julilili42/papers huggingface dataset:
Increased expression of myelin-associated genes in frontal cortex of <i>SNCA</i> overexpressing rats and Parkinson&#x2019;s disease patients
2020-10-05

Parkinson's disease (PD) is an age-dependent neurodegenerative disorder. Besides characteristic motor symptoms, patients suffer from cognitive impairments linked to pathology in cortical areas. Due to obvious challenges in tracing the underlying molecular perturbations in human brain over time, we took advantage of a well-characterized PD rat model. Using RNA sequencing, we profiled the frontocortical transcriptome of post-mortem patient samples and aligned expression changes with perturbation patterns obtained in the model at 5 and 12 months of age reflecting a presymptomatic and symptomatic time point. Integrating cell type-specific reference data, we identified a shared expression signature between both species that pointed to oligodendrocyte-specific, myelin-associated genes. Drawing on longitudinal information from the model, their nearly identical upregulation in both species could be traced to two distinctive perturbance modes. While one mode exhibited age-independent alterations that affected genes including proteolipid protein 1 (<i>PLP1</i>), the other mode, impacting on genes like myelin-associated glycoprotein (<i>MAG</i>), was characterized by interferences of disease gene and adequate expression adaptations along aging. Our results highlight that even for a group of functionally linked genes distinct interference mechanisms may underlie disease progression that cannot be distinguished by examining the terminal point alone but instead require longitudinal interrogation of the system.
Ant foraging strategies vary along a natural resource gradient
2020-10-05

Food selection by foragers is sensitive to the availability of resources, which may vary along geographical gradients. Hence, selectivity of food types by foragers is expected to track these resource gradients. Here we addressed this hypothesis and asked if foraging decisions of seed‐eating ants differ along a geographic gradient of habitat productivity. The study was carried out for two years at five sites along a natural climatic gradient, ranging from arid to Mediterranean, where plant productivity varies six‐fold across a short geographic distance of 250 km. We found that in ant colonies of the genus Messor , collective foraging decisions differed along the gradient. Specifically, at the high‐productivity sites, a stronger association was found between plant seed availability and selectivity, suggesting that colonies respond more accurately to within‐patch variation in food amounts. In contrast, colonies in low‐productivity sites foraged in patches with higher concentration of seeds, suggesting that they respond more accurately to among‐patch variation in food amounts. Moreover, at the high‐productivity sites, colonies were more discriminating in their choice of food and preferred bigger seeds, while in the low‐productivity sites, where smaller seeds were relatively more abundant, food collection depended mostly on seed availability. An experiment with artificial seed patches performed along the same climatic gradient, revealed no difference in food selectivity across sites when food type and availability were similar, and a general preference for bigger over medium‐sized seeds. Overall, our findings suggest that resource availability is an important factor explaining food choice along a climatic gradient and imply that in low‐productivity regions small‐seeded species incur high predation pressure, whereas in high‐productivity regions, large‐seeded species suffer higher predation. This could have important consequences for plant species composition, particularly at the face of climate change, which could dramatically alter the foraging decisions of granivores.
An Exploration of Error-Driven Learning in Simple Two-Layer Networks From a Discriminative Learning Perspective
2020-10-05

Error-driven learning algorithms, which iteratively adjust expectations based on prediction error, are the basis for a vast array of models in the brain and cognitive sciences that often differ widely in their precise form and application: historically, they range from simple models in psychology and cybernetics to current complex deep learning models dominating discussions in machine learning and artificial intelligence. However, despite the ubiquity of this mechanism, detailed theoretical analyses of its basic workings uninfluenced by existing theories or specific research goals are rare in the literature. To address this, we present an exposition and theoretical analysis of error-driven learning - focusing on its simplest form for clarity - and relate this to the historical development of error-driven learning models in the cognitive sciences. Although historically error-driven models have been thought of as associative, such that learning is thought to combine preexisting elemental representations, this analysis will highlight the discriminative nature of learning in these models and the implications of this for the way how learning is conceptualized. We complement our theoretical exposition of error-driven learning with a practical guide to the application of simple error-driven learning models in which we discuss a number of example simulations, that are presented in detail in an accompanying tutorial.
A simple, general, and efficient method for sequential hypothesis testing: The independent segments procedure.
2020-10-05

