julilili42/papers huggingface dataset:
Nationalistic bias among international experts: evidence from professional ski jumping*
2021-06-17

Abstract Ski jumping competitions involve subjective evaluations by judges from different countries. This might lead to nationalistic bias, according to which judges assign higher scores to their compatriots. To test this claim empirically, we exploit within‐performance variation of scores from all World Cup, World Championship, and Olympic Games competitions between the 2010/11 and 2016/17 seasons. Our findings confirm that judges assign significantly higher scores to their compatriots. The magnitude of this nationalistic bias is significantly higher in more corrupt countries. We do not find that judges assign significantly different scores to jumpers whose compatriots are present on the judging panel.
The place beyond the trees: renewed excavations of the Middle Stone Age deposits at Olieboomspoort in the Waterberg Mountains of the South African Savanna Biome
2021-06-17

Abstract Olieboomspoort is one of the few rock shelters in the vast interior of southern Africa documenting pulses of occupation from the Acheulean until the end of the Later Stone Age. Revil Mason excavated the site in 1954 and attributed the large Middle Stone Age (MSA) lithic assemblage to his middle phase of the so-called Pietersburg Industry. Recent work at the site has focused on the Holocene layers, but little is known about the earlier phases of shelter use. Here, we provide some background to the shelter, give a history of past research and present initial results following renewed fieldwork at the site. The MSA deposits contain abundant lithic artefacts and ochre, and we present an initial description of these cultural remains. Palynological analysis reveals limited potential for palaeoenvironmental reconstructions, but some faunal remains indicate open grasslands. We dated two equid teeth that provided highly consistent combined U-series-ESR estimates, resulting in a mean age of 150 ± 14 ka (1σ). Even when considering potential sources of uncertainty such as variations in water-intake, these fossils can securely be dated to Marine Isotopic Stage 6. Our reappraisal of site formation processes highlights the fact that the archaeological assemblage is strongly time-averaged. We discuss these different results in the context of a recently rekindled interest in the so-called Pietersburg Industry.
Serum Amyloid Beta42 Is Not Eliminated by the Cirrhotic Liver: A Pilot Study
2021-06-17

Amyloid-beta (Aβ) deposition in the brain is the main pathological hallmark of Alzheimer disease. Peripheral clearance of Aβ may possibly also lower brain levels. Recent evidence suggested that hepatic clearance of Aβ42 is impaired in liver cirrhosis. To further test this hypothesis, serum Aβ42 was measured by ELISA in portal venous serum (PVS), systemic venous serum (SVS), and hepatic venous serum (HVS) of 20 patients with liver cirrhosis. Mean Aβ42 level was 24.7 ± 20.4 pg/mL in PVS, 21.2 ± 16.7 pg/mL in HVS, and 19.2 ± 11.7 pg/mL in SVS. Similar levels in the three blood compartments suggested that the cirrhotic liver does not clear Aβ42. Aβ42 was neither associated with the model of end-stage liver disease score nor the Child–Pugh score. Patients with abnormal creatinine or bilirubin levels or prolonged prothrombin time did not display higher Aβ42 levels. Patients with massive ascites and patients with large varices had serum Aβ42 levels similar to patients without these complications. Serum Aβ42 was negatively associated with connective tissue growth factor levels (r = −0.580, p = 0.007) and a protective role of Aβ42 in fibrogenesis was already described. Diabetic patients with liver cirrhosis had higher Aβ42 levels (p = 0.069 for PVS, p = 0.047 for HVS and p = 0.181 for SVS), which is in accordance with previous reports. Present analysis showed that the cirrhotic liver does not eliminate Aβ42. Further studies are needed to explore the association of liver cirrhosis, Aβ42 levels, and cognitive dysfunction.
Enrichment of SARM1 alleles encoding variants with constitutively hyperactive NADase in patients with ALS and other motor nerve disorders
2021-06-17

