julilili42/papers huggingface dataset:
Empirical dynamic modelling - a promising tool to assess causal links between water quality time series
2020-03-09

&amp;lt;p&amp;gt;Empirical dynamic modelling (EDM) is a relatively novel method to assess causality from time series in coupled dynamic systems. From the literature, EDM appeared to be useful in a number of applications including analysis of water quality data. It was therefore hypothesized that this technique has a potential to revisit existing long term data of solutes from catchment streams. More specifically, we proposed that causal links between concentration time series could be revealed, which were previously overlooked when only standard linear regression and correlation methods were used. We applied EDM to long term concentrations of dissolved organic carbon (DOC), total Fe and pH from the Lehstenbach stream in Germany, time series that were formerly evaluated using various other techniques in the context of DOC mobilisation from peat catchments. To assess causal links between solute time series, three steps of analysis were conducted. Firstly, the embedding dimension for each time series (that is the number of time lags required for the best possible one-time-step-ahead forecast for a particular time series) was computed. In a second step, using the computed embedding dimension, non-linearity of the system was assessed using a technique called s-mapping to explore if EDM is expected to be a beneficial tool for time series analysis. Finally, convergent cross mapping was applied to test different combinations of variables for causal links. The basic idea of convergent cross mapping is that - if X causes Y - the response variable Y contains information on its driver X but not vice versa (because X is independent of Y) and hence X can be predicted from time series of Y. So X is predicted from Y by mapping nearest neighbours in state space (so called cross mapping). With increasing length of Y, predictions shall improve to a saturation level, that is cross mapping skill converges, which is used as a criterion of causality. We applied EDM to weekly, discharge-corrected, temporal changes of concentration time series. Discharge corrections was conducted to eliminate discharge as a common driver of concentrations. Our data analysis implied a causal interaction between Fe and DOC that was proposed in earlier work. But surprisingly, DOC seems to drive pH but not the other way around, a result that needs to be investigated in more detail, but a likely explanation would be that pH of streamwater is mainly decreasing with acidic inputs of DOC from riparian wetlands. We concluded that using EDM additional insights on the links between catchment time series can be obtained.&amp;lt;/p&amp;gt;
Evolution of a low-relief landscape in the Eastern Alps constrained by low-temperature thermochronology and cosmogenic nuclides
2020-03-09

&amp;lt;p&amp;gt;The relief history of mountain belts is strongly influenced by the interplay of tectonics and surface processes, which both shape Earth&amp;amp;#180;s landscapes. In this context, the quantification of the rates of long-term and short-term processes is key for understanding landscape evolution and requires the application of methods that integrate over different timescales. In this study, we apply low-temperature thermochronology and cosmogenic nuclides to quantify the geological and geomorphic evolution of an elevated low-relief landscape in the Eastern Alps, the so-called Nock Mountains, which are situated to the east of the Tauern Window. The low-temperature thermochronological data yield zircon fission track and zircon (U-Th)/He cooling ages of 93.4&amp;amp;#177;12.9 and 77.8&amp;amp;#177;7.8 Ma, respectively, which we interpret to reflect late Cretaceous cooling after Eo-Alpine metamorphism. Apatite fission track and (U-Th)/He ages are significant younger and range from 36.8 to 31.3 Ma. Time-temperature history modelling of the cooling ages suggests enhanced cooling in the Eocene followed by thermal stagnation. Thus, the rocks of the study area have been in near surface position (2-3 km) since the Late Eocene. Enhanced cooling in the Eocene is probably related to an increasing relief due to shortening, folding and thrusting in the Eastern Alps triggered by the onset of collision between the European margin and the Adriatic microplate. Under the assumption that rock exhumation occurred solely by erosion, the long-term average erosion rate derived from the thermochronological data is ~50-90 mm/kyr. Catchment-wide erosion rates derived from cosmogenic &amp;lt;sup&amp;gt;10&amp;lt;/sup&amp;gt;Be in river sediments&amp;amp;#160; range from 83&amp;amp;#177;7 to 205&amp;amp;#177;18 mm/kyr and hence are lower than in other parts of the Alps. As the &amp;lt;sup&amp;gt;10&amp;lt;/sup&amp;gt;Be-derived erosion rates and the long-term rates derived from thermochronology agree despite the different timescales over which the two methods integrate, our new data suggest that erosion rates did not change significantly over the last ~40 Ma. This is remarkable because within this time span numerous tectonic processes and glacial-interglacial cycles affected the study area. To investigate the deglaciation history after the Last Glacial Maximum in the Nock Mountains, we sampled glacially polished quartz veins for &amp;lt;sup&amp;gt;10&amp;lt;/sup&amp;gt;Be exposure dating. The first four exposure ages obtained so far cluster between 14.5&amp;amp;#177;1.4 and 16.8&amp;amp;#177;1.6 ka. We interpret these ages as the record the retreat of the ice cover in the study area shortly after the Oldest Dryas stadial.&amp;lt;/p&amp;gt;
Glacial cycle ice-sheet evolution controlled by ocean bed properties
2020-03-09

