julilili42/papers huggingface dataset:
Compiling Messages from Neutron Stars
2021-05-03

Compiling Messages from Neutron StarsThe combination of gravitational-wave and x-ray observations of neutron stars provides new insight into the structure of these stars, as well as new confirmation of Einstein's theory of gravity.
COVID-19 vaccine-associated cerebral venous thrombosis in Germany
2021-05-04

Abstract Objective Reports of cerebral sinus and venous thrombosis (CVT) after ChAdOx1 vaccination against SARS-CoV-2 have raised safety concerns. We aimed to estimate the incidence of CVT within one month from first dose administration and the frequency of vaccine-induced immune thrombotic thrombocytopenia (VITT) as the underlying mechanism after vaccination with BNT162b2, ChAdOx1, and mRNA-1273, in Germany. Methods A web-based questionnaire was e-mailed to all Departments of Neurology. We asked to report cases of CVT within one month of a COVID-19 vaccination. Other cerebral events could also be reported. Incidence rates of CVT were calculated by using official statistics of nine German States. Results A total of 45 CVT cases were reported. In addition, 9 primary ischemic strokes, 4 primary intracerebral hemorrhages, and 4 other neurological events were recorded. Of the CVT patients, 35 (77.8%) were female, and 36 (80.0%) were below the age of 60 years. Fifty-three events were observed after vaccination with ChAdOx1 (85.5%), 9 after BNT162b2 (14.5%), and none after mRNA-1273 vaccination. After 7,126,434 first vaccine doses, the incidence rate of CVT within one month from first dose administration was 6.5 (95% CI, 4.4-9.2) per 100,000 person-years for all vaccines and 17.9 (11.8-26.1) for ChAdOx1 (after 2,320,535 ChAdOx1 first doses). The adjusted incidence rate ratio was 9.68 (3.46-34.98) for ChAdOx1 compared to mRNA-based vaccines and 3.14 (1.22-10.65) for women compared to non-women. In 26/45 patients with CVT (57.8%), VITT was graded highly probable. Conclusions Given an incidence of 0.22–1.75 per 100,000 person-years for CVT in the general population, these findings point towards a higher risk for CVT after ChAdOx1 vaccination, especially for women.
The impact of face masks on emotion recognition performance and perception of threat
2021-05-04

Facial emotion recognition is crucial for social interaction. However, in times of a global pandemic, where wearing a face mask covering mouth and nose is widely encouraged to prevent the spread of disease, successful emotion recognition may be challenging. In Study 1, we investigated whether emotion recognition, assessed by a validated emotion recognition task, is impaired for faces wearing a mask compared to uncovered faces, in a sample of 790 participants between 18 and 89 years. Additionally, perception of threat for faces with and without mask was assessed. We found impaired emotion recognition for faces wearing a mask compared to faces without mask, especially for those depicting anger, sadness and disgust. Further, we observed that perception of threat was altered for faces wearing a mask. In Study 2, we compared emotion recognition performance for faces with and without face mask to faces that are occluded by something other than a mask, i.e. a bubble as well as only showing the upper part of the faces. We found that, for most emotions and especially for disgust, there seems to be an effect that can be ascribed to the face mask specifically, both for emotion recognition performance and perception of threat. Methodological constraints as well as the importance of wearing a mask despite temporarily compromised social interaction are discussed.
The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline
2021-05-04

Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use.
New early late Miocene species of Vishnuonyx (Carnivora, Lutrinae) from the hominid locality of Hammerschmiede, Bavaria, Germany
2021-05-04

This study presents a new species of a large-sized lutrine from the upper Miocene hominid locality of Hammerschmiede, Vishnuonyx neptuni sp. nov., reporting the first occurrence of the genus in Europe and its most northern and western record. The new species differs from the already known members of the genus in size (intermediate between the African Vishnuonyx? angololensis and the Asiatic Vishnuonyx chinjiensis) and morphology, in particular in the larger P4 hypocone, the primitive morphology of M1 (paraconule present, enlarged protoconule and metaconule, labial expansion at the paracone area), the shorter and more robust lower premolars and the wider m1 trigonid. We hypothesized that the dispersal event that led to the expansion of the genus in Europe seems to be correlated with the water connection between Paratethys and the Mesopotamian Basin during the Konkian, between 13.4 and 12.65 Ma. In terms of paleoecology, it is here suggested that this form was feeding mainly on fish and less on bivalves or plant material, resembling the extant giant otter, Pteronura brasiliensis.
Phase equilibria of the GeTe−Bi2Te3 quasi-binary system in the range 0–50 mol% Bi2Te3
2021-05-04

The GeTe-GeBi2Te4 part of the GeTe-Bi2Te3 quasi-binary system was re-examined in the 700-1000 K temperature interval by using PXRD, DTA, and SEM techniques, and the corresponding fragment of the phase diagram was constructed. The existence of 4 ternary compounds is confirmed in the system. Ge2Bi2Te5 (863 K) and GeBi2Te4 (854 K) compounds formed by peritectic reactions, while Ge3Bi2Te6 and Ge4Bi2Te7 decompose by solid-phase reactions. The system is also characterized by the formation of large areas of solid solutions based on both modifications of GeTe. Besides, rhombohedral→cubic morphotropic phase transition occurs between 9 and 10 mol% Bi2Te3 compositions. The homogeneity field of the cubic phase does not exceed 2-3 mol% at 700 K and layered phases are formed as the concentration of Bi2Te3 increases. Crystallographic parameters of ternary compounds, as well as solid solutions, were determined by the Rietveld method. A comparative analysis of obtained results with literature data is performed.
Beyond Diophantine Wannier diagrams: Gap labelling for Bloch–Landau Hamiltonians
2021-05-04

