julilili42/papers huggingface dataset:
The ephemeral development of C' shear bands
2021-03-03

&amp;lt;p&amp;gt;C' shear bands are common structures in ductile shear zones but their development is poorly understood. They occur in rocks with a high mechanical strength contrast so we used numerical models of viscoplastic deformation to study the effect of the proportion of weak phase and the phase strength contrast on C' shear band development. We employed simple shear to a finite strain of 18 in 900 steps and recorded the microstructure, stress and strain distribution at each step. We found that C' shear bands form in models with &amp;amp;#8805;5% weak phase when there is a moderate or high phase strength contrast, and they occur in all models with weak phase proportions &amp;amp;#8805;15%. Contrary to previous research, we find that C' shear bands form when layers of weak phase parallel to the shear zone boundary rotate forwards. This occurs due to mechanical instabilities that are a result of heterogeneous distributions of stress and strain rate. C' shear bands form on planes of low strain rate and stress, not in sites of maximum strain rate as has previously been suggested. C' shear bands are ephemeral and they either rotate backwards to the C plane once they are inactive or rotate into the field of shortening and thicken to form X- and triangle- shaped structures.&amp;lt;/p&amp;gt;
An Assessment of Mistletoe-Based Drugs Work in Synergy with Radio-Chemotherapy in the Treatment of Glioma in vitro and in vivo in Glioblastoma Bearing Mice
2021-03-03

Extracts from the mistletoe plant Viscum album L. (VE) are used in the complementary cancer therapy in Europe for decades. VE contain several compounds like the mistletoe lectins (ML) 1-3 and viscotoxins (VT), but also several minor ingredients. ML-1 is suggested to be the main anti-tumor component of VE, VT induce cell death, and some minor compounds can strengthen the anti-tumor activity of ML-1. ML stimulate the immune system, induce cytotoxicity, are able to modify the expression of cancer-associated genes and influence the proliferation and motility of tumor cells. In this study we determine the anti-tumor effects of the VE ISCADOR Qu, of recombinant ML-1 (Aviscumine) and of native ML-1 in the treatment of glioblastoma (GBM), the most common brain tumor in adults. Additionally, we were determined whether a mistletoe-based therapy, if used as adjuvant treatment in combination with temozolomide(TMZ)-or irradiation, provide synergistic effects. The expression of the ML receptor CD75s, which is expressed in GBM specimen and cells, but not in the normal brain, correlates well with the drug-induced cytotoxicity. In GBM cells, the drugs induce cell death in a concentration-dependent manner, induce an arrest in the G2/M phase and provide synergistic and additive anti-tumor effects. A single intratumoral application of Aviscumine prolonged the survival of GBM mice longer than tumor irradiation and was even better if used in combination with radio-chemotherapy. This indicates that an adjuvant treatment of glioma patients with ML-containing drugs might be beneficial.
An Overview of Plant-Derived Drugs in Malaria Treatment
2021-03-03

Treatment of severe malaria continues to rely on two plant derived drugs: artesunate and quinine. In this short overview, the use of effective antimalarial drug combinations against extremely mutable parasite Plasmodium falciparum is reviewed.
Spatial prediction of soil thickness with Gaussian Process Regression using pedological knowledge described by partial differential equations
2021-03-03

