cause the desired elliptical shape.

Phenotype, specificity and avidity of antitumour CD8 T cells in melanoma.

Interactions between T cell receptors (TCRs) and their cognate tumour antigens are central to antitumour immune responses; however, the relationship between phenotypic characteristics and TCR properties is not well elucidated. Here we show, by linking the antigenic specificity of TCRs and the cellular phenotype of melanoma-infiltrating lymphocytes at single-cell resolution, that tumour specificity shapes the expression state of intratumoural CD8 T cells. Non-tumour-reactive T cells were enriched for viral specificities and exhibited a non-exhausted memory phenotype, whereas melanoma-reactive lymphocytes predominantly displayed an exhausted state that encompassed diverse levels of differentiation but rarely acquired memory properties.

Recruitment strategies for a pragmatic cluster randomized oral health trial in pediatric primary care settings.

Objectives: To describe multilevel recruitment strategies for an ongoing clinical trial in pediatric primary care settings, and assess adoption and reach of these strategies via the RE-AIM framework.

Methods: This study is part of a larger pragmatic cluster randomized clinical trial focused on the effectiveness of interventions on the practice, provider, and caregiver levels on dental utilization for Medicaid-enrolled 3-6 year old children. Pediatric practices were recruited according to the proportion of Medicaid-eligible children, geographic region, and County.

Caries disparities among Medicaid-enrolled young children from pediatric primary care settings.

Objectives: The objectives of this study are to determine the overall and racial differences in the extent of caries experience and to examine the association between child and parent/caregiver characteristics and caries among 3-6-year-old Medicaid-enrolled children.

Methods: This study reports baseline cross-sectional data from a larger pragmatic clinical trial in pediatric primary care practices. Child-level clinical dental exams included decayed and filled teeth (dft) using ICDAS criteria and parent/caregiver questionnaire collected information on socio-demographics, child oral health behaviors, oral health related quality of life (OHQoL), and food environment.

Unbiased Screens Show CD8 T Cells of COVID-19 Patients Recognize Shared Epitopes in SARS-CoV-2 that Largely Reside outside the Spike Protein.

Developing effective strategies to prevent or treat coronavirus disease 2019 (COVID-19) requires understanding the natural immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We used an unbiased, genome-wide screening technology to determine the precise peptide sequences in SARS-CoV-2 that are recognized by the memory CD8 T cells of COVID-19 patients. In total, we identified 3-8 epitopes for each of the 6 most prevalent human leukocyte antigen (HLA) types.

Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity.

Understanding humoral responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for improving diagnostics, therapeutics, and vaccines. Deep serological profiling of 232 coronavirus disease 2019 (COVID-19) patients and 190 pre-COVID-19 era controls using VirScan revealed more than 800 epitopes in the SARS-CoV-2 proteome, including 10 epitopes likely recognized by neutralizing antibodies. Preexisting antibodies in controls recognized SARS-CoV-2 ORF1, whereas only COVID-19 patient antibodies primarily recognized spike protein and nucleoprotein.

A comparison of experimental compressive axial loading testing with a numerical simulation of topologically optimized cervical implants made by selective laser melting.

In recent years, the number of cervical interventions has increased. The stress shielding effect is a serious complication in cervical spine interventions. Topological optimization is based on finite element method structural analysis and numerical simulations.

High-Throughput Screening of Kawasaki Disease Sera for Antiviral Antibodies.

Clinical features of Kawasaki disease (KD) display overlap with common pediatric viral illnesses, leading some to hypothesize that a viral infection is the inciting event for KD. To investigate viral infection history in KD patients, we performed comprehensive serological profiling using a high-throughput phage immunoprecipitation sequencing assay covering the complete reference protein sequences of known viruses with human tropism. KD and matched febrile control sera did not demonstrate differences in antiviral antibody profiles.

Measles virus infection diminishes preexisting antibodies that offer protection from other pathogens.

Measles virus is directly responsible for more than 100,000 deaths yearly. Epidemiological studies have associated measles with increased morbidity and mortality for years after infection, but the reasons why are poorly understood. Measles virus infects immune cells, causing acute immune suppression.

T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes.

T cell recognition of specific antigens mediates protection from pathogens and controls neoplasias, but can also cause autoimmunity. Our knowledge of T cell antigens and their implications for human health is limited by the technical limitations of T cell profiling technologies. Here, we present T-Scan, a high-throughput platform for identification of antigens productively recognized by T cells.