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Abstract The rapid and repeatable characterization of individual morphology has advanced automated taxonomic classification. The most direct study of evolutionary processes is, however, not from taxonomic description, but rather of the evolution of the traits that comprise individuals and define species. Repeatable signatures of individual morphology are crucial for analysing the response to selection at scale, and thus tracking evolutionary trajectories through time and across species boundaries. Here, we introduce our 3DKMI—an open‐source MATLAB package designed for the study of morphology using three‐dimensional (3D) Krawtchouk moment invariants. The volumetric features derived from the 3D images remain stable under translation, scaling and rotation and, for an image of size 128 × 128 × 128 can be computed in less than 0.1 s. We applied our package as a case study on a collection of 300 X‐ray computed tomography scans of planktonic foraminifera specimens across five species to (1) assess the invariance of the features under different transformations and (2) analyse morphological differences among species based on the extracted characteristics. We show that 3DKMI has the capacity to efficiently and repeatedly characterize the signatures of individual morphology. In the future, we hope that the 3D feature extraction technique 3DKMI will be widely applied to digital collections to advance research in ecology and evolution.

IntroductionForkhead box P3 (Foxp3) T regulatory cells are critical for maintaining self-tolerance, immune homeostasis, and regulating the immune system.MethodsWe investigated interleukin-4 receptor alpha (IL-4Rα) signalling on T regulatory cells (Tregs) during Listeria monocytogenes (L. monocytogenes) infection using a mouse model on a BALB/c background, specifically with IL-4Rα knockdown in Tregs (Foxp3creIL-4Rα−/lox).ResultsWe showed an impairment of Treg responses, along with a decreased bacterial burden and diminished tissue pathology in the liver and spleen, which translated into better survival. Mechanistically, we observed an enhancement of the Th1 signature, characterised by increased expression of the T-bet transcription factor and a greater number of effector T cells producing IFN-γ, IL-2 following ex-vivo stimulation with heat-killed L. monocytogenes in Foxp3creIL-4Rα-/lox mice. Furthermore, CD8 T cells from Foxp3creIL-4Rα-/lox mice displayed increased cytotoxicity (Granzyme-B) with higher proliferation capacity (Ki-67), better survival (Bcl-2) with concomitant reduced apoptosis (activated caspase 3). In contrast to L. monocytogenes, Foxp3creIL-4Rα-/lox mice displayed similar bacterial burdens, lung pathology and survival during Mycobacterium tuberculosis (M. tuberculosis) infection, despite increased T cell numbers and IFN-γ, TNF and IL-17 production.ConclusionOur results demonstrated that the diminished IL-4Rα signalling on Foxp3+ T regulatory cells resulted in a loss of their functionality, leading to survival benefits in listeriosis but not in tuberculosis.

Abstract Both monocytes and macrophages are heterogeneous populations. It was traditionally understood that Ly6Chi classical (inflammatory) monocytes differentiate into pro-inflammatory Ly6Chi macrophages. Accumulating evidence has suggested that Ly6Chi classical monocytes can also differentiate into Ly6Clo pro-resolving macrophages under certain conditions, while their differentiation trajectory remains to be fully elucidated. The present study with scRNA-seq and flow cytometric analyses reveals that Ly6ChiPD-L2lo classical monocytes recruited to the allergic skin lesion sequentially differentiate into Ly6CloPD-L2hi pro-resolving macrophages, via intermediate Ly6ChiPD-L2hi macrophages but not Ly6Clo non-classical monocytes, in an IL-4 receptor-dependent manner. Along the differentiation, classical monocyte-derived macrophages display anti-inflammatory signatures followed by metabolic rewiring concordant with their ability to phagocytose apoptotic neutrophils and allergens, therefore contributing to the resolution of inflammation. The failure in the generation of these pro-resolving macrophages drives the IL-1α-mediated cycle of inflammation with abscess-like accumulation of necrotic neutrophils. Thus, we clarify the stepwise differentiation trajectory from Ly6Chi classical monocytes toward Ly6Clo pro-resolving macrophages that restrain neutrophilic aggravation of skin allergic inflammation.

