Motivation
Accurate quantitative information about protein abundance is crucial for understanding a biological system and its dynamics. Protein abundance is commonly estimated using label-free, bottom-up mass spectrometry (MS) protocols. Here, proteins are digested into peptides before quantification via MS. However, missing peptide abundance values, which can make up more than 50% of all abundance values, are a common issue. They result in missing protein abundance values, which then hinder accurate and reliable downstream analyses.
Results
To impute missing abundance values, we propose PEPerMINT, a graph neural network model working directly on the peptide level that flexibly takes both peptide-to-protein relationships in a graph format as well as amino acid sequence information into account. We benchmark our method against 11 common imputation methods on 6 diverse datasets, including cell lines, tissue, and plasma samples. We observe that PEPerMINT consistently outperforms other imputation methods. Its prediction performance remains high for varying degrees of missingness, different evaluation approaches, and differential expression prediction. As an additional novel feature, PEPerMINT provides meaningful uncertainty estimates and allows for tailoring imputation to the user’s needs based on the reliability of imputed values.
Weniger anzeigenThe Kieffer model is a widely accepted explanation for seasonal modification of the Martian surface by CO2 ice sublimation and the formation of a "zoo" of intriguing surface features. However, the lack of in situ observations and empirical laboratory measurements of Martian winter conditions hampers model validation and refinement. We present the first experiments to investigate all three main stages of the Kieffer model within a single experiment: (i) CO2 condensation on a thick layer of Mars regolith simulant; (ii) sublimation of CO2 ice and plume, spot, and halo formation; and (iii) the resultant formation of surface features. We find that the full Kieffer model is supported on the laboratory scale as (i) CO2 diffuses into the regolith pore spaces and forms a thin overlying conformal layer of translucent ice. When a buried heater is activated, (ii) a plume and dark spot develop as dust is ejected with pressurized gas, and the falling dust creates a bright halo. During plume activity, (iii) thermal stress cracks form in a network similar in morphology to certain types of spiders, dendritic troughs, furrows, and patterned ground in the Martian high south polar latitudes. These cracks appear to form owing to sublimation of CO2within the substrate, instead of surface scouring. We discuss the potential for this process to be an alternative formation mechanism for "cracked" spider-like morphologies on Mars. Leveraging our laboratory observations, we also provide guidance for future laboratory or in situ investigations of the three stages of the Kieffer model.
Weniger anzeigenBioarchaeological studies provide a valuable contribution to the understanding of the economy and activities of prehistoric populations in mountain regions. The Late Bronze Age in the Caucasus is an epoch of fundamental transformations that is accompanied by the development of a semi-stationary pastoral economy and ultimately by the emergence of combined mountain agriculture. So far, only a few archaeozoological assemblages from this period have been published. The site of Ransyrt-1 in the North Caucasus offers a substantial collection of bone material from the remains of a mountain sanctuary. Analysis of the animal remains as well as preliminary isotopic analyses of strontium, oxygen, and carbon shed light on animal exploitation at this site. Comparisons with slightly later settlements in the North and South Caucasus illustrate the development of intensive livestock management strategies in the Late Bronze Age in this region at the interface between Southwest Asia and the Eurasian steppe.
Weniger anzeigenThe mechanism that causes the rapid uplift and active magmatism of the Hoh-Xil Basin in the northern Tibetan Plateau and hence the outward growth of the proto-plateau is highly debated, more specifically, over the relationship between deep dynamics and surface uplift. Until recently the Hoh-Xil Basin remained uncovered by seismic networks due to inaccessibility. Here, based on linear seismic arrays across the Hoh-Xil Basin, we present a three-dimensional S-wave velocity (VS) model of the crust and uppermost mantle structure beneath the Tibetan Plateau from ambient noise tomography. This model exhibits a widespread partially molten crust in the northern Tibetan Plateau but only isolated pockets in the south manifested as low-VS anomalies in the middle crust. The spatial correlation of the widespread low-VS anomalies with strong uppermost mantle low-VS anomalies and young exposed magmatic rocks in the Hoh-Xil Basin suggests that the plateau grew through lithospheric mantle removal and its driven magmatism.