ABSTRACT SARM1, a protein with critical NADase activity, is a central executioner in a conserved programme of axon degeneration. We report seven rare missense or in-frame microdeletion human SARM1 variant alleles in patients with amyotrophic lateral sclerosis (ALS) or other motor nerve disorders that alter the SARM1 auto-inhibitory ARM domain and constitutively hyperactivate SARM1 NADase activity. The constitutive NADase activity of these seven variants is similar to that of SARM1 lacking the entire ARM domain and greatly exceeds the activity of wild-type SARM1, even in the presence of nicotinamide mononucleotide (NMN), its physiological activator. This rise in constitutive activity alone is enough to promote neuronal degeneration in response to otherwise non-harmful, mild stress. Importantly, these strong gain-of-function alleles are completely patient-specific in the cohorts studied and show a highly significant association with disease at the single gene level. These findings of disease-associated coding variants that alter SARM1 function build on previously reported genome-wide significant association with ALS for a neighbouring, more common SARM1 intragenic single nucleotide polymorphism (SNP) to support a contributory role of SARM1 in these disorders. A broad phenotypic heterogeneity and variable age-of-onset of disease among patients with these alleles also raises intriguing questions about the pathogenic mechanism of hyperactive SARM1 variants.
USING GENERATIVE ADVERSARIAL NETWORKS FOR EXTRACTION OF INSAR SIGNALS FROM LARGE-SCALE SENTINEL-1 INTERFEROGRAMS BY IMPROVING TROPOSPHERIC NOISE CORRECTION
2021-06-17

Abstract. Spatiotemporal variations of pressure, temperature, water vapour content in the atmosphere lead to significant delays in interferometric synthetic aperture radar (InSAR) measurements of deformations in the ground. One of the key challenges in increasing the accuracy of ground deformation measurements using InSAR is to produce robust estimates of the tropospheric delay. Tropospheric models like ERA-Interim can be used to estimate the total tropospheric delay in interferograms in remote areas. The problem with using ERA-Interim model for interferogram correction is that after the tropospheric correction, there are still some residuals left in the interferograms, which can be mainly attributed to turbulent troposphere. In this study, we propose a Generative Adversarial Network (GAN) based approach to mitigate the phase delay caused by troposphere. In this method, we implement a noise to noise model, where the network is trained only with the interferograms corrupted by tropospheric noise. We applied the technique over 116 large scale 800 km long interfergrams formed from Sentinel-1 acquisitions covering a period from 25th October, 2014 to 2nd November, 2017 from descending track numbered 108 over Iran. Our approach reduces the root mean square of the phase values of the interferogram 64% compared to those of the original interferogram and by 55% in comparison to the corresponding ERA-Interim corrected version.
An analogical simulation for teaching electric circuits: a rationale for use in lower secondary school
2021-06-17

Abstract Understanding simple electric DC circuits often represents a great challenge to many students in lower secondary schools. As a result, students’ knowledge of this subject is often dominated by alternative conceptions, even after instruction. One of the reasons for these learning difficulties is the intangibility of key physical quantities and concepts of electric circuits such as the electric potential or the electric current. A potentially effective way of making circuits more accessible to students in introductory electricity lessons represents the use of analogies or models. However, as a brief review shows, there is no single analogy or model that is ideally suited to foster an understanding of all key aspects of simple DC circuits. In order to address this issue and help learners develop a mental model of circuits, a new analogical simulation of simple electric circuits was developed. The simulation is suited for use in combination with the bike chain and the air pressure analogy and aims to support students’ development of a qualitative understanding of potential difference and current in circuits as well as a treatment of circuits as a connected system. Teachers and students can access the 3D simulation free of charge using a modern browser via www.marblemodel.com .
River Erpe (Berlin, Germany) groundwater levels, temperature and 222-radon data set, June 2019
2021-06-17