&amp;lt;p&amp;gt;Recently, there is a growing interest for the soil variable soil thickness in the soil science, geoscience and ecology communities. More and more scientists assume that soil thickness summarizes many different characteristics of the site that are important for plant growth, soil biodiversity and climate change. As such soil thickness can be an indicator of properties like water holding capacity, nutrient cycling, carbon storage, habitat for soil fauna and overall soil quality and productivity. At the same time, it takes a lot of effort to measure soil thickness, especially for larger and heterogeneous areas like mountain regions, which would require dense sampling. For these reasons, it is becoming increasingly important to spatially predict soil thickness as accurately as possible using models. &amp;lt;br&amp;gt;The typical difficulty in predicting variables in environmental sciences is the small number of samples in the field and resulting from this a small number of usable data points to train models in the spatial domain. One possibility to create valid models with sparse spatially distributed soil data is the combination of point measurements with domain knowledge. For soils and their properties such knowledge can be archived from related environmental data, for example, parent material and climate, and their spatial distribution neighboring the sample points. Frequently used machine learning methods for environmental modelling, especially in the geosciences, are the Gaussian Process Regression Models (GPRs), because a spatial correlation can already be implemented via the covariance kernel. One of the great advantages of using GPRs is the possibility to inform this algorithm directly with soil science knowledge. We can claim this knowledge in different ways. &amp;lt;br&amp;gt;In this paper we apply a new approach of implementing geographical knowledge into the Gaussian Processes by means of partial differential equations (PDEs), each describing a pedological process. These PDEs include information on how independent environmental variables influence the searched dependent variable. At first, we calculate for simple correlations between soil thickness and these variables, which we then convert into a PDE. As independent variables we initially use exclusively topographical variables derived from Digital Elevation Models (DEM) such as slope, different curvatures, aspect or the topographic wetness index. In this way, expert knowledge can adapt the GPR model in addition to the already existing assumption of spatial dependency given by prior covariance, where near things are more related than distant. &amp;lt;br&amp;gt;The algorithm will be applied to a data set from Andalusia, Spain, developed by Tobias Rentschler. Among land use information gained from remote sensing, it contains our target variable soil thickness.&amp;lt;/p&amp;gt;
Topographic Kernels for Gaussian Process Regression in Digital Soil Mapping
2021-03-03

&amp;lt;p&amp;gt;Gaussian Processes provide a theoretically well-understood regression framework that is widely used in the context of Digital Soil Mapping. Among the reasons to use Gaussian Process Regression (GPR) are its interpretability, its builtin support for uncertainty quantification, and its ability to handle unevenly spaced and correlated training samples through a user-specified covariance kernel. The base case of GPR is performed with covariance models that are specified functions of Euclidean distance. In order to incorporate information other than the relative positions, regression-kriging extends GPR by an additive regression model of choice, and co-kriging considers a covariance model between covariates and the target variable. In this work, we use the alternative approach of incorporating topographic information directly into the kernel function by use of a non-Euclidean, non-stationary distance function. In particular, we devise kernels based on a path of least effort, where &amp;lt;em&amp;gt;effort&amp;lt;/em&amp;gt; is locally specified as a function constructed from prior knowledge. It can e.g. be derived from local topographic variables. We demonstrate that our candidate models improve prediction accuracy over the base model. This shows that domain knowledge can be integrated into the model by means of handcrafted kernel functions. The approach is not per se restricted to topographic variables, but could be used for any covariate quantity that is available at output resolution.&amp;lt;/p&amp;gt;
Middle Miocene rise of the Greater Himalaya establishing a new orographic barrier
2021-03-03

&amp;lt;p&amp;gt;The Himalaya is the highest and steepest mountain range on Earth and an efficient north-south barrier for moisture-bearing winds. The close coupling of changes in topography, erosion rates, and uplift has previously been interpreted as an expression of a climatic control on tectonic deformation. Here, we present 17 new zircon U/Th-He (ZHe) bedrock-cooling ages from the Sutlej Valley that &amp;amp;#8211; together with &amp;gt;100 previously published mica &amp;lt;sup&amp;gt;40&amp;lt;/sup&amp;gt;Ar/&amp;lt;sup&amp;gt;39&amp;lt;/sup&amp;gt;Ar, zircon and apatite fission track ages &amp;amp;#8211; allow us to constrain the crustal cooling and exhumation history over the last ~20 Myr. Using 1D-thermal modeling, we observe a rapid decrease in exhumation rates from &amp;gt;1 km/Myr to &amp;lt;0.5 km/Myr that initiated at ~17-15 Ma across the entire Greater and Tethyan Himalaya, as far north as the north-Himalayan Leo Pargil gneiss dome. This decrease is recognized both in the hanging and footwall of major Miocene shear zones and suggests that cooling is associated to surface erosion rather than to tectonic unroofing. We explain the middle Miocene deceleration of exhumation with major reorganization of Himalayan deformation and the onset of the growth of the Lesser Himalayan duplex. This resulted in accelerated uplift of the Greater Himalaya above a mid-crustal ramp, and thus forming a new efficient orographic barrier. The period of slow exhumation in the upper Sutlej Valley coincides with a period of internal drainage in the south-Tibetan Zada Basin further upstream, which we interpret to be a consequence of tectonic damming of the upper Sutlej River. External drainage of the Zada Basin was re-established ~1 Ma, when we observe exhumation rates in the upper Sutlej Valley to accelerate again. Our new finding document that the location of tectonic deformation processes control the first order spatial pattern of both climatic zones and erosion across the orogen.&amp;lt;/p&amp;gt;
Dataset (III) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
2021-03-03

