Proliferating macrophages in human tumours show characteristics of monocytes responding to myelopoietic growth factors.

Macrophages play essential roles in maintaining tissue homeostasis and immune defence. However, their extensive infiltration into tumours has been linked to adverse outcomes in multiple human cancers. Within the tumour microenvironment (TME), tumour-associated macrophages (TAMs) promote tumour growth and metastasis, making them prime targets for cancer immunotherapy. Recent single-cell analysis suggest that proliferating TAMs accumulate in human cancers, yet their origins and differentiation pathways remain uncertain. Here, we show that a subpopulation of CD163+ TAMs proliferates in situ within the TME of melanoma, lung cancer, and breast cancer. Consistent with their potential role in suppressing anti-tumour activities of T cells, CD163+ TAMs express a range of potent immunosuppressive molecules, including PD-L1, PD-L2, IL-10, and TGF-ß. Other phenotypic markers strongly suggested that these cells originate from CD14+ CCR2+ monocytes, a cell population believed to have minimal capacity for proliferation. However, we demonstrate in vitro that certain myelopoietic cytokines commonly available within the TME induce robust proliferation of human monocytes, especially the combination of interleukin 3 (IL-3) and Macrophage Colony-Stimulating Factor 1 (M-CSF). Monocytic cells cultured with these cytokines efficiently modulate T cell proliferation, and their molecular phenotype recapitulates that of CD163+ TAMs. IL-3-driven proliferation of monocytic cells can be completely blocked by IL-4, associated with the induction of CDKN1A, alongside the upregulation of transcription factors linked to dendritic cell function, such as BATF3 and IRF4. Taken together, our work suggests several novel therapeutic routes to reducing immunosuppressive TAMs in human tumours, from blocking chemokine-mediated recruitment of monocytes to blocking their proliferation.

Organophosphate pesticide exposure and risk of SARS-CoV-2 infection.

Several studies have reported immune modulation by organophosphate (OP) pesticides, but the relationship between OP exposure and SARS-CoV-2 infection is yet to be studied. We used two different measures of OP pesticide exposure (urinary biomarkers (N = 154) and residential proximity to OP applications (N = 292)) to examine the association of early-childhood and lifetime exposure to OPs and risk of infection of SARS-CoV-2 using antibody data. Our study population consisted of young adults (ages 18-21 years) from the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) Study, a longitudinal cohort of families from a California agricultural region. Urinary biomarkers reflected exposure from in utero to age 5 years. Residential proximity reflected exposures between in utero and age 16 years. SARS-CoV-2 antibodies in blood samples collected between June 2022 and January 2023 were detected via two enzyme linked immunosorbent assays, each designed to bind to different SARS-CoV-2 antigens. We performed logistic regression for each measure of pesticide exposure, adjusting for covariates from demographic data and self-reported questionnaire data. We found increased odds of SARS-CoV-2 infection among participants with higher urinary biomarkers of OPs in utero (OR = 1.94, 95% CI: 0.71, 5,58) and from age 0-5 (OR = 1.90, 95% CI: 0.54, 6.95).

Neoantigen Landscape Supports Feasibility of Personalized Cancer Vaccine for Follicular Lymphoma.

Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that 'polyvalent' vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole exome sequencing (WES) and RNA sequencing (RNA-Seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-Seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by alignment of B-cell receptor (BCR) CDR3 regions from RNA-Seq data, grouping at the protein level, and comparison to the BCR repertoire from healthy individuals using RNA-Seq data. An average of 52 somatic mutations per patient (range: 2-172) were identified, and two or more (median: 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide (SLP) vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all four patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field.

The inflammasome pathway is activated by dengue virus non-structural protein 1 and is protective during dengue virus infection.

Dengue virus (DENV) is a medically important flavivirus causing an estimated 50-100 million dengue cases annually, some of whom progress to severe disease. DENV non-structural protein 1 (NS1) is secreted from infected cells and has been implicated as a major driver of dengue pathogenesis by inducing endothelial barrier dysfunction. However, less is known about how DENV NS1 interacts with immune cells and what role these interactions play. Here we report that DENV NS1 can trigger activation of inflammasomes, a family of cytosolic innate immune sensors that respond to infectious and noxious stimuli, in mouse and human macrophages. DENV NS1 induces the release of IL-1ß in a caspase-1 dependent manner. Additionally, we find that DENV NS1-induced inflammasome activation is independent of the NLRP3, Pyrin, and AIM2 inflammasome pathways, but requires CD14. Intriguingly, DENV NS1-induced inflammasome activation does not induce pyroptosis and rapid cell death; instead, macrophages maintain cellular viability while releasing IL-1ß. Lastly, we show that caspase-1/11-deficient, but not NLRP3-deficient, mice are more susceptible to lethal DENV infection. Together, these results indicate that the inflammasome pathway acts as a sensor of DENV NS1 and plays a protective role during infection.