Weniger anzeigenEocene hyperthermal events reflect profound perturbations of the global carbon cycle. Most of our knowledge about their onset, timing, and rates originates from marine records. Hence, the pacing and magnitude of hyperthermal continental warming remains largely unaccounted for due to a lack of high-resolution climate records. Here we use terrestrial biomarkers and carbon isotopes retrieved from varved lake deposits of the UNESCO World Heritage site ‘Messel Fossil Pit’ (Germany) to quantify sub-millennial to millennial-scale temperature and carbon isotope changes across hyperthermal event C21n-H1 (47.2 million years ago). Our results show maximum warming of ca. 3.5 °C during C21n-H1. We propose that two components are responsible for the warming pattern across the hyperthermal: (1) the massive release of greenhouse gases into the atmosphere-ocean system and (2) half-precession orbital forcing indicated by ~12.000-year temperature cycles. The carbon isotope record of bulk organic matter indicates a sharp, 7‰ decrease at the peak of the hyperthermal, corresponding to increased organic carbon content and a shift in the lake algal community. Collectively, our proxy data reveal the structure of continental temperature response during the hyperthermal event that is characterized by overall warming with a superimposed pattern of sub-orbital scale temperature fluctuations.
Weniger anzeigenPrevious research finds that recent immigrants are healthier than the native-born, while more established immigrants exhibit worse health, suggesting a process of unhealthy assimilation. However, previous literature is mostly based on cross-sectional data or on longitudinal analyses similarly failing to disentangle individual-level variation from between-individual confounding. Moreover, previous longitudinal studies are often limited in their study of different health outcomes (few and mostly subjective health), populations (sometimes only elderly individuals), time periods (short panels) and geographical contexts (mostly Australia, Canada and USA). We address these limitations by comparing the health trajectories of adult immigrants and natives in Germany over extended periods, using data from years 2002–2021 of the German Socio-Economic Panel (SOEP), and investigating a wide range of health outcomes, including self-assessed physical and mental health measures, diagnosed illnesses, and health behaviors. We employ a longitudinal approach that stratifies immigrants by age at arrival, and compares them to natives of the same age. This allows us to estimate both Hierarchical Linear Models and more rigorous Fixed Effects models to further address confounding. Cross-sectionally, we confirm previous literature's findings: recent immigrants are healthier than natives and established immigrants. Longitudinally, we find support for the unhealthy assimilation hypothesis concerning subjective health and mental health, but not for the others health indicators or behaviors. We interpret these findings as possible evidence of immigrants' reduced access to timely health care and emphasize the need for greater longitudinal research investigating migrant gaps in various health outcomes.
Weniger anzeigenLung diseases are one of the leading causes of global mortality. Advances in induced pluripotent stem cell (iPSC) differentiation have enabled the creation of bronchiolar and alveolar lung organoids, advancing research on lung conditions. Traditional Matrigel encapsulation, reliant on the spontaneous assembly and propagation of cells with limited external intervention, often results in variability and low reproducibility. The absence of hyaluronic acid (HA) in Matrigel, a key lung extracellular matrix component, limits bronchiolar and alveolar cell differentiation, reducing the efficacy and reproducibility of iPSC-derived organoid generation. To address this, a novel hybrid hydrogel combining HA and 23% Matrigel, inspired by the natural lung environment, is developed. This hydrogel offers improved biochemical support and viscoelastic properties, significantly accelerating organoid development. Within eight days, the hydrogel produces uniformly sized organoids containing both bronchiolar and alveolar epithelial cells. Increased levels of active mechanosensors and transducers, including PIEZO1, Integrin, and Myosin, suggest that the hydrogel's altered viscoelasticity triggers a mechanotransduction cascade. This bioinspired hydrogel provides a robust, fast model for biomedical research, facilitating rapid drug screening, respiratory disease treatment studies, and surfactant trafficking investigations. Furthermore, it enables the exploration of underlying biomechanical mechanisms to enhance the controllability of organoid generation and maturation.
