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Today, the University of Oxford and AstraZeneca researchers present a pooled analysis of Phase 3 trials of a vaccine against SARS-CoV-2 across two different dose regimens, resulting in an average efficacy of 70.4%. The new study published in the Lancet is the first peer-reviewed publication of phase 3 data from studies of a vaccine against the coronavirus.
Unveiling sub-populations in critical care settings: a real-world data approach in COVID-19.
BackgroundDisease presentation and progression can vary greatly in heterogeneous diseases, such as COVID-19, with variability in patient outcomes, even within the hospital setting. This variability underscores the need for tailored treatment approaches based on distinct clinical subgroups.ObjectivesThis study aimed to identify COVID-19 patient subgroups with unique clinical characteristics using real-world data (RWD) from electronic health records (EHRs) to inform individualized treatment plans.Materials and methodsA Factor Analysis of Mixed Data (FAMD)-based agglomerative hierarchical clustering approach was employed to analyze the real-world data, enabling the identification of distinct patient subgroups. Statistical tests evaluated cluster differences, and machine learning models classified the identified subgroups.ResultsThree clusters of COVID-19 in patients with unique clinical characteristics were identified. The analysis revealed significant differences in hospital stay durations and survival rates among the clusters, with more severe clinical features correlating with worse prognoses and machine learning classifiers achieving high accuracy in subgroup identification.ConclusionBy leveraging RWD and advanced clustering techniques, the study provides insights into the heterogeneity of COVID-19 presentations. The findings support the development of classification models that can inform more individualized and effective treatment plans, improving patient outcomes in the future.
Characterising the Behaviour of a Structured PDE Model of the Cell Cycle in Contrast to a Corresponding ODE System.
Experimental results have shown that anti-cancer therapies, such as radiotherapy and chemotherapy, can modulate the cell cycle and generate cell cycle phase-dependent responses. As a result, obtaining a detailed understanding of the cell cycle is one possible path towards improving the efficacy of many of these therapies. Here, we consider a basic structured partial differential equation (PDE) model for cell progression through the cell cycle, and derive expressions for key quantities, such as the population growth rate and cell phase proportions. These quantities are shown to be periodic and, as such, we compare the PDE model to a corresponding ordinary differential equation (ODE) model in which the parameters are linked by ensuring that the long-term ODE behaviour agrees with the average PDE behaviour. By design, we find that the ODE model does an excellent job of representing the mean dynamics of the PDE model within just a few cell cycles. However, by probing the parameter space we find cases in which this mean behaviour is not a good measure of the PDE population growth. Our analytical comparison of two caricature models (one PDE and one ODE system) provides insight into cases in which the simple ODE model is an appropriate approximation to the PDE model.
Activity-Based Protein Profiling (ABPP) of Cellular DeISGylating Enzymes and Inhibitor Screening.
A detailed methodology platform is described for activity-based protein profiling (ABPP) of cellular deISGylating enzymes using a specific activity-based interferon-stimulated gene 15 (ISG15) probe. Manual and semi-automated workflows for medium- to high-throughput applications are outlined in this chapter, with western blotting and proteomics-based techniques as the main readouts. This methodology informs us of endogenous deISGylating enzyme expression and activity in a cellular context, including USP18, the type I interferon (IFN-I)-inducible deISGylase, and several constitutively expressed deubiquitinases (DUBs), such as USP5, USP14, USP16, and USP36, that exert cross-reactivity to ISG15. ISG15-ABPP also enables the identification and characterization of potent and selective deISGylating enzyme modulators.
Spatial distribution and population structure of the invasive Anopheles stephensi in Kenya from 2022 to 2024.
This study analyzes the distribution, genetic diversity, and spread of Anopheles stephensi in Kenya following initial detection in December 2022. A total of 114 larval and 33 adult An. stephensi samples were confirmed in 7 of 18 surveyed counties majorly along transportation routes. Genetic analyses revealed three distinct genetic compositions with different levels of genetic diversity, suggesting multiple introductions into the country. The genetic composition of mosquitoes in most counties resembled southern Ethiopian populations, while those from Turkana showed a unique haplotype. A species distribution model predicts a more extensive range than currently observed, with low precipitation and minimal seasonal temperature variations as key factors influencing distribution. Challenges in adult sampling were noted, with larval sampling revealing co-occurrence with native Anopheles species. The findings have implications for surveillance and control strategies, emphasizing the need for continued monitoring, refined sampling techniques to inform bionomics, and cross-border collaboration.