Biomechanical, physiological and anthropometrical predictors of performance in recreational runners.

Background: The maximal running speed (VMAX) determined on a graded treadmill test is well-recognized as a running performance predictor. However, few studies have assessed the variables that predict VMAX in recreationally active runners. Methods: We used a mathematical procedure combining Fick's law and metabolic cost analysis to verify the relation between (1) VMAX versus anthropometric and physiological determinants of running performance and, (2) theoretical metabolic cost versus running biomechanical parameters. Linear multiple regression and bivariate correlation were applied. We aimed to verify the biomechanical, physiological, and anthropometrical determinants of VMAX in recreationally active runners. Fifteen recreationally active runners participated in this observational study. A Conconi and a stead-steady running test were applied using a heart rate monitor and a simple video camera to register the physiological and mechanical variables, respectively. Results: Statistical analysis revealed that the speed at the second ventilatory threshold, theoretical metabolic cost, and fat-mass percentage confidently estimated the individual running performance as follows: VMAX = 58.632 + (-0.183 * fat percentage) + (-0.507 * heart rate percentage at second ventilatory threshold) + (7.959 * theoretical metabolic cost) (R2 = 0.62, p = 0.011, RMSE = 1.50 km.h-1). Likewise, the theoretical metabolic cost was significantly explained (R2 = 0.91, p = 0.004, RMSE = 0.013 a.u.) by the running spatiotemporal and elastic-related parameters (contact and aerial times, stride length and frequency, and vertical oscillation) as follows: theoretical metabolic cost = 10.421 + (4.282 * contact time) + (-3.795 * aerial time) + (-2.422 * stride length) + (-1.711 * stride frequency) + (0.107 * vertical oscillation). Conclusion: Critical determinants of elastic mechanism, such as maximal vertical force and vertical and leg stiffness were unrelated to the metabolic economy. VMAX, a valuable marker of running performance, and its physiological and biomechanical determinants can be effectively evaluated using a heart rate monitor, treadmill, and a digital camera, which can be used in the design of training programs to recreationally active runners.

Extending beyond individual caves: a graph theory approach broadening conservation priorities in Amazon iron ore caves.

The Amazon is renowned worldwide for its biological significance, but it also harbors substantial mineral reserves. Among these, the ferruginous geosystems of the region are critical for iron ore extraction, accounting for 10% of Brazil's export revenue. Additionally, this region holds a significant speleological heritage with more than 1,000 caves. However, cave conservation efforts are often in conflict with land use, necessitating mediation through environmental regulations. While conservation decisions typically consider only the caves' characteristics, such an approach fails to account for the interactions among cave communities and their surrounding landscape. This poses a challenge to reserve design for cave conservation purposes. To address this issue, we assessed the predictors that influence the similarity among cave communities, suggesting the use of this parameter as a proxy for subterranean connectivity. Applying graph theory, we proposed a tool to aid in the selection of priority caves for conservation purposes. Our study involved the sampling of invertebrates in 69 iron ore caves and analyzing 28 environmental variables related to these subterranean habitats and adjacent landscape. Our analysis revealed that landscape and habitat characteristics are more important than geographical distance in determining patterns of similarity among caves. Our graph approach highlighted densely interconnected clusters based on similarity. However, specific caves stood out for harboring exclusive fauna and/or exhibiting habitat specificity, making them unique in the study area. Thus, we recommend prioritizing cave clusters for conservation, assembling both singular caves and others that influence them. It is crucial to note that protocols for the protection of subterranean biodiversity must consider measures that encompass both the caves and the surrounding landscape. Our methodology provides insights into the connectivity among caves, identifies existing groups, highlights singular (or unique) cavities that require preservation, and recognizes those influencing these unique habitats. This methodological advancement is crucial for the development of better conservation policies for the speleological heritage in areas under constant economic pressure.