Weniger anzeigenThe Koopman–von Neumann equation describes the evolution of a complex-valued wavefunction corresponding to the probability distribution given by an associated classical Liouville equation. Typically, it is defined on the whole Euclidean space. The investigation of bounded domains, particularly in practical scenarios involving quantum-based simulations of dynamical systems, has received little attention so far. We consider the Koopman–von Neumann equation associated with an ordinary differential equation on a bounded domain whose trajectories are contained in the set's closure. Our main results are the construction of a strongly continuous semigroup together with the existence and uniqueness of solutions of the associated initial value problem. To this end, a functional-analytic framework connected to Sobolev spaces is proposed and analyzed. Moreover, the connection of the Koopman–von Neumann framework to transport equations is highlighted.
Weniger anzeigenEndothelial cells, which line the lumen of blood vessels, locally sense and respond to blood flow. In response to altered blood flow dynamics during early embryonic development, these cells undergo shape changes that directly affect vessel geometry: In the dorsal aorta of zebrafish embryos, elongation of endothelial cells in the direction of flow between 48 and 72 hours post fertilization (hpf) reduces the vessel’s diameter. This remodeling process requires Endoglin; excessive endothelial cell growth in the protein’s absence results in vessel diameter increases. To understand how these changes in vessel geometry emerge from morphological changes of individual endothelial cells, we developed a novel mathematical approach that allows 3D reconstruction and quantification of both dorsal aorta geometry and endothelial cell surface morphology. Based on fluorescently marked endothelial cell contours, we inferred cross-sections of the dorsal aorta that accounted for dorsal flattening of the vessel. By projection of endothelial cell contours onto the estimated cross-sections and subsequent triangulation, we finally reconstructed 3D surfaces of the individual cells. By simultaneously reconstructing vessel cross-sections and cell surfaces, we found in an exploratory analysis that morphology varied between endothelial cells located in different sectors of the dorsal aorta in both wild-type and Endoglin-deficient zebrafish embryos: In wild-types, ventral endothelial cells were smaller and more elongated in flow direction than dorsal endothelial cells at both 48 hpf and 72 hpf. Although dorsal and ventral endothelial cells in Endoglin-deficient embryos had similar sizes at 48 hpf, dorsal endothelial cells were much larger at 72 hpf. In Endoglin-deficient embryos, elongation in flow direction increased between 48 hpf and 72 hpf in ventral endothelial cells but hardly changed in dorsal endothelial cells. Hereby, we provide evidence that dorsal endothelial cells contribute most to the disparate changes in dorsal aorta diameter in wild-type and Endoglin-deficient embryos between 48 hpf and 72 hpf.
Weniger anzeigenHydration and dehydration reactions play pivotal roles in plate tectonics and the deep water cycle, yet many facets of (de)hydration reactions remain unclear. Here, we study (de)hydration reactions where associated solid density changes are predominantly balanced by porosity changes, with solid rock deformation playing a minor role. We propose a hypothesis for three scenarios of (de)hydration front propagation and test it using one-dimensional hydro-mechanical-chemical models. Our models couple porous fluid flow, solid rock volumetric deformation, and (de)hydration reactions described by equilibrium thermodynamics. We couple our transport model with reactions through fluid pressure: the fluid pressure gradient governs porous flow and the fluid pressure magnitude controls the reaction boundary. Our model validates the hypothesized scenarios and shows that the change in solid density across the reaction boundary, from lower to higher pressure, dictates whether hydration or dehydration fronts propagate: decreasing solid density causes dehydration front propagation in the direction opposite to fluid flow while increasing solid density enables both hydration and dehydration front propagation in the same direction as fluid flow. Our models demonstrate that reactions can drive the propagation of (de)hydration fronts, characterized by sharp porosity fronts, into a viscous medium with zero porosity and permeability; such propagation is impossible without reactions, as porosity fronts become trapped. We apply our model to serpentinite dehydration reactions with positive and negative Clapeyron slopes and granulite hydration (eclogitization). We use the results of systematic numerical simulations to derive a new equation that allows estimating the transient, reaction-induced permeability of natural (de)hydration zones.