&amp;lt;p&amp;gt;Shortcomings in the description of ice dynamics have been recognized as a major limitation for projecting the evolution of the Greenland and Antarctic ice sheets. If current sea-level rise rates continue unabated, up to 630 million people will be at annual flood risk by 2100; making improved ice-sheet model projections a priority and of high socio-economic impact. Since the boundary condition at the underside of the ice-sheet is poorly known, improving constraints on the basal ice/bed properties is essential for accurate prediction of ice-sheet stability and grounding line positions. Furthermore, the history of grounding-line positions since the Last Glacial Maximum has proven challenging to understand due to uncertainties in bed conditions. Here we use a 3D full-Stokes ice-sheet model to investigate the effect of differing ocean bed properties on ice-sheet advance and retreat over a glacial cycle of 40,000 years. We do this for the Ekstr&amp;amp;#246;m Ice Shelf catchment, East Antarctica. We find that predicted ice volumes differ by &amp;gt;50 % under almost equal forcing when comparing (low-friction) sediment-covered with (high-friction) crystalline ocean beds. Grounding-line positions differ by &amp;gt;100 % (49 km), show significant hysteresis, and migrate non-steadily in both scenarios with long quiescent phases disrupted by leaps of rapid migration. Our new modelling framework extends the applicability of 3D full-Stokes ice-sheet models by an order of magnitude to previous studies. The simulations predict evolution of two entirely different catchment geometries (namely thick and slow vs. thin and fast), triggered exclusively by variable ocean-bed properties. This highlights that constraints not only for the bathymetry but also its geological properties are urgently needed for predicting ice-sheet evolution and sea level change.&amp;lt;/p&amp;gt;
Polystyrene microplastics do not affect juvenile brow trout (Salmo trutta f. fario) or modulate effect of the pesticide methiocarb
2020-03-09

<title>Abstract</title> Background There has been a rising interest within the scientific community and the public about the environmental risk related to the abundance of microplastics in aquatic environments. Up to now, however, scientific knowledge in this context has been scarce and insufficient for a reliable risk assessment. To remedy this scarcity of data, we investigated possible adverse effects of polystyrene particles (10^4 particles/L) and the pesticide methiocarb (1 mg/L) in juvenile brow trout (Salmo trutta f. fario) both by themselves as well as in combination after a 96 h laboratory exposure. PS beads (density 1.05 g/mL) were cryogenically milled and fractionated resulting in irregular shaped particles (&lt;50 μm). Besides body weight of the animals, biomarkers for proteotoxicity (stress protein family Hsp70), oxidative stress (superoxide dismutase, lipid peroxidation), and neurotoxicity (acetylcholinesterase, carboxylesterases) were analysed. As an indicator of overall health, histopathological effects were studied in liver and gills of exposed fish. Results Polystyrene particles by themselves did not influence any of the investigated biomarkers. In contrast, the exposure to methiocarb led to a significant reduction of the activity of acetylcholinesterase and the two carboxylesterases. Moreover, the tissue integrity of liver and gills was impaired by the pesticide. Body weight, the oxidative stress and the stress protein levels were not influenced by methiocarb. Effects caused by co-exposure of polystyrene microplastics and methiocarb were the same as those caused by methiocarb alone. Conclusions Overall, methiocarb led to negative effects in juvenile brown trout. In contrast, polystyrene microplastics in the tested concentration did not affect the health of juvenile brown trout and did not modulate the toxicity of methiocarb in this fish species.
The substrate specificity switch FlhB assembles onto the export gate to regulate type three secretion
2020-03-10

