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Abstract The characteristics of data produced by omics technologies are pivotal, as they critically influence the feasibility and effectiveness of computational methods applied in downstream analyses, such as data harmonization and differential abundance analyses. Furthermore, variability in these data characteristics across datasets plays a crucial role, leading to diverging outcomes in benchmarking studies, which are essential for guiding the selection of appropriate analysis methods in all omics fields. Additionally, downstream analysis tools are often developed and applied within specific omics communities due to the presumed differences in data characteristics attributed to each omics technology. In this study, we investigate over ten thousand datasets to understand how proteomics, metabolomics, lipidomics, transcriptomics, and microbiome data vary in specific data characteristics. We were able to show patterns of data characteristics specific to the investigated omics types and provide a tool that enables researchers to assess how representative a given omics dataset is for its respective discipline. Moreover, we illustrate how data characteristics can impact analyses at the example of normalization in the presence of sample-dependent proportions of missing values. Given the variability of omics data characteristics, we encourage the systematic inspection of these characteristics in benchmark studies and for downstream analyses to prevent suboptimal method selection and unintended bias.

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.

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).

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.

One of the major consequences of schistosomiasis is its impact on brain function, and despite its severity, the underlying mechanism(s) remain inadequately understood, highlighting a knowledge gap in the disease. The symptoms can vary from headaches to profound cognitive impairment. Besides, the potential influence of physical exercise in mitigating cognitive deficits has received little attention. In our study, we utilized a murine model of Schistosoma mansoni infection to investigate the cognitive impact of schistosomiasis. Our aims were multifaceted: to pinpoint the specific cognitive domains affected during the infection in adult mice, to unravel the complex interplay between glial and immune cells within the central nervous system (CNS), and crucially, to explore the potential therapeutic role of regular physical exercise in counteracting the deleterious effects of schistosomiasis on the CNS. Our findings unveiled that while acute infection did not disrupt simple and complex learning or spatial reference memory, it did induce significant deficits in recall memory—a critical aspect of cognitive function. Furthermore, our investigation unearthed profound alterations in the immune and glial cell populations within the CNS. Notably, we observed marked changes in CD4+ T cells and eosinophils in the meninges, as well as alterations in glial cell dynamics within the hippocampus and other brain regions. These alterations were characterized by heightened microglial activation, diminished astrocyte reactivity and a shift towards a proinflammatory milieu within the CNS. We also provided insights into the transformative potential of regular moderate physical exercise in partially alleviating cognitive and neuroinflammatory consequences of schistosomiasis. Remarkably, exercise decreased glial cell production of TNFα, suggesting a shift towards a less pro-inflammatory environment. Collectively, our study provided compelling evidence of the intricate interplay between schistosomiasis infection and cognitive function, underscoring the critical need for further exploration in this area. Furthermore, our findings demonstrated the positive effects of physical activities on mitigating the cognitive burden of schistosomiasis, offering new hope for patients afflicted by this debilitating disease. [ABSTRACT FROM AUTHOR]

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.

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.

The characteristics of data produced by omics technologies are pivotal, as they critically influence the feasibility and effectiveness of computational methods applied in downstream analyses, such as data harmonization and differential abundance analyses. Furthermore, variability in these data characteristics across datasets plays a crucial role, leading to diverging outcomes in benchmarking studies, which are essential for guiding the selection of appropriate analysis methods in all omics fields. Additionally, downstream analysis tools are often developed and applied within specific omics communities due to the presumed differences in data characteristics attributed to each omics technology. In this study, we investigate over ten thousand datasets to understand how proteomics, metabolomics, lipidomics, transcriptomics, and microbiome data vary in specific data characteristics. We were able to show patterns of data characteristics specific to the investigated omics types and provide a tool that enables researchers to assess how representative a given omics dataset is for its respective discipline. Moreover, we illustrate how data characteristics can impact analyses at the example of normalization in the presence of sample-dependent proportions of missing values. Given the variability of omics data characteristics, we encourage the systematic inspection of these characteristics in benchmark studies and for downstream analyses to prevent suboptimal method selection and unintended bias. [ABSTRACT FROM AUTHOR]

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.

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.