We propose a new sequential hypothesis testing procedure in which data are collected and analyzed in a series of independent segments. As in fixed-sample hypothesis testing and in previous sequential procedures, the overall α level can be set to any desired value. Like other sequential procedures, the independent segments procedure generally requires smaller samples than fixed-sample procedures-often approximately 30% smaller-to achieve the same α level and statistical power. Relative to other sequential procedures, the new method has the advantages that it is simpler to use, requires fewer assumptions, and can be used with a wider array of statistical tests. Thus, in some circumstances the independent segments procedure may provide an attractive option for increasing the efficiency of statistical testing. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
Intermediate phenotype of ATP13A2 mutation in two Chilean siblings: Towards a continuum between parkinsonism and hereditary spastic paraplegia
2020-10-05

•ATP13A2 mutations have been described in several apparently independent neurodegenerative movement disorders. •Two patients with an intermediate phenotype combining parkinsonism and spastic paraplegia carry mutations in ATP13A2. •The term ATP13A2-associated disorder may better define a genetic entity with heterogeneous and overlapping clinical features.
WLD: A Wavelet and Learning based Line Descriptor for Line Feature Matching
2020-10-05

We present a machine learning based and wavelet enhanced line feature descriptor for line feature matching. Therefor we trained a neural network to compute a descriptor for a line, given preprocessed information from the image area around the line. In the preprocessing step we utilize wavelets to extract meaningful information from the image for the descriptor. This process is inspired by the human vision system. We used the Unreal Engine 4 and multiple different freely available scenes to create our training data. We conducted the evaluation on ground truth labeled images of our own and from the Middlebury Stereo Dataset. To show the advancement of our method in terms of matching quality, we compare it to the Line Band Descriptor (LBD), to the Deep Learning Based Line Descriptor (DLD), which we used as a starting point for this work, and to the Learnable Line Segment Descriptor for Visual SLAM (LLD). We publish the project on github to support the community: https://github.com/manuellange/WLD
Obtaining deeper insights into microbiome diversity using a simple method to block host and non-targets in amplicon sequencing
2020-10-05

Abstract Microbiome profiling is revolutionizing our understanding of biological mechanisms such as metaorganismal (host+microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci is an instrumental tool for characterization of the highly diverse microbiomes of natural systems. Investigations in many study systems are hindered by loss of essential sequencing depth due to amplification of non-target DNA from hosts or overabundant microorganisms. This issue requires urgent attention to address ecologically relevant problems using high throughput, high resolution microbial profiling. Here, we introduce a simple, low cost and highly flexible method using standard oligonucleotides (“blocking oligos”) to block amplification of non-targets and an R package to aid in their design. They can be dropped into practically any two-step amplicon sequencing library preparation pipeline. We apply them in leaves, a system presenting exceptional challenges with host and non-target microbial amplification. Blocking oligos designed for use in eight target loci reduce undesirable amplification of host and non-target microbial DNA by up to 90%. In addition, 16S and 18S “universal” plant blocking oligos efficiently block most plant hosts, leading to increased microbial alpha diversity discovery without biasing beta diversity measurements. By blocking only chloroplast 16S amplification, we show that blocking oligos do not compromise quantitative microbial load information inherent to plant-associated amplicon sequencing data. Using these tools, we generated a near-complete survey of the Arabidopsis thaliana leaf microbiome based on diversity data from eight loci and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. The blocking oligo approach has potential to make new questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems-based insights into microbial discovery.
Single depolymerizing and transport kinesins stabilize microtubule ends
2020-10-05

ABSTRACT Microtubules are highly dynamic cellular filaments and many intracellular processes like cell division depend on an accurate control of their length. Among other factors, microtubule length is actively modulated by motors from the kinesin superfamily. For example, yeast kinesin-8, Kip3, depolymerizes microtubules in a collective manner by a force- and length-dependent mechanism. However, whether single motors depolymerize or stabilize microtubule ends is unclear. Here, using interference reflection microscopy, we measured the influence of single kinesin motors on the stability of microtubules in an in vitro assay. Surprisingly, using unlabeled, stabilized microtubules, we found that both single kinesin-8 and non-depolymerizing kinesin-1 transport motors stabilized microtubule ends further by reducing the spontaneous microtubule depolymerization rate. Since we observed this effect for two very different kinesins, it implies a more general stabilization mechanism. For Kip3, this behavior is contrary to the collective force-dependent depolymerization activity of multiple motors. The complex, concentration-dependent interaction with microtubule ends provides new insights into the molecular mechanism of kinesin-8 and its regulatory function of microtubule length.
Statistical Analysis of Bistatic Rural Terrain Clutter
2020-10-05