Use of Interactive Visualization and 3D Printing in the Repair of Complex Congenital Heart Disease Presenting in Adult Life.

We report a case of a 25-year-old male with a heterotaxy-like constellation of congenital heart defects consisting of complete atrioventricular septal defect, transposition of the great arteries, subpulmonary stenosis, L-looped ventricles, hypoplastic right ventricle, and a distant aorta arising from the right ventricle. This case demonstrates how 3D printing and interactive 3D visualization may facilitate a unique surgical repair.

Perspectives on the role of nutrition in influencing academy soccer player development and performance: A qualitative case study of key stakeholders from an English category one soccer academy.

This study aimed to explore player and stakeholder perceptions of the role of nutrition in influencing the development of male academy soccer players. Semi-structured interviews (28 ± 13 mins in length) were conducted with 31 participants from an English category one academy, including players (Youth Development Phase, YDP: n = 6; Professional Development Phase, PDP: n = 4), parents/guardians (n = 10), coaches (n = 3), sport scientists (n = 3), physiotherapists (n = 3), and catering (n = 2). Via reflexive thematic analysis, data demonstrate an apparent lack of understanding and awareness on the role of nutrition in influencing player development, especially in relation to growth, maturation and reducing injury risk. Players highlighted the influence of their parents on their dietary behaviours, whilst parents also called for education to better support their sons. Notably, players and stakeholders perceived that the daily schedule of an academy soccer player presents as "too busy to eat", especially in relation to before school, and before and after training. The results demonstrate the necessity for the co-creation of player and stakeholder specific nutrition education programmes as an initial step towards positively impacting the nutrition culture associated with the academy soccer environment.

Plant trait and vegetation data along a 1314 m elevation gradient with fire history in Puna grasslands, Perú.

Alpine grassland vegetation supports globally important biodiversity and ecosystems that are increasingly threatened by climate warming and other environmental changes. Trait-based approaches can support understanding of vegetation responses to global change drivers and consequences for ecosystem functioning. In six sites along a 1314 m elevational gradient in Puna grasslands in the Peruvian Andes, we collected datasets on vascular plant composition, plant functional traits, biomass, ecosystem fluxes, and climate data over three years. The data were collected in the wet and dry season and from plots with different fire histories. We selected traits associated with plant resource use, growth, and life history strategies (leaf area, leaf dry/wet mass, leaf thickness, specific leaf area, leaf dry matter content, leaf C, N, P content, C and N isotopes). The trait dataset contains 3,665 plant records from 145 taxa, 54,036 trait measurements (increasing the trait data coverage of the regional flora by 420%) covering 14 traits and 121 plant taxa (ca. 40% of which have no previous publicly available trait data) across 33 families.

On the multiphoton ionisation photoelectron spectra of phenol.

The phenol molecule is a prototype for non-adiabatic dynamics and the excited-state photochemistry of biomolecules. In this article, we report a joint theoretical and experimental investigation on the resonance enhanced multiphoton ionisation photoelectron (REMPI) spectra of the two lowest ionisation bands of phenol. The focus is on the theoretical interpretation of the measured spectra using quantum dynamics simulations. These were performed by numerically solving the time-dependent Schrödinger equation using the multi-layer variant of the multiconfiguration time-dependent Hartree algorithm together with a vibronic coupling Hamiltonian model. The ionising laser pulse is modelled explicitly within the ionisation continuum model to simulate experimental femtosecond 1+1 REMPI photoelectron spectra. These measured spectra are sensitive to very short lived electronically excited states, providing a rigorous benchmark for our theoretical methods. The match between experiment and theory allows for an interpretation of the features of the spectra at different wavelengths and shows that there are features due to both 'direct' and 'indirect' ionisation, resulting from non-resonant and resonant excitation by the pump pulse.

The Role of the Ophthalmic Genetics Multidisciplinary Team in the Management of Inherited Retinal Degenerations-A Case-Based Review.

