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Abstract: Manila clam (Ruditapes philippinarum) harvests from Willapa Bay, Washington, USA have increased by an order of magnitude over two decades. This increased yield of a non-native species has been supported by natural recruitment as well as some planting of small clams. Manila clam settlement was recorded over three years in clam spat collectors (mesh bags containing gravel) and occurred in June to October at water temperatures >13°C. At 16 sites in the bay, clam abundance was measured at multiple life stages. Distributions of early-stage larvae during a spawning peak were well-correlated with wild populations of adult clams, with both stages highest in the southwest region having long residence time and little direct freshwater input. In contrast, settlement of these larvae 1–2 weeks later was correlated neither with early-stage larval distributions nor with one year-old recruits a year later; instead, settlement was spread more evenly between southeast and southwest regions, possibly due to mixing during larval development. Therefore, higher natural clam production in west than east may stem from differential post-settlement survival over the first winter, whereas low densities of all life stages in northern regions may be set by larval supply due to water residence time constraints. Despite an extended settlement period of several months, clams were no more abundant after one year than were measured for one week in clam spat collectors, suggesting generally high post-settlement losses in addition to factors that are spatially variable and break down correlations among life stages. [Copyright &y& Elsevier]

The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens and found an association with beneficial response to PD-1 blockade. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcome. This hub is distinct from mature tertiary lymphoid structures and is enriched for stem-like TCF7 + PD-1 + CD8 + T cells, activated CCR7 + LAMP3 + dendritic cells and CCL19 + fibroblasts as well as chemokines that organize these cells. Within the stem-immunity hub, we find preferential interactions between CXCL10 + macrophages and TCF7 - CD8 + T cells as well as between mature regulatory dendritic cells and TCF7 + CD4 + and regulatory T cells. These results provide a picture of the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Background: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse-transcription PCR (RT-qPCR). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce. To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction., Methods: We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance., Results: After optimization, SwabExpress has a low limit of detection at 2-4 molecules/µL, 100% sensitivity, and 99.4% specificity when compared side by side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time., Conclusion: SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics., (© American Association for Clinical Chemistry 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)