&lt;p&gt;Time series of groundwater levels and temperature, chloride concentrations as well as 222-radon activities in piezometers P0 to P9 and P11 located close to Heidem&uuml;hle at the River Erpe, Berlin, Germany, collected between June and November 2019. In &quot;Rn_eql_incubations.csv&quot;, &quot;mea&quot; denotes the mean activity and &quot;sdd&quot; the associated standard deviation.&lt;/p&gt;
River Erpe (Berlin, Germany) groundwater levels, temperature and 222-radon data set, June 2019
2021-06-17

Time series of groundwater levels and temperature, chloride concentrations as well as 222-radon activities in piezometers P0 to P9 and P11 located close to Heidemühle at the River Erpe, Berlin, Germany, collected between June and November 2019. In "Rn_eql_incubations.csv", "mea" denotes the mean activity and "sdd" the associated standard deviation.
Data for "MorphVAE: Generating Neural Morphologies from 3D-Walks using Variational Autoencoder with Spherical Latent Space"
2021-06-17

&lt;p&gt;The reconstructions and the processed data that accompany the publication &lt;/p&gt;\\n\\n&lt;p&gt;&lt;strong&gt;MorphVAE: Generating Neural Morphologies from 3D-Walks using a Variational Autoencoder with Spherical Latent Space&lt;/strong&gt;&lt;/p&gt;\\n\\n&lt;p&gt;Sophie Laturnus, Philipp Berens&lt;/p&gt;\\n\\n&lt;p&gt;https://www.biorxiv.org/content/10.1101/2021.06.14.448271v1&lt;/p&gt;\\n\\n&lt;p&gt;doi: https://doi.org/10.1101/2021.06.14.448271&lt;/p&gt;
Fe(II) Redox Chemistry in the Environment
2021-06-18

Iron (Fe) is the fourth most abundant element in the earth's crust and plays important roles in both biological and chemical processes. The redox reactivity of various Fe(II) forms has gained increasing attention over recent decades in the areas of (bio) geochemistry, environmental chemistry and engineering, and material sciences. The goal of this paper is to review these recent advances and the current state of knowledge of Fe(II) redox chemistry in the environment. Specifically, this comprehensive review focuses on the redox reactivity of four types of Fe(II) species including aqueous Fe(II), Fe(II) complexed with ligands, minerals bearing structural Fe(II), and sorbed Fe(II) on mineral oxide surfaces. The formation pathways, factors governing the reactivity, insights into potential mechanisms, reactivity comparison, and characterization techniques are discussed with reference to the most recent breakthroughs in this field where possible. We also cover the roles of these Fe(II) species in environmental applications of zerovalent iron, microbial processes, biogeochemical cycling of carbon and nutrients, and their abiotic oxidation related processes in natural and engineered systems.
Myeloid-Derived Suppressor Cells as a Potential Biomarker and Therapeutic Target in COVID-19
2021-06-18

Clinical presentations of COVID-19 are highly variable, yet the precise mechanisms that govern the pathophysiology of different disease courses remain poorly defined. Across the spectrum of disease severity, COVID-19 impairs both innate and adaptive host immune responses by activating innate immune cell recruitment, while resulting in low lymphocyte counts. Recently, several reports have shown that patients with severe COVID-19 exhibit a dysregulated myeloid cell compartment, with increased myeloid-derived suppressor cells (MDSCs) correlating with disease severity. MDSCs, in turn, promote virus survival by suppressing T-cell responses and driving a highly pro-inflammatory state through the secretion of various mediators of immune activation. Here, we summarize the evidence on MDSCs and myeloid cell dysregulation in COVID-19 infection and discuss the potential of MDSCs as biomarkers and therapeutic targets in COVID-19 pneumonia and associated disease.
Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element
2021-06-18

A combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30- to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 × 10-31).
Harnessing self-labeling enzymes for selective and concurrent A-to-I and C-to-U RNA base editing
2021-06-18