Vaccine effects on in-hospital COVID-19 outcomes.
Here, we posit that studies comparing outcomes of patients hospitalized with COVID-19 by vaccination status are important descriptive epidemiologic studies, but contrast two groups that are not comparable with regard to causal analyses. We use the principal stratification framework to show that these studies can estimate a causal vaccine effect only for the subgroup of individuals who would be hospitalized with or without vaccination. Further, we describe the methodology for, and present sensitivity analyses of, this effect. Using this approach can change the interpretation of studies only reporting the standard analyses that condition on observed hospital admission status - that is, analyses comparing outcomes for all hospitalised COVID-19 patients by vaccination status.
Crystallographic fragment screening reveals ligand hotspots in TRIM21 PRY-SPRY domain.
Tripartite motif-containing protein 21 (TRIM21), and particularly its PRY-SPRY protein interaction domain, plays a critical role in the immune response by recognizing intracellular antibodies targeting them for degradation. In this study, we performed a crystallographic fragment screening (CFS) campaign to identify potential small molecule binders targeting the PRY-SPRY domain of TRIM21. Our screen identified a total of 109 fragments binding to TRIM21 that were distributed across five distinct binding sites. These fragments have been designed to facilitate straightforward follow-up chemistry, making them ideal starting points for further chemical optimization. A subsequent fragment merging approach demonstrated improved activity. To enable functional validation of compounds with full length human TRIM21, we established a NanoBRET assay suitable for measuring target engagement to the main Fc binding site in life cells. The high-resolution structural data and observed binding modes across the different sites highlight the versatility of the PRY-SPRY domain as a target for small-molecule intervention. The presented data provide a solid foundation for structure-guided ligand design, enabling the rational design of more potent and selective compounds, with the goal to develop bivalent molecules such as Proteolysis Targeting Chimeras (PROTACs).
Acceptability and feasibility of glucose-6-phosphate dehydrogenase (G6PD) testing using SD Biosensor by village malaria workers in Cambodia: a qualitative study.
IntroductionPlasmodium vivax is the predominant cause of malaria in the Greater Mekong Subregion. To ensure safe treatment with primaquine, point-of-care glucose-6-phosphate dehydrogenase (G6PD) testing was rolled out in Cambodia at the health facility level, although most malaria patients are diagnosed in the community. The current study aims to explore the acceptability and feasibility of implementing community-level G6PD testing in Cambodia.MethodsSemistructured interviews and focus group discussions (FGD) were conducted. Across eight study sites in three provinces, 142 respondents, including policymakers, programme officers, healthcare providers and patients, participated in 67 interviews and 19 FGDs in 2022 and 2023. Data were analysed thematically using an adapted framework derived from Bowen et al's feasibility framework and Sekhon et al's acceptability framework.ResultsAll stakeholders attributed value to the intervention. Acknowledging an intervention's different values can help discern policy implications for an intervention's successful implementation. Building and maintaining confidence in the device, end users, infrastructure and health systems were found to be key elements of acceptability. In general, health centre workers and village malaria workers (VMWs) had confidence that VMWs could conduct the test and administer treatment given appropriate initial training, monthly refresher training and the test's repeated use. More is required to build policymakers' confidence, while some implementation challenges, including the test's regulatory approval, stability above 30°C and cost, need to be overcome.ConclusionImplementation of G6PD testing at the community level in Cambodia is an acceptable and potentially feasible option but requires addressing implementation challenges and building and maintaining confidence among stakeholders.
Structure and stabilization of the antigenic glycoprotein building blocks of the New World mammarenavirus spike complex.
