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Stimulus data and experimental design for a self-paced reading study on emoji-word substitutions
(2022)
This data paper presents the experimental design and stimuli from an online self-paced reading study on the processing of emojis substituting lexically ambiguous nouns. We recorded reading times for the target ambiguous nouns and for emojis depicting either the intended target referent or a contextually inappropriate homophonous noun. Furthermore, we recorded comprehension accuracy, demographics and a self-assessment of the participants' emoji usage frequency. The data includes all stimuli used, the raw data, the full JavaScript code for the online experiment, as well as Python and R code for the data analysis. We believe that our dataset may give important insights related to the comprehension mechanisms involved in the cognitive processing of emojis. For interpretation and discussion of the experiment, please see the original article entitled "The processing of emoji-word substitutions: A self-paced-reading study".
Landslides in deglaciated and deglaciating mountains represent a major hazard, but their distribution at the spatial scale of entire mountain belts has rarely been studied. Traditional models of landslide distribution assume that landslides are concentrated in the steepest, wettest, and most tectonically active parts of the orogens, where glaciers reached their greatest thickness.
However, based on mapping large landslides (>0.9 km(2)) over an unprecedentedly large area of Southern Patagonia (similar to 305,000 km(2)), we show that the distribution of landslides can have the opposite trend.
We show that the largest landslides within the limits of the former Patagonian Ice Sheet (PIS) cluster along its eastern margins occupying lower, tectonically less active, and arid part of the Patagonian Andes. In contrast to the heavily glaciated, highest elevations of the mountain range, the peripheral regions have been glaciated only episodically, leaving a larger volume of unstable sedimentary and volcanic rocks that are subject to ongoing slope instability.
Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein's coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyr(CUA) were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs).
The benefits of counting butterflies: recommendations for a successful citizen science project
(2022)
Citizen science (CS) projects, being popular across many fields of science, have recently also become a popular tool to collect biodiversity data. Although the benefits of such projects for science and policy making are well understood, relatively little is known about the benefits participants get from these projects as well as their personal backgrounds and motivations. Furthermore, very little is known about their expectations. We here examine these aspects, with the citizen science project "German Butterfly Monitoring" as an example. A questionnaire was sent to all participants of the project and the responses to the questionnaire indicated the following: center dot Most transect walkers do not have a professional background in this field, though they do have a high educational level, and are close to retirement, with a high number of females; center dot An important motivation to join the project is to preserve the natural environment and to contribute to scientific knowledge; center dot Participants benefit by enhancing their knowledge about butterflies and especially their ability to identify different species (taxonomic knowledge); center dot Participants do not have specific expectations regarding the project beyond proper management and coordination, but have an intrinsic sense of working for a greater good. The willingness to join a project is higher if the project contributes to the solution of a problem discussed in the media (here, insect decline). Based on our findings from the analysis of the questionnaire we can derive a set of recommendations for establishing a successful CS project. These include the importance of good communication, e.g., by explaining what the (scientific) purpose of the project is and what problems are to be solved with the help of the data collected in the project. The motivation to join a CS project is mostly intrinsic and CS is a good tool to engage people during difficult times such as the COVID-19 pandemic, giving participants the feeling of doing something useful.
In this paper, we employ an experimental paradigm using insights from the psychology of reasoning to investigate the question whether certain modals generate and draw attention to alternatives. The article extends and builds on the methodology and findings of Mascarenhas & Picat (2019). Based on experimental results, they argue that the English epistemic modal might raises alternatives. We apply the same methodology to the English modal allowed to to test different hypotheses regarding the involvement of alternatives in deontic modality. We find commonalities and differences between the two modals we tested. We discuss theoretical consequences for existing semantic analyses of these modals, and argue that reasoning tasks can serve as a diagnostic tool to discover which natural language expressions involve alternatives.
So far, various studies have aimed at decomposing the integrated terrestrial water storage variations observed by satellite gravimetry (GRACE, GRACE-FO) with the help of large-scale hydrological models. While the results of the storage decomposition depend on model structure, little attention has been given to the impact of the way that vegetation is represented in these models. Although vegetation structure and activity represent the crucial link between water, carbon, and energy cycles, their representation in large-scale hydrological models remains a major source of uncertainty. At the same time, the increasing availability and quality of Earth-observation-based vegetation data provide valuable information with good prospects for improving model simulations and gaining better insights into the role of vegetation within the global water cycle. In this study, we use observation-based vegetation information such as vegetation indices and rooting depths for spatializing the parameters of a simple global hydrological model to define infiltration, root water uptake, and transpiration processes. The parameters are further constrained by considering observations of terrestrial water storage anomalies (TWS), soil moisture, evapotranspiration (ET) and gridded runoff ( Q) estimates in a multi-criteria calibration approach. We assess the implications of including varying vegetation characteristics on the simulation results, with a particular focus on the partitioning between water storage components. To isolate the effect of vegetation, we compare a model experiment in which vegetation parameters vary in space and time to a baseline experiment in which all parameters are calibrated as static, globally uniform values. Both experiments show good overall performance, but explicitly including varying vegetation data leads to even better performance and more physically plausible parameter values. The largest improvements regarding TWS and ET are seen in supply-limited (semi-arid) regions and in the tropics, whereas Q simulations improve mainly in northern latitudes. While the total fluxes and storages are similar, accounting for vegetation substantially changes the contributions of different soil water storage components to the TWS variations. This suggests an important role of the representation of vegetation in hydrological models for interpreting TWS variations. Our simulations further indicate a major effect of deeper moisture storages and groundwater-soil moisture-vegetation interactions as a key to understanding TWS variations. We highlight the need for further observations to identify the adequate model structure rather than only model parameters for a reasonable representation and interpretation of vegetation-water interactions.