Abstract The SNAP-ADAR tool enables precise and efficient A-to-I RNA editing in a guideRNA-dependent manner by applying the self-labeling SNAP-tag enzyme to generate RNA-guided editases in cell culture. Here, we extend this platform by combining the SNAP-tagged tool with further effectors steered by the orthogonal HALO-tag. Due to their small size (ca. 2 kb), both effectors are readily integrated into one genomic locus. We demonstrate selective and concurrent recruitment of ADAR1 and ADAR2 deaminase activity for optimal editing with extended substrate scope and moderate global off-target effects. Furthermore, we combine the recruitment of ADAR1 and APOBEC1 deaminase activity to achieve selective and concurrent A-to-I and C-to-U RNA base editing of endogenous transcripts inside living cells, again with moderate global off-target effects. The platform should be readily transferable to further epitranscriptomic writers and erasers to manipulate epitranscriptomic marks in a programmable way with high molecular precision.
Kinetics of Equilibrium Passive Sampling of Organic Chemicals with Polymers in Diverse Mammalian Tissues
2021-06-18

Equilibrium passive sampling employing polydimethylsiloxane (PDMS) as a sampling phase can be used for the extraction of complex mixtures of organic chemicals from lipid-rich biota. We extended the method to lean tissues and more hydrophilic chemicals by implementing a mass-balance model for partitioning between lipids, proteins, and water in tissues and by accelerating uptake kinetics with a custom-built stirrer that effectively decreased time to equilibrium to less than 8 days even for a homogenized liver tissue with an only 4% lipid content. The partition constants log <i>K</i><sub>lipid/PDMS</sub> between tissues and PDMS were derived from measured concentration in PDMS and the mass-balance model and were very similar for 40 neutral chemicals with octanol-water partition constants 1.4 < log <i>K</i><sub>ow</sub> < 8.7, that is, log <i>K</i><sub>lipid/PDMS</sub> of 1.26 (95% CI, 1.13-1.39) for the adipose tissue, 1.16 (1.00-1.33) for the liver, and 0.58 (0.42-0.73) for the brain. This conversion factor can be applied to interpret chemical analysis and <i>in vitro</i> bioassays after additionally accounting for a small fraction of coextracted lipids of <0.7% of the PDMS weight. PDMS is more widely applicable for passive sampling of mammalian tissues than previously thought, both, in terms of diversity of chemicals and the range of lipid contents of tissues and, therefore, an ideal method for human biomonitoring to be combined with <i>in vitro</i> bioassays.
Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?
2021-06-18

Environmental omics and molecular-biological data have been proposed to yield improved quantitative predictions of biogeochemical processes. The abundances of functional genes and transcripts relate to the number of cells and activity of microorganisms. However, whether molecular-biological data can be quantitatively linked to reaction rates remains an open question. We present an enzyme-based denitrification model that simulates concentrations of transcription factors, functional-gene transcripts, enzymes, and solutes. We calibrated the model using experimental data from a well-controlled batch experiment with the denitrifier Paracoccous denitrificans . The model accurately predicts denitrification rates and measured transcript dynamics. The relationship between simulated transcript concentrations and reaction rates exhibits strong non-linearity and hysteresis related to the faster dynamics of gene transcription and substrate consumption, relative to enzyme production and decay. Hence, assuming a unique relationship between transcript-to-gene ratios and reaction rates, as frequently suggested, may be an erroneous simplification. Comparing model results of our enzyme-based model to those of a classical Monod-type model reveals that both formulations perform equally well with respect to nitrogen species, indicating only a low benefit of integrating molecular-biological data for estimating denitrification rates. Nonetheless, the enzyme-based model is a valuable tool to improve our mechanistic understanding of the relationship between biomolecular quantities and reaction rates. Furthermore, our results highlight that both enzyme kinetics (i.e., substrate limitation and inhibition) and gene expression or enzyme dynamics are important controls on denitrification rates.
Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export
2021-06-18