Weniger anzeigenRecognizing that no central authority can combat climate change, scholars have pointed to the potential of polycentric governance in tackling climate change. Yet, empirical evidence for such a claim is scarce, particularly in the Global South. This study analyzes the characteristics, promises, and pitfalls of polycentric governance to promote climate mitigation efforts in three Indian states. Our contribution is twofold: (1) conceptually, we propose a framework to investigate the promises and pitfalls of polycentric climate governance in a federalist system with a particular focus on aspects of scaling and institutionalization, and (2) empirically, we compare solar power development across three Indian states with favorable conditions for solar power but varying performance. Based on a qualitative analysis of interviews and documents, we show how state governments with different party backgrounds have been vital in implementing policy changes and overcoming political barriers. Still, very few bottom-up initiatives exist and were successfully institutionalized.
Weniger anzeigenIn a hypergraph ℋ = (V, ℰ) with vertex set V and edge set ℰ, a real-valued function f: V → [0, 1] is a fractional transversal if ∑v ∈ E f(v) ≥ 1 holds for every E ∈ ℰ. Its size is |f| := ∑v ∈ V f(v), and the fractional transversal number τ*(ℋ) is the smallest possible |f|.
We consider a game scenario where two players have opposite goals, one of them trying to minimize and the other to maximize the size of a fractional transversal constructed incrementally. We prove that both players have strategies to achieve their common optimum, and they can reach their goals using rational weights.
Weniger anzeigenWhen subjects navigate through spatial environments, grid cells exhibit firing fields that are arranged in a triangular grid pattern. Direct recordings of grid cells from the human brain are rare. Hence, functional magnetic resonance imaging (fMRI) studies proposed an indirect measure of entorhinal grid-cell activity, quantified as hexadirectional modulation of fMRI activity as a function of the subject’s movement direction. However, it remains unclear how the activity of a population of grid cells may exhibit hexadirectional modulation. Here, we use numerical simulations and analytical calculations to suggest that this hexadirectional modulation is best explained by head-direction tuning aligned to the grid axes, whereas it is not clearly supported by a bias of grid cells toward a particular phase offset. Firing-rate adaptation can result in hexadirectional modulation, but the available cellular data is insufficient to clearly support or refute this option. The magnitude of hexadirectional modulation furthermore depends considerably on the subject’s navigation pattern, indicating that future fMRI studies could be designed to test which hypothesis most likely accounts for the fMRI measure of grid cells. Our findings also underline the importance of quantifying the properties of human grid cells to further elucidate how hexadirectional modulations of fMRI activity may emerge.
Weniger anzeigenThe transition towards more just and sustainable food systems is a major challenge which requires persuasive policy narratives for motivation and coordination. However, research about how relevant European actor groups view crucial elements of food system transitions is scarce. The consultation on the European Commission's Farm-to-Fork Strategy provided an opportunity to analyze how elements of food system transitions are represented and connected in the policy narratives of European stakeholders. A deductive-inductive content analysis of 164 public responses, using an analytical framework based on the multi-level-perspective of food system transitions, found twelve distinct narratives, mostly focused on agricultural production. Ten of them showed clear connections to three established agricultural policy discourses: neomercantilism, multi-functionalism and market liberalism. While the narratives together provided a comprehensive account of transition drivers, challenges, opportunities and responses, individually they presented rather partial perspectives. For example, market-liberal narratives emphasized the role of value chain actors and “consumer choice”, whereas multifunctionalist narratives called for more regulation. Farmers' associations mainly deployed neomercantilist, NGOs multi-functional and industry representatives market-liberal narratives, revealing dissent on the importance and desirability of change. The findings indicate that shifting the discussion venue away from core agriculture policy arenas broadened entrenched discourses only marginally.