In this paper we present the statistical analysis of bistatic rural ground clutter for different terrain types. Compared to state-of-the-art analysis we present clutter models for subdivisions of rural environments. Therefore, four measurement campaigns have been carried out during summer of 2019 in four different rural terrain types, namely a field with low vegetation, with high vegetation, plantation of small trees and forest environment representing a typical rural German environment. The measurements have been carried out in the radar relevant X-Band at a center frequency of 8.85GHz and with a bandwidth of 100MHz. The distinction of the rural terrain into different types enables a more precise and accurate clutter analysis and modelling of the statistical properties as shown in the presented results. The statistical properties are derived from the calculated probability density functions and the corresponding cumulative density functions for each of the four terrain types from the measured range-Doppler domain data.
The eROSITA X-ray telescope on SRG
2020-10-06

eROSITA (extended ROentgen Survey with an Imaging Telescope Array) is the primary instrument on the Spectrum-Roentgen-Gamma (SRG) mission, which was successfully launched on July 13, 2019, from the Baikonour cosmodrome. After the commissioning of the instrument and a subsequent calibration and performance verification phase, eROSITA started a survey of the entire sky on December 13, 2019. By the end of 2023, eight complete scans of the celestial sphere will have been performed, each lasting six months. At the end of this program, the eROSITA all-sky survey in the soft X-ray band (0.2–2.3 keV) will be about 25 times more sensitive than the ROSAT All-Sky Survey, while in the hard band (2.3–8 keV) it will provide the first ever true imaging survey of the sky. The eROSITA design driving science is the detection of large samples of galaxy clusters up to redshifts z &gt; 1 in order to study the large-scale structure of the universe and test cosmological models including Dark Energy. In addition, eROSITA is expected to yield a sample of a few million AGNs, including obscured objects, revolutionizing our view of the evolution of supermassive black holes. The survey will also provide new insights into a wide range of astrophysical phenomena, including X-ray binaries, active stars, and diffuse emission within the Galaxy. Results from early observations, some of which are presented here, confirm that the performance of the instrument is able to fulfil its scientific promise. With this paper, we aim to give a concise description of the instrument, its performance as measured on ground, its operation in space, and also the first results from in-orbit measurements.
Histological Evidence for the Enteric Nervous System and the Choroid Plexus as Alternative Routes of Neuroinvasion by SARS-CoV2
2020-10-06

Evidence is mounting that the novel corona virus SARS-CoV2 inflicts neurological symptoms in a subgroup of COVID-19 patients. While plenty of theories on the route of neuroinvasion have been proposed, little histological evidence has been presented supporting any of these hypotheses. Therefore, we carried out immunostainings for ACE2 and TMPRSS2, two proteinases crucial for the entry of SARS-CoV2 into host cells, in the human enteric nervous system (ENS), as well as in the choroid plexus of the lateral ventricles. Both of these sites are important, yet often neglected entry gates to the nervous system. We found that ACE2 and TMPRSS2 are expressed by enteric neurons and glial cells of the small and large intestine, as well as choroid plexus epithelial cells, indicating that these cells meet the molecular requirements for viral entry. Together, our results are fundamental histological evidence substantiating current theories of neuroinvasion by SARS-CoV2.
A Multi-Omics Approach Identifies Key Regulatory Pathways Induced by Long-Term Zinc Supplementation in Human Primary Retinal Pigment Epithelium
2020-10-06

In age-related macular degeneration (AMD), both systemic and local zinc levels decline. Elevation of zinc in clinical studies delayed the progression to end-stage AMD. However, the molecular pathways underpinning this beneficial effect are not yet identified. In this study, we used differentiated primary human fetal retinal pigment epithelium (RPE) cultures and long-term zinc supplementation to carry out a combined transcriptome, proteome and secretome analysis from three genetically different human donors. After combining significant differences, we identified the complex molecular networks using Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathway Analysis (IPA). The cell cultures from the three donors showed extensive pigmentation, development of microvilli and basal infoldings and responded to zinc supplementation with an increase in transepithelial electrical resistance (TEER) (apical supplementation: 443.2 ± 79.3%, basal supplementation: 424.9 ± 116.8%, compared to control: 317.5 ± 98.2%). Significant changes were observed in the expression of 1044 genes, 151 cellular proteins and 124 secreted proteins. Gene set enrichment analysis revealed changes in specific molecular pathways related to cell adhesion/polarity, extracellular matrix organization, protein processing/transport, and oxidative stress response by zinc and identified a key upstream regulator effect similar to that of TGFB1.
How Do Newly-Amended Biochar Particles Affect Erodibility and Soil Water Movement?—A Small-Scale Experimental Approach
2020-10-06