The spillover of New World (NW) arenaviruses from rodent reservoirs into human populations poses a continued risk to human health. NW arenaviruses present a glycoprotein (GP) complex on the envelope surface of the virion, which orchestrates host cell entry and is a key target of the immune response arising from infection and immunization. Each protomer of the trimeric GP is composed of a stable signal peptide, a GP1 attachment glycoprotein, and a GP2 fusion glycoprotein. To glean insights into the architecture of this key therapeutic target, we determined the crystal structures of NW GP1-GP2 heterodimeric complexes from Junín virus and Machupo virus. Due to the metastability of the interaction between GP1 and GP2, structural elucidation required the introduction of a disulfide bond at the GP1-GP2 complex interface, but no other stabilizing modifications were required. While the overall assembly of NW GP1-GP2 is conserved with that presented by Old World (OW) arenaviruses, including Lassa virus and lymphocytic choriomeningitis virus, NW GP1-GP2 complexes are structurally distinct. Indeed, we note that when compared to the OW GP1-GP2 complex, the globular portion of NW GP1 undergoes limited structural alterations upon detachment from its cognate GP2. We further demonstrate that our engineered GP1-GP2 heterodimers are antigenically relevant and recognized by neutralizing antibodies. These data provide insights into the distinct assemblies presented by NW and OW arenaviruses, as well as provide molecular-level blueprints that may guide vaccine development.IMPORTANCEAlthough the emergence of New World (NW) hemorrhagic fever mammarenaviruses poses an unceasing threat to human health, there is a paucity of reagents capable of protecting against the transmission of these pathogens from their natural rodent reservoirs. This is, in part, attributed to our limited understanding of the structure and function of the NW glycoprotein spike complex presented on the NW arenavirus surface. Here, we provide a detailed molecular-level description of how the two major components of this key therapeutic target assemble to form a key building block of the NW arenaviral spike complex. The insights gleaned from this work provide a framework for guiding the structure-based development of NW arenaviral vaccines.
Identifying context-specific determinants to inform improvement of antimicrobial stewardship implementation in healthcare facilities in Asia: results from a scoping review and web-based survey among local experts.
International guidelines are available for the assessment and improvement of antimicrobial stewardship (AMS) programmes: an important strategy to address the escalating global antimicrobial resistance problem. However, existing AMS assessment tools lack contextual specificity for resource-limited settings, leading to limited applicability in Asia. This project aimed to identify relevant themes from current guidance documents to help develop a context-specific assessment tool that can be applied by healthcare facilities (HCFs) to improve local implementation.We performed a sequential approach of a scoping review to identify relevant assessment themes for Asia and an expert survey for getting feedback on the relevance of assessment stems developed from the scoping review. We reviewed English-language published documents discussing AMS implementation or assessment at HCFs globally and in Asia. Themes were derived through content analysis and classified following the predefined context dimensions to develop assessment stems, defined as containing one identified determinant that may influence implementation outcomes. The survey consisting of identified assessment stems was reviewed by 20 locally identified experts in Asia who rated the level of relevance of these stems in AMS implementation in the region.National leadership, training and technical support, and policy and guidance were the most commonly identified themes among 100 themes identified from 73 reviewed documents. From these themes, we developed 131 assessment stems for the expert survey. Of the 131 assessment stems, 117 (89%) were considered relevant for AMS implementation in Asia by at least 80% of respondents. These stems were included in the process of developing a global AMS assessment tool to support HCFs to improve their programmes.In conclusion, national leadership and support represent a distinct and important aspect affecting AMS implementation in HCFs in Asia. The identified assessment themes have substantial value for the formulation of locally relevant implementation strategies tailored to the Asian context.
TCR and inflammatory signals tune human MAIT cells to exert specific tissue repair and effector functions
SUMMARYMAIT cells are an abundant T-cell population enriched in peripheral tissues such as the liver. They are activated both through TCR-dependent and - independent mechanisms. However, the different specific functional responses of MAIT cells to these distinct signals remain elusive. We examined the impact of combinations of TCR-dependent and -independent signals in blood and tissue-derived human MAIT cells. TCR-independent activation of MAIT cells from blood and gut was maximised by extending the panel of cytokines to including TNF-superfamily member TL1A. RNAseq experiments revealed that TCR-dependent and -independent signals drive MAIT cells to exert overlapping and unique effector functions, impacting both host defence and tissue homeostasis. While TCR-triggering alone is insufficient to drive sustained activation, TCR-triggered MAIT cells did show specific enrichment of tissue-repair functions at the level of gene expression, protein production and in in vitro assays and these functions were amplified by cytokine costimulation. Taken together, these data indicate the blend of TCR-dependent and -independent signalling to MAIT cells may play a role in controlling the balance between healthy and pathological processes of tissue inflammation and repair.