MD simulation data ofCmpd 2 related to the publication Pantsar et al.:Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors. (Other datasets related to this publication:10.5281/zenodo.4572444;10.5281/zenodo.4568113;10.5281/zenodo.4563896) Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files).
Dataset (I) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
2021-03-03

MD simulation data ofCmpd 1 related to the publication Pantsar et al.:Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors. (Other datasets related to this publication:10.5281/zenodo.4572444;10.5281/zenodo.4563896;10.5281/zenodo.4561797) Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files).
Stereolithography vs. Direct Light Processing for Rapid Manufacturing of Complete Denture Bases: An In Vitro Accuracy Analysis
2021-03-04

The topical literature lacks any comparison between stereolithography (SLA) and direct light processing (DLP) printing methods with regard to the accuracy of complete denture base fabrication, thereby utilizing materials certified for this purpose. In order to investigate this aspect, 15 denture bases were printed with SLA and DLP methods using three build angles: 0°, 45° and 90°. The dentures were digitalized using a laboratory scanner (D2000, 3Shape) and analyzed in analyzing software (Geomagic Control X, 3D systems). Differences between 3D datasets were measured using the root mean square (RMS) value for trueness and precision and mean and maximum deviations were obtained for each denture base. The data were statistically analyzed using two-way ANOVA and Tukey’s multiple comparison test. A heat map was generated to display the locations of the deviations within the intaglio surface. The overall tendency indicated that SLA denture bases had significantly higher trueness for most build angles compared to DLP (p &lt; 0.001). The 90° build angle may provide the best trueness for both SLA and DLP. With regard to precision, statistically significant differences were found in the build angles only. Higher precision was revealed in the DLP angle of 0° in comparison to the 45° and 90° angles.
Delirium REduction after administration of melatonin in acute ischemic stroke (DREAMS): A propensity score–matched analysis
2021-03-04

Abstract Background and purpose Poststroke delirium (PSD) comprises a common and severe complication after stroke. However, treatment options for PSD remain insufficient. We investigated whether prophylactic melatonin supplementation may be associated with reduced risk for PSD. Methods Consecutive patients admitted to the Tübingen University Stroke Unit, Tübingen, Germany, with acute ischemic stroke (AIS), who underwent standard care between August 2017 and December 2017, and patients who additionally received prophylactic melatonin (2 mg per day at night) within 24 h of symptom onset between August 2018 and December 2018 were included. Primary outcomes were (i) PSD prevalence in AIS patients and (ii) PSD risk and PSD‐free survival in patients with cerebral infarction who underwent melatonin supplementation compared to propensity score–matched (PSM) controls. Secondary outcomes included time of PSD onset and PSD duration. Results Out of 465 (81.2%) patients with cerebral infarction and 108 (18.8%) transient ischemic attack (TIA) patients, 152 (26.5%) developed PSD (median time to onset [IQR]: 16 [8–32] h; duration 24 [8–40] h). Higher age, cerebral infarction rather than TIA, and higher National Institutes of Health Stroke Scale score and aphasia on admission were significant predictors of PSD. After PSM (164 melatonin‐treated patients with cerebral infarction versus 164 matched controls), 42 (25.6%) melatonin‐treated patients developed PSD versus 60 (36.6%) controls (odds ratio, 0.597; 95% confidence interval, 0.372–0.958; p = 0.032). PSD‐free survival differed significantly between groups ( p = 0.027), favoring melatonin‐treated patients. In patients with PSD, no between‐group differences in the time of PSD onset and PSD duration were noted. Conclusions Patients prophylactically treated with melatonin within 24 h of AIS onset had lower risk for PSD than patients undergoing standard care. Prospective randomized trials are warranted to corroborate these findings.
Deoxyribonuclease 1-Mediated Clearance of Circulating Chromatin Prevents From Immune Cell Activation and Pro-inflammatory Cytokine Production, a Phenomenon Amplified by Low Trap1 Activity: Consequences for Systemic Lupus Erythematosus
2021-03-04