Deep learning has emerged as a robust tool for automating feature extraction from three-dimensional images, offering an efficient alternative to labour-intensive and potentially biased manual image segmentation methods. However, there has been limited exploration into the optimal training set sizes, including assessing whether artficial expansion by data augmentation can achieve consistent results in less time and how consistent these benefits are across different types of traits. In this study, we manually segmented 50 planktonic foraminifera specimens from the genus Menardella to determine the minimum number of training images required to produce accurate volumetric and shape data from internal and external structures. The results reveal unsurprisingly that deep learning models improve with a larger number of training images with eight specimens being required to achieve 95% accuracy. Furthermore, data augmentation can enhance network accuracy by up to 8.0%. Notably, predicting both volumetric and shape measurements for the internal structure poses a greater challenge compared with the external structure, owing to low contrast differences between different materials and increased geometric complexity. These results provide novel insight into optimal training set sizes for precise image segmentation of diverse traits and highlight the potential of data augmentation for enhancing multivariate feature extraction from three-dimensional images.

Schistosomiasis remains the most devastating neglected tropical disease, affecting over 240 million people world-wide. The disease is caused by the eggs laid by mature female worms that are trapped in host’s tissues, resulting in chronic Th2 driven fibrogranulmatous pathology. Although the disease can be treated with a relatively inexpensive drug, praziquantel (PZQ), re-infections remain a major problem in endemic areas. There is a need for new therapeutic drugs and alternative drug treatments for schistosomiasis. The current study hypothesized that cysteinyl leukotrienes (cysLTs) could mediate fibroproliferative pathology during schistosomiasis. Cysteinyl leukotrienes (cysLTs) are potent lipid mediators that are known to be key players in inflammatory diseases, such as asthma and allergic rhinitis. The present study aimed to investigate the role of cysLTR1 during experimental acute and chronic schistosomiasis using cysLTR1-/- mice, as well as the use of cysLTR1 inhibitor (Montelukast) to assess immune responses during chronic Schistosoma mansoni infection. Mice deficient of cysLTR1 and littermate control mice were infected with either high or low dose of Schistosoma mansoni to achieve chronic or acute schistosomiasis, respectively. Hepatic granulomatous inflammation, hepatic fibrosis and IL-4 production in the liver was significantly reduced in mice lacking cysLTR1 during chronic schistosomiasis, while reduced liver pathology was observed during acute schistosomiasis. Pharmacological blockade of cysLTR1 using montelukast in combination with PZQ reduced hepatic inflammation and parasite egg burden in chronically infected mice. Combination therapy led to the expansion of Tregs in chronically infected mice. We show that the disruption of cysLTR1 is dispensable for host survival during schistosomiasis, suggesting an important role cysLTR1 may play during early immunity against schistosomiasis. Our findings revealed that the combination of montelukast and PZQ could be a potential prophylactic treatment for chronic schistosomiasis by reducing fibrogranulomatous pathology in mice. In conclusion, the present study demonstrated that cysLTR1 is a potential target for host-directed therapy to ameliorate fibrogranulomatous pathology in the liver during chronic and acute schistosomiasis in mice.

The challenge of global food security in the face of population growth, conflict, and climate change requires a comprehensive understanding of cropped areas, irrigation practices, and the distribution of major commodity crops like maize and wheat. However, such understanding should preferably be updated at seasonal intervals for each agricultural system rather than relying on a single annual assessment. Here we present the European Space Agency-funded WorldCereal system, a global, seasonal, and reproducible crop and irrigation mapping system that addresses existing limitations in current global-scale crop and irrigation mapping. WorldCereal generates a range of global products, including temporary crop extent, seasonal maize and cereal maps, seasonal irrigation maps, seasonal active cropland maps, and model confidence layers providing insights into expected product quality. The WorldCereal product suite for the year 2021 presented here serves as a global demonstration of the dynamic open-source WorldCereal system. Validation of the products was done based on best available reference data per product. A global statistical validation for the temporary crop extent product resulted in user's and producer's accuracies of 88.5 % and 92.1 %, respectively. For crop type, a verification was performed against a newly collected street view dataset (overall agreement 82.5 %) and a limited number of publicly available in situ datasets (reaching minimum agreement of 80 %). Finally, global irrigated-area estimates were derived from available maps and statistical datasets, revealing the conservative nature of the WorldCereal irrigation product. The WorldCereal system provides a vital tool for policymakers, international organizations, and researchers to better understand global crop and irrigation patterns and to inform decision-making related to food security and sustainable agriculture. Our findings highlight the need for continued community efforts such as additional reference data collection to support further development and to push the boundaries for global agricultural mapping from space. The global products are available at https://doi.org/10.5281/zenodo.7875104 (Van Tricht et al., 2023).