Weniger anzeigenCrimean Congo hemorrhagic fever (CCHF) is a tick-borne zoonotic disease caused by CCHF virus (CCHFV). The disease has a complex transmission cycle that involves a wide range of hosts including mammalian and some species of birds. We implemented a sero-epidemiological study in Isiolo County, Kenya, to determine relative seroprevalences of CCHFV in humans, livestock and in wild animals. In addition, we identified subject and environment level factors that could promote exposure to CCHFV. Humans (n = 580) and livestock (n = 2,137) were recruited into the study through a multistage random sampling technique, and in addition, various species of wild animals (n = 87) were also sampled conveniently. Serum samples from all recruited humans and animals were collected and screened for CCHFV antibodies using ID Screen multispecies, double-antigen IgG enzyme-linked immunosorbent assay (ELISA). The overall anti-CCHFV IgG seroprevalences in humans, cattle, goats, sheep and camels were 7.2% [95% CI: 3.1–15.8%], 53.9% [95% CI: 30.7–50.9%], 11.6% [95% CI: 7.2–22.5%], 8.6% [95% CI: 3–14%] and 89.7% [95% CI: 78–94%], respectively. On average, the sampled wild animals had CCHFV seroprevalence of 41.0% [95% CI: 29.1–49.4%]; giraffes had the highest mean CCHF seroprevalence followed by buffaloes, while impala had very low exposure levels. Statistical analyses using mixed effects logistic regression models showed that CCHFV exposure in humans was significantly associated with male gender, being over 30 years of age and belonging to a household with a seropositive herd. In livestock, a combination of animal- and environment level factors including older animals, being in an area with high normalized difference vegetation index (NDVI) and high vapour pressure deficit were significantly associated with CCHFV infection. Age, sex and species of wild animals were considered as the key risk factors in the analysis, but none of these variables was significant (P-value = 0.891, 0.401 and 0.664, respectively). Additionally, RT-qPCR analysis revealed the presence of CCHFV RNA in camels (30%), cattle (14.3%), and goats (3.8%), but not in humans, sheep, or wild animals. This study demonstrates that environmental factors, such as NDVI and vapor pressure deficit, affect CCHFV exposure in livestock, while the presence of infected livestock is the key determinant of human exposure at the household level. These findings underscore the importance of using One Health approaches to control the disease in human-livestock-wildlife interfaces. For instance, the existing CCHF surveillance measures could be enhanced by incorporating algorithms that simulate disease risk based on the environmental factors identified in the study. Additionally, tick control in livestock, such as the use of acaricides, could reduce CCHFV exposure in livestock and, consequently, in humans.
Weniger anzeigenBackground The anterolateral thigh (ALT) flap plays a crucial role in reconstructive surgeries, providing versatile and reliable soft-tissue coverage. Flap thickness is a critical determinant of tissue volume and quality. Vascular factors, including the vascular diameter of the perforators and the length of the vascular pedicle, significantly influence flap viability and postrepair outcomes. To enhance preoperative assessment, this study integrated gender and body mass index (BMI) to analyze the anatomical characteristics of ALT flaps.
Methods This study used somatic penetrating ultrasonography to examine bilateral ALT flaps in patients. This study analyzed the relationship between gender and ALT flap thickness, vascular diameter of the perforators, and vascular pedicle length. Chi-square test was used to assess variations in age and gender. Multiple t-tests compared flap thickness, vascular diameter, and pedicle length between men and women in different BMI groups.
Results A total of 158 patients were included in this study from January 2018 to December 2022. In BMI < 24 and BMI ≥ 24.0 groups, males had lower ALT flap thickness than females (p < 0.0001 in each subgroup). Similarly, the vascular diameter of the perforators followed the same trend, with females having larger vascular diameters than males in BMI < 24 and BMI ≥ 24.0 groups. In terms of vascular pedicle length, males had longer pedicle length than females in both BMI < 24 and BMI ≥ 24.0 groups (p < 0.05 in each subgroup).
Conclusions Females demonstrate greater ALT flap thickness and larger vascular diameter of the perforators than males, whereas males have a longer length of the vascular pedicle.
Weniger anzeigenDeep learning applications in taxonomic classification for animals and plants from images have become popular, while those for microorganisms are still lagging behind. Our study investigated the potential of deep learning for the taxonomic classification of hundreds of filamentous fungi from colony images, which is typically a task that requires specialized knowledge. We isolated soil fungi, annotated their taxonomy using standard molecular barcode techniques, and took images of the fungal colonies grown in petri dishes (n = 606). We applied a convolutional neural network with multiple training approaches and model architectures to deal with some common issues in ecological datasets: small amounts of data, class imbalance, and hierarchically structured grouping. Model performance was overall low, mainly due to the relatively small dataset, class imbalance, and the high morphological plasticity exhibited by fungal colonies. However, our approach indicates that morphological features like color, patchiness, and colony extension rate could be used for the recognition of fungal colonies at higher taxonomic ranks (i.e. phylum, class, and order). Model explanation implies that image recognition characters appear at different positions within the colony (e.g. outer or inner hyphae) depending on the taxonomic resolution. Our study suggests the potential of deep learning applications for a better understanding of the taxonomy and ecology of filamentous fungi amenable to axenic culturing. Meanwhile, our study also highlights some technical challenges in deep learning image analysis in ecology, highlighting that the domain of applicability of these methods needs to be carefully considered.