The Canadian Alliance for Healthy Hearts and Minds: How Well Does It Reflect the Canadian Population?
BackgroundThe intent of the Canadian Alliance for Healthy Hearts and Minds (CAHHM) cohort is to understand the early determinants of subclinical cardiac and vascular disease and progression in adults selected from existing cohorts-the Canadian Partnership for Tomorrow's Health, the Prospective Urban and Rural Evaluation (PURE) cohort, and the Montreal Heart Institute Biobank. We evaluated how well the CAHHM-Health Services Research (CAHHM-HSR) subcohort reflects the Canadian population.MethodsA cross-sectional design was used among a prospective cohort of community-dwelling adults aged 35-69 years who met the CAHHM inclusion criteria, and a cohort of adults aged 35-69 years who responded to the 2015 Canadian Community Health Survey-Rapid Response module. The INTERHEART risk score was calculated at the individual level with means and proportions reported at the overall and provincial level.ResultsThere are modest differences between CAHHM-HSR study participants and the 2015 Canadian Community Health Survey-Rapid Response respondents in age (56.3 vs 51.7 mean years), proportion of men (44.9% vs 49.3%), and mean INTERHEART risk score (9.7 vs 10.1). Larger differences were observed in postsecondary education (86.8% vs 70.2%), Chinese ethnicity (11.0% vs 3.3%), obesity (23.2% vs 29.3%), current smoker status (6.1% vs 18.4%), and having no cardiac testing (30.4% vs 55.9%).ConclusionsCAHHM-HSR participants are older, of higher socioeconomic status, and have a similar mean INTERHEART risk score, compared with participants in the Canadian Community Health Survey. Differing sampling strategies and missing data may explain some differences between the CAHHM-HSR cohort and Canadian community-dwelling adults and should be considered when using the CAHHM-HSR for scientific research.
AMG 701 induces cytotoxicity of multiple myeloma cells and depletes plasma cells in cynomolgus monkeys.
Multiple myeloma (MM) is a hematologic malignancy that is characterized by the accumulation of abnormal plasma cells (PCs) in the bone marrow (BM). Patient outcome may be improved with BiTE (bispecific T-cell engager) molecules, which redirect T cells to lyse tumor cells. B-cell maturation antigen (BCMA) supports PC survival and is highly expressed on MM cells. A half-life extended anti-BCMA BiTE molecule (AMG 701) induced selective cytotoxicity against BCMA-expressing MM cells (average half-maximal effective concentration, 18.8 ± 14.8 pM), T-cell activation, and cytokine release in vitro. In a subcutaneous mouse xenograft model, at all doses tested, AMG 701 completely inhibited tumor formation (P < .001), as well as inhibited growth of established tumors (P ≤ .001) and extended survival in an orthotopic MM model (P ≤ .01). To evaluate AMG 701 bioactivity in cynomolgus monkeys, a PC surface phenotype and specific genes were defined to enable a quantitative digital droplet polymerase chain reaction assay (sensitivity, 0.1%). Dose-dependent pharmacokinetic and pharmacodynamic behavior was observed, with depletion of PC-specific genes reaching 93% in blood and 85% in BM. Combination with a programmed cell death protein 1 (PD-1)-blocking antibody significantly increased AMG 701 potency in vitro. A model of AMG 701 binding to BCMA and CD3 indicates that the distance between the T-cell and target cell membranes (ie, the immunological synapse) is similar to that of the major histocompatibility complex class I molecule binding to a T-cell receptor and suggests that the synapse would not be disrupted by the half-life extending Fc domain. These data support the clinical development of AMG 701.
The immunomodulatory drugs lenalidomide and pomalidomide enhance the potency of AMG 701 in multiple myeloma preclinical models.