Manipulating the motion of individual trapped ions at the single quantum level has become standard practice in radio-frequency ion traps, enabling sweeping advances in quantum information processing and precision metrology. The key step for motional-state engineering is ground-state cooling. Full motional control also bears great potential to explore another regime of sensitivities for fundamental physics tests in Penning traps. Here we demonstrate the key enabling step by implementing resolved-sideband cooling on the axial mode of a single ^{9}Be^{+} ion in a 5 Tesla cryogenic Penning trap. The system has been developed for the implementation of high-precision antimatter experiments to test the fundamental symmetries of the standard model with the highest accuracy in the baryonic sector. We measure an axial phonon number of n[over ¯]_{z}=0.10(4) after cooling and demonstrate that the axial heating rate in our system is compatible with the implementation of quantum logic spectroscopy of (anti-)protons.

Many students around the world are exposed to a rote teaching style in mathematics that emphasizes memorization of procedures. Students are frequently presented with standard types of equations in their textbooks, in which the equal sign is immediately preceding the answer (a + b = c). This exposure can lead to many misconceptions, such as thinking that the equal sign means "do something" or "the answer is." This paper describes students' understanding of the equal sign when solving nonstandard equations in Jordan on the Early Grade Mathematics Assessment (EGMA) and in India on a number sense screener. Common misconceptions are shared, as well as strategies for improving instruction with the equal sign and non-standard equations to prevent future errors.

This study was motivated by a desire to help working-age individuals gain a better understanding of their daily nutritional intakes with a new self-reported dietary assessment method because an unhealthy eating behavior increases the risks of developing chronic diseases. In this study, we present the design and evaluation of NutriColoring, a food diary that leverages doodling on sketches to report and reflect on everyday diet in the working context. Through a 2-week field study involving 18 participants, the usefulness of NutriColoring in facilitating dietary assessment was tested by making comparisons with the typical bullet diary method. Our quantitative results showed that NutriColoring provided users with improved dietary assessment experience and intrinsic motivations, with significantly low task frustration and high enjoyment. Because of the freedom and playfulness in reporting intakes at work, the interview findings showed a high acceptance of employing NutriColoring at work. This article is concluded with a set of implications for the design and development of a Doodling toolkit to support healthy eating behaviors among office workers.

Abstract Atopic dermatitis (AD) is a common pruritic inflammatory skin disease with complex environmental and genetic predisposing factors. Primary skin barrier dysfunction and aberrant T helper 2 (TH2) responses to common allergens, together with increased serum IgE antibodies, characterise the disease. B and T cells are essential in the disease manifestation, however, the exact mechanism of how these cells is involved is unclear. Targeting interleukin 4 receptor alpha (IL-4Rα), an IL-4/IL-13 signalling axis, with dupilumab shows efficacy in AD. We investigated the importance of IL-4Rα signalling specifically on B and T cells during acute and chronic models of AD. We used House dust mite (HDM) and Ovalbumin (OVA) in chronic models and a low-calcemic analog of vitamin D (MC903) for acute models of AD. We used mb1creIL-4Rα−/lox, iLCKcreIL-4Rα−/lox, LCKcreIL-4Rα−/lox, CD4creIL-4Rα−/lox, Foxp3creIL-4Rα−/lox and IL-4Rα−/lox littermate controls. IL-4Rα-responsive B cells were essential in serum IgE levels, but not in epidermal thickening in both chronic and acute models. IL-4Rα-responsive T cells were essential in epidermal thickening in the pan-T cell, but not CD4 or CD8 T cells suggesting the importance of γδT cells during acute AD. Our results suggest that IL-4Rα responsiveness on innate T cells regulates acute atopic dermatitis, while on B cells it regulates IgE.