Weniger anzeigenElectron paramagnetic resonance–on-a-chip (EPRoC) devices use small voltage-controlled oscillators (VCOs) for both the excitation and detection of the EPR signal, allowing access to unique sample environments by lifting the restrictions imposed by resonator-based EPR techniques. EPRoC devices have been successfully used at multiple frequencies (7 to 360 gigahertz) and have demonstrated their utility in producing high-resolution spectra in a variety of spin centers. To enable quantitative measurements using EPRoC devices, the spatial distribution of the B1 field produced by the VCOs must be known. As an example, the field distribution of a 12-coil VCO array EPRoC operating at 14 gigahertz is described in this study. The frequency modulation–recorded EPR spectra of a “point”-like and a thin-film sample were investigated while varying the position of both samples in three directions. The results were compared to COMSOL simulations of the B1-field intensity. The EPRoC array sensitive volume was determined to be ~19 nanoliters. Implications for possible EPR applications are discussed.
Weniger anzeigenHabitat loss is the main driver of biodiversity decline worldwide. An immediate consequence can be extinction debt, i.e. time-delayed extinction of species following habitat loss. We tested extinction debt in terricolous lichen communities in 45 patches of lowland open dry habitats in the western Po Plain (northern Italy) considering richness of four species groups: total, red-listed, rare, and common species. The distance from the currently nearest patch and the annual precipitation correlated – negatively and positively, respectively – with all the groups. Total, red-listed, and rare species were positively related to the oldest available patch extent (1954). Common species were positively related to the current (2020) patch extent. Total and red-listed species were negatively related to the extent difference (1954–2020). Results reveal an extinction debt which has not yet been completely paid and that could be exacerbated by climate change. To counteract this trend, management should conserve habitat patches with the highest species richness, improve connectivity between habitat patches, and provide suitable microrefugia for species with different ecological requirements.
Weniger anzeigenThe synthesis of the Al2SiO5 polymorphs kyanite, sillimanite and andalusite in a pure Al2O3–SiO2–H2O (ASH) system has long been known to be impeded. In order to decipher individual aspects of the reaction: corundum + SiO2aq, which repeatedly fails to produce thermodynamically stable Al2SiO5, we conducted experiments within the stability fields of kyanite and sillimanite (500–800 ℃; 0.2–1 GPa) with the aim of forming reaction coronas on corundum. Results showed that metastable corundum + quartz assemblages form persistently in pure ASH, even in Al2SiO5 seeded experiments, despite the presence of catalyzing fluid and evidence of fast reaction kinetics. Coronas on corundum spontaneously formed when additional components (Na, K, N, and Mg) were added to the experiment. In a similar experiment with baddeleyite (ZrO2) instead of corundum in silica saturated water, a zircon corona formed readily. This implies that nucleation and growth of Al2SiO5 is obstructed under conditions of Al and Si saturation in aqueous fluid, while both corundum and quartz saturated aqueous fluid are willing participants in other reactions towards stable corona formation. Instead of Al2SiO5 precipitation, an unexpected fluid-aided silica diffusion process into corundum was documented. The latter included the formation of nanometer wide hydrous silicate layers along the basal plane of the corundum host, which enhanced the silica diffusion rate drastically, leading to silica supersaturation in the host mineral, and ultimately to precipitation of quartz inside corundum. We conclude that the natural metastable assemblage of quartz and corundum is not necessarily the result of dry or fluid absent conditions, given that the aqueous fluid in experiments does not promote Al2SiO5 formation, but rather seems to support the formation and preservation of a metastable assemblage.
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