We investigated here the novel immunomodulation and anti-multiple myeloma (MM) function of T cells engaged by the bispecific T-cell engager molecule AMG 701, and further examined the impact of AMG 701 in combination with immunomodulatory drugs (IMiDs; lenalidomide and pomalidomide). AMG 701 potently induced T-cell-dependent cellular cytotoxicity (TDCC) against MM cells expressing B-cell maturation antigen, including autologous cells from patients with relapsed and refractory MM (RRMM) (half maximal effective concentration, <46.6 pM). Besides inducing T-cell proliferation and cytolytic activity, AMG 701 also promoted differentiation of patient T cells to central memory, effector memory, and stem cell-like memory (scm) phenotypes, more so in CD8 vs CD4 T subsets, resulting in increased CD8/CD4 ratios in 7-day ex vivo cocultures. IMiDs and AMG 701 synergistically induced TDCC against MM cell lines and autologous RRMM patient cells, even in the presence of immunosuppressive bone marrow stromal cells or osteoclasts. IMiDs further upregulated AMG 701-induced patient T-cell differentiation toward memory phenotypes, associated with increased CD8/CD4 ratios, increased Tscm, and decreased interleukin 10-positive T and T regulatory cells (CD25highFOXP3high), which may downregulate T effector cells. Importantly, the combination of AMG 701 with lenalidomide induced sustained inhibition of MM cell growth in SCID mice reconstituted with human T cells; tumor regrowth was eventually observed in cohorts treated with either agent alone (P < .001). These results strongly support AMG 701 clinical studies as monotherapy in patients with RRMM (NCT03287908) and the combination with IMiDs to improve patient outcomes in MM.
Characterization of a Novel FLT3 BiTE Molecule for the Treatment of Acute Myeloid Leukemia.
Despite advances in the treatment of acute myeloid leukemia (AML), novel therapies are needed to induce deeper and more durable clinical response. Bispecific T-cell Engager (BiTE) molecules, which redirect patient T cells to lyse tumor cells, are a clinically validated modality for hematologic malignancies. Due to broad AML expression and limited normal tissue expression, fms-related tyrosine kinase 3 (FLT3) is proposed to be an optimal BiTE molecule target. Expression profiling of FLT3 was performed in primary AML patient samples and normal hematopoietic cells and nonhematopoietic tissues. Two novel FLT3 BiTE molecules, one with a half-life extending (HLE) Fc moiety and one without, were assessed for T-cell-dependent cellular cytotoxicity (TDCC) of FLT3-positive cell lines in vitro, in vivo, and ex vivo FLT3 protein was detected on the surface of most primary AML bulk and leukemic stem cells but only a fraction of normal hematopoietic stem and progenitor cells. FLT3 protein detected in nonhematopoietic cells was cytoplasmic. FLT3 BiTE molecules induced TDCC of FLT3-positive cells in vitro, reduced tumor growth and increased survival in AML mouse models in vivo Both molecules exhibited reproducible pharmacokinetic and pharmacodynamic profiles in cynomolgus monkeys in vivo, including elimination of FLT3-positive cells in blood and bone marrow. In ex vivo cultures of primary AML samples, patient T cells induced TDCC of FLT3-positive target cells. Combination with PD-1 blockade increased BiTE activity. These data support the clinical development of an FLT3 targeting BiTE molecule for the treatment of AML.
Findings from an in-Depth Annual Tree-Ring Radiocarbon Intercomparison
ABSTRACTThe radiocarbon (14C) calibration curve so far contains annually resolved data only for a short period of time. With accelerator mass spectrometry (AMS) matching the precision of decay counting, it is now possible to efficiently produce large datasets of annual resolution for calibration purposes using small amounts of wood. The radiocarbon intercomparison on single-year tree-ring samples presented here is the first to investigate specifically possible offsets between AMS laboratories at high precision. The results show that AMS laboratories are capable of measuring samples of Holocene age with an accuracy and precision that is comparable or even goes beyond what is possible with decay counting, even though they require a thousand times less wood. It also shows that not all AMS laboratories always produce results that are consistent with their stated uncertainties. The long-term benefits of studies of this kind are more accurate radiocarbon measurements with, in the future, better quantified uncertainties.
The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0–55 cal kBP)
ABSTRACTRadiocarbon (14C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric14C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international14C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable14C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the14C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine14C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.