C57BL/6 mice are one of the most widely used inbred strains in biomedical research. Early separation of the breeding colony has led to the development of several sub-strains. Colony separation led to genetic variation development driving numerous phenotypic discrepancies. The reported phenotypic behavior differences between the sub-strains were, however; not consistent in the literature, suggesting the involvement of factors other than host genes. Here, we characterized the cognitive and affective behavior of C57BL/6J and C57BL/6N mice in correlation with the immune cell profile in the brain. Furthermore, faecal microbiota transfer and mice co-housing techniques were used to dissect microbial and environmental factors’ contribution, respectively, to cognitive and affective behavior patterns. We first noted a unique profile of locomotor activity, immobility pattern, and spatial and non-spatial learning and memory abilities between the two sub-strains. The phenotypic behavior profile was associated with a distinct difference in the dynamics of type 2 cytokines in the meninges and brain parenchyma. Analysing the contribution of microbiome and environmental factors to the noted behavioral profile, our data indicated that while immobility pattern was genetically driven, locomotor activity and cognitive abilities were highly sensitive to alterations in the gut microbiome and environmental factors. Changes in the phenotypic behavior in response to these factors were associated with changes in immune cell profile. While microglia were highly sensitive to alteration in gut microbiome, immune cells in meninges were more resilient. Collectively, our findings demonstrated a direct impact of environmental conditions on gut microbiota which subsequently impacts the brain immune cell profile that could modulate cognitive and affective behavior. Our data further highlight the importance of characterizing the laboratory available strain/sub-strain to select the most appropriate one that fits best the study purpose.

Foraminifera are one of the few taxa that preserve their entire ontogeny in their fossilised remains. Revealing this ontogeny through micro-computed tomography (CT) of fossil planktonic foraminifera has greatly improved our understanding of their life history and allows accurate quantification of total shell volume, growth rates and developmental constraints throughout an individual's life. Studies using CT scans currently mainly focus on chamber size, but the wealth of three-dimensional data generated by CT scans has the potential to reconstruct complete growth trajectories. Here we present an open-source R package to analyse growth in three-dimensional space. Using only the centroid xyz coordinates of every chamber, the functions determine the growth sequence and check that chambers are in the correct order. Once the order of growth has been verified, the functions calculate distances and angles between subsequent chambers, determine the total number of whorls and the number of chambers in the final whorl at the time each chamber was built, and, for the first time, quantify trochospirality. The applications of this package will enable repeatable analysis of large data sets and quantification of key taxonomic traits and ultimately provide new insights into the effects of ontogeny on evolution.