Increased concentrations of circulating chromatin, especially oligo-nucleosomes, are observed in sepsis, cancer and some inflammatory autoimmune diseases like systemic lupus erythematosus (SLE). In SLE, circulating nucleosomes mainly result from increased apoptosis and decreased clearance of apoptotic cells. Once released, nucleosomes behave both as an autoantigen and as a damage-associated molecular pattern (DAMP) by activating several immune cells, especially pro-inflammatory cells. Deoxyribonuclease 1 (DNase1) is a major serum nuclease whose activity is decreased in mouse and human lupus. Likewise, the mitochondrial chaperone tumor necrosis factor (TNF) receptor-associated protein-1 (Trap1) protects against oxidative stress, which is increased in SLE. Here, using wild type, DNase1-deficient and DNase1/Trap1-deficient mice, we demonstrate that DNase1 is a major serum nuclease involved in chromatin degradation, especially when the plasminogen system is activated. In vitro degradation assays show that chromatin digestion is strongly impaired in serum from DNase1/Trap1-deficient mice as compared to wild type mice. In vivo , after injection of purified chromatin, clearance of circulating chromatin is delayed in DNase1/Trap1-deficient mice in comparison to wild type mice. Since defective chromatin clearance may lead to chromatin deposition in tissues and subsequent immune cell activation, spleen cells were stimulated in vitro with chromatin. Splenocytes were activated by chromatin, as shown by interleukin (IL)-12 secretion and CD69 up-regulation. Moreover, cell activation was exacerbated when Trap1 is deficient. Importantly, we also show that cytokines involved in lupus pathogenesis down-regulate Trap1 expression in splenocytes. Therefore, combined low activities of both DNase1 and Trap1 lead to an impaired degradation of chromatin in vitro , delayed chromatin clearance in vivo and enhanced activation of immune cells. This situation may be encountered especially, but not exclusively, in SLE by the negative action of cytokines on Trap1 expression.
First record of mawsoniid coelacanths (Actinistia, Sarcopterygii) from the marine Rhaetian (Upper Triassic) of Bonenburg, Germany
2021-03-04

Coelacanths are represented today by a single genus, Latimeria. They are known to be 'living fossils', because their evolutionary history dates back into the Devonian. Through the Upper Triassic, coelacanths are represented by two families, the Latimeriidae and Mawsoniidae. While latimeriids represent their marine lineage, mawsoniids were, until recently (Deesri et al., 2018), thought to be exclusively freshwater inhabitants. Through the Late Triassic, mawsoniids originated in freshwater environments of America, and only little is known about their evolution in Europe during this time period. Here we report on two morphotypes of mawsoniid basisphenoids from the marine Rhaetian (Upper Triassic) Bonenburg locality (Kreis Höxter, North Rhine-Westphalia, Germany) showing that (1) Late Triassic coelacanths from Germany can be assigned to the family level, specifically to Mawsoniidae, (2) mawsoniid coelacanths were already present in Europe in the Late Triassic, and (3) these inhabited marine environments at the end of the Triassic, supporting the affinities of habitat preference of previous finds from France (Deesri et al., 2018). The results strengthen the hypothesis an intermediate marine phase between the origin of Mawsoniidae in freshwater environments of nowadays North America during the Late Triassic and their final occurrence in continental deposits of Western Gondwana (Africa and South America) and nowadays Europe in the Late Cretaceous (Cavin et al., 2019).
Development and Validation of an In Silico Decision Tool To Guide Optimization of Intravenous Artesunate Dosing Regimens for Severe Falciparum Malaria Patients
2021-03-04