Abstract Protein secretion through type-three secretion systems (T3SS) is critical for motility and virulence of many bacteria. Proteins are transported through an export gate containing three proteins (FliPQR in flagella, SctRST in virulence systems). A fourth essential T3SS protein (FlhB/SctU) functions to “switch” secretion substrate specificity once the growing hook/needle reach their determined length. Here, we present the cryo-electron microscopy structure of an export gate containing the switch protein from a Vibrio flagellar system at 3.2 Å resolution. The structure reveals that FlhB/SctU extends the helical export gate with its four predicted transmembrane helices wrapped around FliPQR/SctRST. The unusual topology of the FlhB/SctU helices creates a loop wrapped around the bottom of the closed export gate. Structure-informed mutagenesis suggests that this loop is critical in gating secretion and we propose that a series of conformational changes in the T3SS trigger opening of the gate through interactions between FlhB/SctU and FliPQR/SctRST.
Primary Human Chondrocytes Affected by Cigarette Smoke—Therapeutic Challenges
2020-03-10

Although several researchers have attested deleterious effects of smoking to the musculoskeletal system, the association between smoking and the onset of osteoarthritis (OA) remains unclear. Here, we investigate the effect of cigarette smoke extract (CSE) on primary human chondrocytes. The present study demonstrates that physiological concentrations of CSE (0.1%–10%) inhibit the viability, proliferation, and matrix formation of chondrocytes in a dose- and time-dependent manner. Significant amounts of free radicals were generated by 10% of CSE and led to cell death. A clinical dosage (4 mg/mL) of dexamethasone (Dex) showed toxic effects on chondrocytes, and the long-time treatment by lower doses (4–400 μg/mL) induced hypertrophic changes in the chondrocytes. To substitute Dex, diclofenac (Dic, 1 μg/mL) and acetaminophen (Ace, 10 μg/mL) were tested and did not worsen the metabolic activity of CSE-exposed chondrocytes. Hyaluronic acid (HA, 5 mg/mL) combined with Dic or Ace significantly inhibited the oxidative stress and enhanced the viability and matrix formation of CSE-exposed chondrocytes. This study shows for the first time that CSE mediates the disruption of cartilage through inducing cell death by increasing oxidative stress, and that this effect is fortified by Dex. The deleterious effects of CSE on chondrocytes could be reversed by treatment with HA combined with first-line analgesic/anti-inflammatory agents.
Testing the individual and social learning abilities of task-naïve captive chimpanzees (Pan troglodytes sp.) in a nut-cracking task
2020-03-10

Nut-cracking is often cited as one of the most complex behaviours observed in wild chimpanzees. However, the cognitive mechanisms behind its acquisition are still debated. The current null hypothesis is that the form of nut-cracking behaviour relies on variants of social learning, with some researchers arguing, more precisely, that copying variants of social learning mechanisms are necessary. However, to date, very few experiments have directly investigated the potentially sufficient role of individual learning in explaining the behavioural form of nut-cracking. Despite this, the available data provides some evidence for the spontaneous acquisition of nut-cracking by chimpanzees; later group acquisition was then found to be at least facilitated by (unspecified) variants of social learning. The latter findings are in line with both suggested hypotheses, i.e., that copying social learning is required and that other (non-copying) social learning mechanisms are at play. Here we present the first study which focused (initially) on the role of individual learning for the acquisition of the nut-cracking behavioural form in chimpanzees. We tested task-naïve chimpanzees ( N = 13) with an extended baseline condition to examine whether the behaviour would emerge spontaneously. After the baseline condition (which was unsuccessful), we tested for the role of social learning by providing social information in a step-wise fashion, culminating in a full action demonstration of nut-cracking by a human demonstrator (this last condition made it possible for the observers to copy all actions underlying the behaviour). Despite the opportunities to individually and/or socially learn nut-cracking, none of the chimpanzees tested here cracked nuts using tools in any of the conditions in our study; thus, providing no conclusive evidence for either competing hypothesis. We conclude that this failure was the product of an interplay of factors, including behavioural conservatism and the existence of a potential sensitive learning period for nut-cracking in chimpanzees. The possibility remains that nut-cracking is a behaviour that chimpanzees can individually learn. However, this behaviour might only be acquired when chimpanzees are still inside their sensitive learning period, and when ecological and developmental conditions allow for it. The possibility remains that nut-cracking is an example of a culture dependent trait in non-human great apes. Recommendations for future research projects to address this question are considered.
Association between metabolic syndrome and hip osteoarthritis in middle-aged men and women from the general population
2020-03-10