To determine the role that the IL-4/IL13 receptor plays in the development of alternatively activated macrophages (AAM or M2) and their role in the regulation of immunity to the extraintestinal phase of the helminth parasite Taenia crassiceps, we followed the infection in a mouse strain lacking the IL-4Rα gene (IL-4Rα−/−) and in the macrophage/neutrophil-specific IL-4Rα-deficient mouse strain (LysMcreIL-4Rα−/lox or cre/LoxP). While 100% of T. crassiceps-infected IL-4Rα+/+ (WT) mice harbored large parasite loads, more than 50% of th eIL-4Rα−/− mice resolved the infection. Approximately 88% of the LysMcreIL-4Rα−/lox mice displayed a sterilizing immunity to the infection. The remaining few infected cre/LoxP mice displayed the lowest number of larvae in their peritoneal cavity. The inability of the WT mice to control the infection was associated with antigen-specific Th2-type responses with higher levels of IgG1, IL-4, IL-13, and total IgE, reduced NO production, and increased arginase activity. In contrast, IL-4Rα−/− semi-resistant mice showed a Th1/Th2 combined response. Furthermore, macrophages from the WT mice displayed higher transcripts for Arginase-1 and RELM-α, as well as increased expression of PD-L2 with robust suppressive activity over anti-CD3/CD28 stimulated T cells; all of these features are associated with the AAM or M2 macrophage phenotype. In contrast, both the IL-4Rα−/− and LysMcreIL-4Rα−/lox mice did not fully develop AAM or display suppressive activity over CD3/CD28 stimulated T cells, reducing PDL2 expression. Additionally, T-CD8+ but no T-CD4+ cells showed a suppressive phenotype with increased Tim-3 and PD1 expression in WT and IL-4Rα−/−, which were absent in T. crassiceps-infected LysMcreIL-4Rα−/lox mice. These findings demonstrate a critical role for the IL-4 signaling pathway in sustaining AAM and its suppressive activity during cysticercosis, suggesting a pivotal role for AAM in favoring susceptibility to T. crassiceps infection. Thus, the absence of these suppressor cells is one of the leading mechanisms to control experimental cysticercosis successfully.

Obesity-associated metabolic inflammation drives the development of insulin resistance and type 2 diabetes, notably through modulating innate and adaptive immune cells in metabolic organs. The nutrient sensor liver kinase B1 (LKB1) has recently been shown to control cellular metabolism and T cell priming functions of DCs. Here, we report that hepatic DCs from high-fat diet–fed (HFD-fed) obese mice display increased LKB1 phosphorylation and that LKB1 deficiency in DCs (CD11cΔLKB1) worsened HFD-driven hepatic steatosis and impaired glucose homeostasis. Loss of LKB1 in DCs was associated with increased expression of Th17-polarizing cytokines and accumulation of hepatic IL-17A+ Th cells in HFD-fed mice. Importantly, IL-17A neutralization rescued metabolic perturbations in HFD-fed CD11cΔLKB1 mice. Mechanistically, deficiency of the canonical LKB1 target AMPK in HFD-fed CD11cΔAMPKα1 mice recapitulated neither the hepatic Th17 phenotype nor the disrupted metabolic homeostasis, suggesting the involvement of other and/or additional LKB1 downstream effectors. We indeed provide evidence that the control of Th17 responses by DCs via LKB1 is actually dependent on both AMPKα1 and salt-inducible kinase signaling. Altogether, our data reveal a key role for LKB1 signaling in DCs in protection against obesity-induced metabolic dysfunctions by limiting hepatic Th17 responses.

IntroductionLines of least resistance, or the direction of maximum phenotypic variation, are reliable predictive tools for directions of evolutionary divergence through time. However, the consistency of trait covariation patterns through space, i.e. in different populations of the same taxa inhabiting different environmental settings, remains poorly established.MethodsTo test whether the predicted direction of evolutionary change is the same through time as it is across space, we compare within- and among-population trait covariation patterns across six Atlantic populations of two planktonic foraminifera species. Our study interval is 600,000 years long, spans the Neogene/Quaternary boundary and includes Earth’s most recent major natural shift in global climate state: the intensification of Northern Hemisphere Glaciation.ResultsWe show that, despite powerful global temporal changes in climate, there is a strong spatial signal in the evolutionary response. Population-specific trait covariation slopes vary among sites, climate phases and core/edge position within the species’ biogeographic range.DiscussionOur results imply that the direction of expected evolutionary change does not align across populations. This suggests that trait covariation patterns in the study species are driven by adaptation to local environmental settings rather than species-wide constraints. Single populations should therefore not be used to predict the response of other populations, even if they are faced with similar environmental conditions. We caution against using individual populations to project future response of other/global populations unless the underlying mechanism for trait covariation is shown to be universal.

Data independent acquisition (DIA) has been gaining momentum in clinical proteomics. Here, the authors create a benchmark dataset comprising inter-patient heterogeneity to compare popular DIA data analysis workflows for identifying differentially abundant proteins.