Most deaths from severe falciparum malaria occur within 24 h of presentation to a hospital. Intravenous (i.v.) artesunate is the first-line treatment for severe falciparum malaria, but its efficacy may be compromised by delayed parasitological responses.
Nemertean, brachiopod and phoronid neuropeptidomics reveals ancestral spiralian signalling systems
2021-03-04

Abstract Neuropeptides are diverse signalling molecules in animals commonly acting through G-protein coupled receptors (GPCRs). Neuropeptides and their receptors underwent extensive diversification in bilaterians and the relationships of many peptide-receptor systems have been clarified. However, we lack a detailed picture of neuropeptide evolution in lophotrochozoans as in-depth studies only exist for molluscs and annelids. Here we analyse peptidergic systems in Nemertea, Brachiopoda and Phoronida. We screened transcriptomes from thirteen nemertean, six brachiopod and four phoronid species for proneuropeptides and neuropeptide GPCRs. With mass spectrometry from the nemertean Lineus longissimus , we validated several predicted peptides and identified novel ones. Molecular phylogeny combined with peptide-sequence and gene-structure comparisons allowed us to comprehensively map spiralian neuropeptide evolution. We found most mollusc and annelid peptidergic systems also in nemerteans, brachiopods and phoronids. We uncovered previously hidden relationships including the orthologies of spiralian CCWamides to arthropod agatoxin-like peptides and of mollusc APGWamides to RGWamides from annelids, with orthologues systems in nemerteans, brachiopods and phoronids. We found that pleurin neuropeptides previously only found in molluscs are also present in nemerteans and brachiopods. We also identified cases of gene family duplications and losses. These include a protostome-specific expansion of RFamide/Wamide signalling, a spiralian expansion of GnRH-related peptides, and duplications of vasopressin/oxytocin before the divergence of brachiopods, phoronids and nemerteans. This analysis expands our knowledge of peptidergic signalling in spiralians and protostomes. Our annotated dataset of nearly 1,300 proneuropeptide sequences and 600 GPCRs presents a useful resource for further studies of neuropeptide signalling in protostomes.
Post-depositional processes visible in the integration of EGRIP high-resolution water isotope record and visual stratigraphy
2021-03-04

&amp;lt;p&amp;gt;With recent advances in analytical techniques, water stable isotope ratios can be measured in astounding detail in ice core records (~mm scale or equivalent to subannual resolution). While this has enabled the study of past climates across a vast range of timescales, the full set of processes driving the highest frequency variability in these water isotope records remains poorly understood. In the EastGRIP ice core, we observe a strong relationship between high-frequency water isotope anomalies (sharp transitions on the scale of cms) and variability in the visual stratigraphy of the ice. The water isotope timeseries reveals these anomalies that would otherwise be missed using traditional lower resolution discrete sampling methods (5-50 cm scale).&amp;amp;#160; A comparison with the dark-field imaging of stratigraphic layers (high-resolution line-scanning system; 50&amp;amp;#181;m/pix) from the EGRIP ice core indicates a correlation between bubble-free ice layers and the sharp transitions observed in the isotope record.&amp;amp;#160; Prior to this comparison, such anomalies in high-resolution isotope records were often dismissed as analytical artifacts. The striking correspondence to the bubble-free ice layers, which is a parameter measured independently from the isotopes, suggests the isotope variability is real. We are investigating a range of depositional and post-depositional processes that may may be able to explain the origin of this variability and its relationship to the physical properties of the ice. This study has implications for frequency analysis of the isotope data, and the related analysis of isotope diffusion and its effects on the recorded climate signal. Understanding these anomalies opens new doors to the interpretation of climate signals in ice cores.&amp;lt;/p&amp;gt;
A posteriori error estimation and space-time adaptivity for a linear stochastic PDE with additive noise
2021-03-04

Abstract We present a strong residual-based a posteriori error estimate for a finite element-based space-time discretization of the linear stochastic convected heat equation with additive noise. This error estimate is used for an adaptive algorithm that automatically selects deterministic mesh parameters in space and time. For every , we find a new time-step , a new spatial mesh terminating within finitely many iterations and a finite element value approximation on this spatial mesh, which then approximates strongly the solution of the stochastic partial differential equation (SPDE) within a prescribed tolerance.