The compound metabolic syndrome showed no association with osteoarthritis of the hip joint. Age was the only parameter to be dependently and independently associated to osteoarthritis of both hip joints, while elevated blood glucose was independently associated with degeneration of the right hip joint.
The Impact of an Audience Response System on a Summative Assessment, a Controlled Field Study
2020-03-10

<title>Abstract</title> <bold>Background:</bold> Audience response systems allow to activate the audience and to receive a direct feedback of participants during lectures. Modern systems do not require any proprietary hardware anymore. Students can directly respond on their smartphone. Several studies reported about a high level of satisfaction of students when audience response systems are used, however their impact on learning success is still unclear.<bold>Methods:</bold> In order to evaluate the impact of an audience response system on the learning success we implemented the audience response system eduVote into a seminar series and performed a controlled crossover study on its impact on assessments. 154 students in nine groups were taught the same content. In five groups, eduVote was integrated for the first topic while four groups were taught this topic without the audience response systems. For a second topic, the groups were switched: Those groups who were taught before using eduVote were now taught without the audience response system and vice versa. We then analyzed the impact of the audience response system on the students’ performance in a summative assessment and specifically focused on questions dealing with the topic, for which the audience response system was used during teaching. We further assessed the students’ perception on the use of eduVote using questionnaires.<bold>Results:</bold> In our controlled crossover study we could not confirm an impact of the audience response system eduVote on long-term persistence i.e. the students’ performance in the summative assessment. Our evaluation revealed that students assessed the use of eduVote very positively, felt stronger engaged and better motivated to deal with the respective topics and would prefer their integration into additional courses as well. In particular we identified, that “shy students” profit from the use of an audience response system during teaching.<bold>Conclusions:</bold> Audience response systems motivate and activate students and increase their engagement during classes. However, their impact on long-term persistence and summative assessments may be limited. Audience response systems, however, specifically allow activating students which cannot be reached by the traditional way of asking questions without such an anonymous tool.
Application of polarimetric radar to infer ice fabric anisotropy
2020-03-10