Twisted stalks are morphologically unique bacterial extracellular organo-metallic structures containing Fe(III) oxyhydroxides that are produced by microaerophilic Fe(II)-oxidizers belonging to the Betaproteobacteria and Zetaproteobacteria. Understanding the underlying genetic and physiological mechanisms of stalk formation is of great interest based on their potential as novel biogenic nanomaterials and their relevance as putative biomarkers for microbial Fe(II) oxidation on ancient Earth. Despite the recognition of these special biominerals for over 150 years, the genetic foundation for the stalk phenotype has remained unresolved. Here we present a candidate gene cluster for the biosynthesis and secretion of the stalk organic matrix that we identified with a trait-based analyses of a pan-genome comprising 16 Zetaproteobacteria isolate genomes. The “ s talk f ormation in Z etaproteobacteria” (sfz) cluster comprises six genes ( sfz1-sfz6 ), of which sfz1 and sfz2 were predicted with functions in exopolysaccharide synthesis, regulation, and export, sfz4 and sfz6 with functions in cell wall synthesis manipulation and carbohydrate hydrolysis, and sfz3 and sfz5 with unknown functions. The stalk-forming Betaproteobacteria Ferriphaselus R-1 and OYT-1, as well as dread-forming Zetaproteobacteria Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8 contain distant sfz gene homologs, whereas stalk-less Zetaproteobacteria and Betaproteobacteria lack the entire gene cluster. Our pan-genome analysis further revealed a significant enrichment of clusters of orthologous groups (COGs) across all Zetaproteobacteria isolate genomes that are associated with the regulation of a switch between sessile and motile growth controlled by the intracellular signaling molecule c-di-GMP. Potential interactions between stalk-former unique transcription factor genes, sfz genes, and c-di-GMP point toward a c-di-GMP regulated surface attachment function of stalks during sessile growth.
Representational exchange in human social learning: Balancing efficiency and flexibility
2021-06-18

What makes human social learning so powerful? While past accounts have sometimes prioritized finding the single capacity that makes the largest difference, our social learning abilities span a wide spectrum of capacities from the high-fidelity imitation of behaviors to inferring and learning from hidden mental states. Here, we propose that the power of human social learning lies not within a single capacity, but in our ability to flexibly arbitrate between different computations and to integrate their outputs. In particular, learners can directly copy the demonstrator’s actions in the absence of causal insight (policy imitation), infer their instrumental values (value inference), or infer their model of the world and intrinsic rewards (belief inference and reward inference). Each of these strategies trades off the cost of computation against the flexibility and compositionality of its outputs. Crucially, we have the capacity to arbitrate and exchange information between these representational formats. Human social learning, we suggest, is powerful not just because of the way it moves information between minds, but also because of the way it flexibly moves information within them.
Iodine-catalyzed electrophilic substitution of indoles: Synthesis of (un)symmetrical diindolylmethanes with a quaternary carbon center
2021-06-18

A novel, versatile approach for the synthesis of unsymmetrical 3,3'-diindolylmethanes (DIMs) with a quaternary carbon center has been developed via iodine-catalyzed coupling of trifluoromethyl(indolyl)phenylmethanols with indoles. In contrast to previously reported methods, the new procedure is characterized by chemoselectivity, mild conditions, high yields, and scalability to obtain gram amounts for biological studies. Selected compounds were found to display affinity for cannabinoid receptors, which are promising drug targets for the treatment of inflammatory and neurodegenerative diseases.
Which species discovers novel food sources first? A camera trap study in a natural environment
2021-06-18

Abstract Birds underlie a predation-starvation risk, and foraging should show a diurnal/circadian pattern. Camera traps were used to study visitation patterns and discovery of a novel food source in woodland birds in SW Germany. A total of 18 species occurred at feeders with nine of them being exploratory species. Great Tits ( Parus major ) discovered novel food sources first in most instances, and first discoveries occurred on average at 10:38, while it took 97 h for the first detection of the food source. Population size was correlated with discovery. The study supports the predation-starvation risk hypothesis with discovery of food sources in the morning.