Biochar amendment changes chemical and physical properties of soils and influences soil biota. It is, thus, assumed that it can also affect soil erosion and erosion-related processes. In this study, we investigated how biochar particles instantly change erodibility by rain splash and the initial movement of soil water in a small-scale experiment. Hydrothermal carbonization (HTC)-char and Pyrochar were admixed to two soil substrates. Soil erodibility was determined with Tübingen splash cups under simulated rainfall, soil hydraulic conductivity was calculated from texture and bulk soil density, and soil water retention was measured using the negative and the excess pressure methods. Results showed that the addition of biochar significantly reduced initial soil erosion in coarse sand and silt loam immediately after biochar application. Furthermore, biochar particles were not preferentially removed from the substrate surface, but increasing biochar particle sizes partly showed decreasing erodibility of substrates. Moreover, biochar amendment led to improved hydraulic conductivity and soil water retention, regarding soil erosion control. In conclusion, this study provided evidence that biochar amendments reduce soil degradation by water erosion. Furthermore, this effect is detectable in a very early stage, and without long-term incorporation of biochar into soils.
Heat treatment significantly increases the sharpness of silcrete stone tools
2020-10-06

Humans were regularly heat‐treating stone tool raw materials as early as 130,000 years ago. The late Middle Stone Age (MSA) and Late Stone Age (LSA) of South Africa's Western Cape region provides some of the earliest and most pervasive archaeological evidence for this behaviour. While archaeologists are beginning to understand the flaking implications of raw material heat treatment, its potential functional benefits remain unanswered. Using silcrete from the Western Cape region, we investigate the impact of heat treatment on stone tool cutting performance. We quantify the sharpness of silcrete in its natural, unheated form, before comparing it with silcrete heated in three different conditions. Results show that heat‐treated silcrete can be significantly sharper than unheated alternatives, with cutting forces halving and energy requirements reducing by approximately two‐thirds. The data suggest that silcrete may have been heat treated during the South African MSA and LSA to increase the sharpness and performance of stone cutting edges. This early example of material engineering has implications for understanding Stone Age populations’ technological capabilities, inventiveness and raw material choices. We predict that heat‐treatment behaviours in other prehistoric and ethnographic contexts may also be linked to increases in edge sharpness and concerns about functional performance.
SppI Forms a Membrane Protein Complex with SppA and Inhibits Its Protease Activity in Bacillus subtilis
2020-10-06

Our study presents new insights into the molecular mechanism that regulates the activity of SppA, a widely conserved bacterial membrane protease. We show that the membrane proteins SppA and SppI form a complex in the Gram-positive model bacterium B. subtilis and that SppI inhibits SppA protease activity in vitro and in vivo . Furthermore, we demonstrate that the C-terminal domain of SppI is involved in SppA inhibition. Since SppA, through its protease activity, contributes directly to resistance to lantibiotic peptides and cationic antibacterial peptides, we propose that the conserved SppA-SppI complex could play a major role in the evasion of bactericidal peptides, including those produced as part of human innate immune defenses.
Migration jumps of planets in transition discs
2020-10-06

Context. Transition discs form a special class of protoplanetary discs that are characterised by a deficiency of disc material close to the star. In a subgroup, inner holes in these discs can stretch out to a few tens of au while there is still mass accretion onto the central star observed at the same time. Aims. We analyse the proposition that this type of wide transition disc is generated by the interaction of the disc with a system of embedded planets. Methods. We performed two-dimensional hydrodynamics simulations of a flat disc. Different equations of state were used including locally isothermal models and more realistic cases that consider viscous heating, radiative cooling, and stellar heating. Two massive planets (with masses of between three and nine Jupiter masses) were embedded in the disc and their dynamical evolution due to disc–planet interaction was followed for over 100 000 yr. The simulations account for mass accretion onto the star and planets. We included models with parameters reminiscent of the system PDS 70. To assess the observability of features in our models we performed synthetic ALMA observations. Results. For systems with a more massive inner planet, there are phases where both planets migrate outward engaged in a 2:1 mean motion resonance via the Masset-Snellgrove mechanism. In sufficiently massive discs, the resulting formation of a vortex and the interaction with it can trigger rapid outward migration of the outer planet where its distance can increase by tens of au in a few thousand years. After another few thousand years, the outer planet rapidly migrates back inwards into resonance with the inner planet. We call this emerging composite phenomenon a migration jump. Outward migration and the migration jumps are accompanied by a high mass accretion rate onto the star. The synthetic images reveal numerous substructures depending on the type of dynamical behaviour. Conclusions. Our results suggest that the outward migration of two embedded planets is a prime candidate for the explanation of the observed high stellar mass accretion rate in wide transition discs. The models for PDS 70 indicate it is not currently undergoing a migration jump but might very well be in a phase of outward migration.