&amp;lt;p&amp;gt;Understanding ice flow of ice sheets is not only important to predict their future evolution, but is also required for finding future ice-core sites with an intact stratigraphy and a constrained age-depth relationship of the corresponding climate record. Anisotropic ice flow, induced through the formation of aligned Crystal Orientation Fabric (COF), is in this context important as it may cause ice overturning and folding at larger depths. Here, we use a synthetic radar forward model to explore the feasibility of detecting the crystal orientation fabric orientation and strength using coherent, polarimetric ice-penetrating radar data (ApRES). We compare our results, with ApRES data collected in Antarctica. Some of the sites are located near deep drill ice-core sites (e.g., Dome C), and we validate our approach with ice-core data.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;In multilayer models, we distinguish between birefringence (caused by ray propagation through anisotropic COF with unknown strength and orientation) and anisotropic scattering (caused by an unknown depth variability of anisotropic COF). We show analytically that the scattering ratio is determined by the angular dependence of co-polarization extinction nodes. Building on previous work, we infer COF orientation using the depolarization component, and COF strength from the gradient of polarimetric coherence, respectively.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;We apply this approach to polarimetric ApRES datasets. We show COF orientation can often reliably be inferred as long as it does not change significantly with depth. Rotation of principal axis with depth, on the other hand, causes a complicated radar response that is not straightforwardly interpreted. At dome positions, where the ice anisotropy develops more gently compared to flank-flow settings, the degree of anisotropy can be estimated with the phase gradient method. This becomes increasingly more difficult for flank-flow settings where phase unwrapping is required. We delineate a number of anisotropic scattering zones which likely correspond to COF patterns changing abruptly. In some cases, boundaries between anisotropic scattering zones coincide with climate transitions within the ice.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;We provide our model code in the form of a user-friendly GUI, enabling to quickly explore a wide range of possible COF patterns and their corresponding imprint in the radar data. This is useful both for scientific and educational purposes. Our analysis underlines the potential of coherent, polarimetric radars to infer the COF orientation of ice sheets also away from ice core sites. This will provide important data for the inclusion of ice anisotropy in ice-flow models in the future.&amp;lt;/p&amp;gt;
Zinc and Nickel signature for abiogenic and biogenic magnetite: implications for the origin of magnetite in banded iron formations
2020-03-10

&amp;lt;p&amp;gt;There are longstanding and ongoing controversies about the abiogenic or biogenic origin of magnetite in banded iron formations (BIFs). The trace element composition of magnetite was proposed as a promising tracer for distinguishing biogenic from abiogenic magnetite, which, however, remains to be explored quantitatively. Here, we compared the partitioning of trace elements Zinc (Zn) and Nickel (Ni) in both abiogenic and biogenic magnetite produced either by an abiotic reaction of ferrihydrite with by Fe&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt;&amp;lt;sub&amp;gt;aq&amp;lt;/sub&amp;gt; or by Fe(III)-reducing bacteria &amp;lt;em&amp;gt;Shewanella oneidensis&amp;lt;/em&amp;gt; MR-1. We compared the transformation of three different ferrihydrite (Fh) starting materials: 1) Control Fh without added trace elements, 2) ferrihydrite with co-precipitated Zn (ZnFh) and 3) ferrihydrite with co-precipitated Ni (NiFh) &amp;amp;#8211; both in either NaHCO&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; or HEPES buffer. We monitored Fe concentration and speciation in both aqueous and solid phases over time using the spectrophotometric ferrozine assay, analyzed Fh transformation products by M&amp;amp;#246;ssbauer spectroscopy as well as X-ray diffraction and quantified Zn and Ni in solution and in the minerals by iCAP-Qc quadrupole mass spectrometer after acidic dissolution of the minerals. In summary our results revealed that both Zn and Ni are much more depleted in abiogenic magnetite than those in biogenic magnetite, independent of whether magnetite was precipitated in NaHCO&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; or HEPES buffer. Although further analyses are needed, this suggests that the trace element distribution could be a chemical signature to distinguish biogenic from abiogenic magnetite in BIFs.&amp;lt;/p&amp;gt;
Modern plate tectonic cycles are inherited from Hadean mantle convection
2020-03-10

&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Earth&amp;amp;#8217;s oldest preserved crustal archive, the Jack Hills zircon of Western Australia, has been controversial to interpret in terms of the onset of plate tectonics. Here we conduct time series analysis on hafnium isotopes of the Jack Hills zircon and reveal an array of statistically significant cycles that are reminiscent of plate tectonics, i.e., subduction. At face value, such cycles may suggest early Earth conditions similar to today&amp;amp;#8212;the uniformitarian &amp;amp;#8220;day one&amp;amp;#8221; hypothesis. On the other hand, in the context of expected secular changes due to planetary evolution and geological observations, the cycles could instead imply that modern plate tectonic subduction inherited convective harmonics already facilitated by an early phase of stagnant-lid delamination&amp;amp;#8212;the &amp;amp;#8220;lid-to-plates&amp;amp;#8221; hypothesis. Either way, any model for the initiation of plate tectonics must begin in Hadean time.&amp;lt;/strong&amp;gt;&amp;lt;/p&amp;gt;