(1) Background: Inherited retinal degenertions are rare conditions which may have a dramatic impact on the daily life of those affected and how they interact with their environment. Coordination of clinical services via an ophthalmic genetics multidisciplinary team (OG-MDT) allows better efficiency of time and resources to reach diagnoses and facilitate patient needs. (2) Methods: This clinical case series was conducted by a retrospective review of patient records for patients enrolled in the Target 5000 programme and managed by the OG-MDT, at the Mater Hospital Dublin, Ireland (n = 865) (3) Results: Herein we describe clinical cases and how the use of the OG-MDT optimizes care for isolated and syndromic IRD pedigrees. (4) Conclusions: this paper demonstrates the benefits of an OG-MDT to patients with IRDs resulting in the holistic resolution of complex and syndromic cases. Furthermore, we demonstrate that this format can be adopted/developed by similar centres around the world, bringing with it the myriad benefits.

Shifts in the incidence of shark bites and efficacy of beach-focussed mitigation in Australia.

Shark-human interactions are some of the most pervasive human-wildlife conflicts, and their frequencies are increasing globally. New South Wales (Australia) was the first to implement a broad-scale program of shark-bite mitigation in 1937 using shark nets, which expanded in the late 2010s to include non-lethal measures. Using 196 unprovoked shark-human interactions recorded in New South Wales since 1900, we show that bites shifted from being predominantly on swimmers to 79 % on surfers by the 1980s and increased 2-4-fold. We could not detect differences in the interaction rate at netted versus non-netted beaches since the 2000s, partly because of low incidence and high variance. Although shark-human interactions continued to occur at beaches with tagged-shark listening stations, there were no interactions while SMART drumlines and/or drones were deployed. Our effect-size analyses show that a small increase in the difference between mitigated and non-mitigated beaches could indicate reductions in shark-human interactions. Area-based protection alone is insufficient to reduce shark-human interactions, so we propose a new, globally transferable approach to minimise risk of shark bite more effectively.

Toward a Cenozoic history of atmospheric CO2.

The geological record encodes the relationship between climate and atmospheric carbon dioxide (CO2) over long and short timescales, as well as potential drivers of evolutionary transitions. However, reconstructing CO2 beyond direct measurements requires the use of paleoproxies and herein lies the challenge, as proxies differ in their assumptions, degree of understanding, and even reconstructed values. In this study, we critically evaluated, categorized, and integrated available proxies to create a high-fidelity and transparently constructed atmospheric CO2 record spanning the past 66 million years. This newly constructed record provides clearer evidence for higher Earth system sensitivity in the past and for the role of CO2 thresholds in biological and cryosphere evolution.

Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma.

The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified >95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL. SIGNIFICANCE: Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient.

Low-Performing Students Confidently Overpredict Their Grade Performance throughout the Semester.

When asked to predict how they will perform on an upcoming exam, students are often poorly calibrated, typically in the direction of overpredicting their performance. Research shows that low-performing students' calibration tends to remain poor across multiple tests over the course of a semester. We tested whether these students remain confident in these erroneously high grade predictions across the semester or whether their confidence wanes, suggesting some degree of metacognitive awareness. In two studies, students made grade predictions prior to taking four in-class exams and then rated their level of confidence in their predictions. Results from both studies showed that miscalibration and confidence remained stable across tests, suggesting that low-performing students continued to believe that they would perform well on upcoming exams despite prior evidence to the contrary.

The Inflammasome Pathway is Activated by Dengue Virus Non-structural Protein 1 and is Protective During Dengue Virus Infection.

Dengue virus (DENV) is a medically important flavivirus causing an estimated 50-100 million dengue cases annually, some of whom progress to severe disease. DENV non-structural protein 1 (NS1) is secreted from infected cells and has been implicated as a major driver of dengue pathogenesis by inducing endothelial barrier dysfunction. However, less is known about how DENV NS1 interacts with immune cells and what role these interactions play. Here we report that DENV NS1 can trigger activation of inflammasomes, a family of cytosolic innate immune sensors that respond to infectious and noxious stimuli, in mouse and human macrophages. DENV NS1 induces the release of IL-1ß in a caspase-1 dependent manner. Additionally, we find that DENV NS1-induced inflammasome activation is independent of the NLRP3, Pyrin, and AIM2 inflammasome pathways, but requires CD14. Intriguingly, DENV NS1-induced inflammasome activation does not induce pyroptosis and rapid cell death; instead, macrophages maintain cellular viability while releasing IL-1ß. Lastly, we show that caspase-1/11-deficient, but not NLRP3-deficient, mice are more susceptible to lethal DENV infection. Together, these results indicate that the inflammasome pathway acts as a sensor of DENV NS1 and plays a protective role during infection.