Satellite-measured tidal magnetic signals are of growing importance. These fields are mainly used to infer Earth's mantle conductivity, but also to derive changes in the oceanic heat content. We present a new Kalman filter-based method to derive tidal magnetic fields from satellite magnetometers: KALMAG. The method's advantage is that it allows to study a precisely estimated posterior error covariance matrix. We present the results of a simultaneous estimation of the magnetic signals of 8 major tides from 17 years of Swarm and CHAMP data. For the first time, robustly derived posterior error distributions are reported along with the reported tidal magnetic fields. The results are compared to other estimates that are either based on numerical forward models or on satellite inversions of the same data. For all comparisons, maximal differences and the corresponding globally averaged RMSE are reported. We found that the inter-product differences are comparable with the KALMAG-based errors only in a global mean sense. Here, all approaches give values of the same order, e.g., 0.09 nT-0.14 nT for M2. Locally, the KALMAG posterior errors are up to one order smaller than the inter-product differences, e.g., 0.12 nT vs. 0.96 nT for M2.
Planned decommissioning of coal-fired plants in Europe requires innovative technical and economic strategies to support coal regions on their path towards a climate-resilient future. The repurposing of open pit mines into hybrid pumped hydro power storage (HPHS) of excess energy from the electric grid, and renewable sources will contribute to the EU Green Deal, increase the economic value, stabilize the regional job market and contribute to the EU energy supply security. This study aims to present a preliminary phase of a geospatial workflow used to evaluate land suitability by implementing a multi-criteria decision making (MCDM) technique with an advanced geographic information system (GIS) in the context of an interdisciplinary feasibility study on HPHS in the Kardia lignite open pit mine (Western Macedonia, Greece). The introduced geospatial analysis is based on the utilization of the constraints and ranking criteria within the boundaries of the abandoned mine regarding specific topographic and proximity criteria. The applied criteria were selected from the literature, while for their weights, the experts' judgement was introduced by implementing the analytic hierarchy process (AHP), in the framework of the ATLANTIS research program. According to the results, seven regions were recognized as suitable, with a potential energy storage capacity from 1.09 to 5.16 GWh. Particularly, the present study's results reveal that 9.27% (212,884 m(2)) of the area had a very low suitability, 15.83% (363,599 m(2)) had a low suitability, 23.99% (550,998 m(2)) had a moderate suitability, 24.99% (573,813 m(2)) had a high suitability, and 25.92% (595,125 m(2)) had a very high suitability for the construction of the upper reservoir. The proposed semi-automatic geospatial workflow introduces an innovative tool that can be applied to open pit mines globally to identify the optimum design for an HPHS system depending on the existing lower reservoir.
Full-length transcriptome
(2021)
Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relying on genome alignments of related species. Based on cell heterogeneity and known markers, we characterized four cell types: T cells, B cells, monocytes/macrophages (Mo/M phi) and NCC (non-specific cytotoxic cells). Further analysis indicated the presence of two subsets of Mo/M phi including M1 and M2 type, as well as four subsets in B cells, i.e. mature B cells, immature B cells, pre B cells and early-pre B cells. Our research will provide new clues for understanding biological characteristics, development and function of immune cell populations of teleost. Furthermore, our approach provides a reliable alternative for scRNA-seq data analysis in teleost for which no reference genome is currently available.
We study the first-arrival (first-hitting) dynamics and efficiency of a one-dimensional random search model performing asymmetric Levy flights by leveraging the Fokker-Planck equation with a delta-sink and an asymmetric space-fractional derivative operator with stable index alpha and asymmetry (skewness) parameter beta.
We find exact analytical results for the probability density of first-arrival times and the search efficiency, and we analyse their behaviour within the limits of short and long times.
We find that when the starting point of the searcher is to the right of the target, random search by Brownian motion is more efficient than Levy flights with beta <= 0 (with a rightward bias) for short initial distances, while for beta>0 (with a leftward bias) Levy flights with alpha -> 1 are more efficient.
When increasing the initial distance of the searcher to the target, Levy flight search (except for alpha=1 with beta=0) is more efficient than the Brownian search. Moreover, the asymmetry in jumps leads to essentially higher efficiency of the Levy search compared to symmetric Levy flights at both short and long distances, and the effect is more pronounced for stable indices alpha close to unity.