It is well known that, given a 2d purely magnetic Landau Hamiltonian with a constant magnetic field b which generates a magnetic flux \\varphi per unit area, then any spectral island \\sigma_b consisting of M infinitely degenerate Landau levels carries an integrated density of states \\mathcal{I}_b=M \\varphi . Wannier later discovered a similar Diophantine relation expressing the integrated density of states of a gapped group of bands of the Hofstadter Hamiltonian as a linear function of the magnetic field flux with integer slope. We extend this result to a gap labelling theorem for any 2d Bloch–Landau operator H_b which also has a bounded \\mathbb{Z}^2 -periodic electric potential. Assume that H_b has a spectral island \\sigma_b which remains isolated from the rest of the spectrum as long as \\varphi lies in a compact interval [\\varphi_1,\\varphi_2] . Then \\mathcal{I}_b=c_0+c_1\\varphi on such intervals, where the constant c_0\\in\\mathbb{Q} while c_1\\in \\mathbb{Z} . The integer c_1 is the Chern marker of the spectral projection onto the spectral island \\sigma_b . This result also implies that the Fermi projection on \\sigma_b , albeit continuous in b in the strong topology, is nowhere continuous in the norm topology if either c_1\\ne0 or c_1=0 and \\varphi is rational. Our proofs, otherwise elementary, do not use non-commutative geometry but are based on gauge covariant magnetic perturbation theory which we briefly review for the sake of the reader. Moreover, our method allows us to extend the analysis to certain non-covariant systems having slowly varying magnetic fields.
Technical comment on the paper of Dessert et al. "The dark matter interpretation of the 3.5 keV line is inconsistent with blank-sky observations"
2021-05-04

An unidentified line at energy around 3.5 keV was detected in the spectra of dark matter-dominated objects. Recent work [1] used 30~Msec of XMM-Newton blank-sky observations to constrain the admissible line flux, challenging its dark matter decay origin. We demonstrate that these bounds are overestimated by more than an order of magnitude due to improper background modeling. Therefore, the dark matter interpretation of the 3.5~keV signal remains viable.
Exploring single-path Architecture Search ranking correlations
2021-05-04

Recently presented benchmarks for Neural Architecture Search (NAS) provide the results of training thousands of different architectures in a specific search space, thus enabling the fair and rapid comparison of different methods. Based on these results, we quantify the ranking correlations of single-path architecture search methods in different search space subsets and under several training variations; studying their impact on the expected search results. The experiments support the few-shot approach and Linear Transformers, provide evidence against disabling cell topology sharing during the training phase or using strong regularization in the NAS-Bench-201 search space, and show the necessity of further research regarding super-network size and path sampling strategies.
Adversarial Privacy Preservation in MRI Scans of the Brain
2021-05-04

De-identification of magnetic resonance imagery (MRI) is intrinsically difficult since, even with all metadata removed, a person's face can easily be rendered and matched against a database. Existing de-identification methods tackle this task by obfuscating or removing parts of the face, but they either fail to reliably hide the patient's identity or they remove so much information that they adversely affect further analyses in the 3D space surrounding the face. In this work, we describe a new class of MRI de-identification techniques that remodel privacy-sensitive facial features as opposed to removing them.To accomplish this, we propose a conditional, multi-scale, 3D GAN architecture that takes a patient's MRI scan as input and generates a 3D volume in which the brain is not modified but the face has been de-identified. Compared to the classical removal-based techniques, our deep learning framework preserves privacy more reliably without adversely affecting downstream medical analyses on the brain, including segmentation and age prediction.
Light-triggered and phosphorylation-dependent 14-3-3 association with NON-PHOTOTROPIC HYPOCOTYL 3 is required for hypocotyl phototropism
2021-05-04

Abstract NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) is a key component of the auxin-dependent plant phototropic growth response. We show that NPH3 directly binds polyacidic phospholipids, required for plasma membrane association in darkness. We further demonstrate that blue light induces an immediate phosphorylation of a C-terminal 14-3-3 binding motif in NPH3. Subsequent association of 14-3-3 proteins is causal for the light-induced release of NPH3 from the membrane and required for NPH3 dephosphorylation. In the cytosol, NPH3 dynamically transitions into membrane-less condensate-like structures. The dephosphorylated state of the 14-3-3 binding site and NPH3 membrane recruitment are recoverable in darkness. NPH3 variants that constitutively localize either to the membrane or to condensates are non-functional, revealing a fundamental role of the 14-3-3 mediated dynamic change in NPH3 localization for auxin-dependent phototropism. This novel mechanism of regulation might be of general nature, given that several members of the NPH3-like family interact with 14-3-3 via a C-terminal motif.
A Unifying Perspective on Neighbor Embeddings along the Attraction-Repulsion Spectrum
2021-05-04

Neighbor embeddings are a family of methods for visualizing complex high-dimensional datasets using kNN graphs. To find the low-dimensional embedding, these algorithms combine an attractive force between neighboring pairs of points with a repulsive force between all points. One of the most popular examples of such algorithms is t-SNE. Here we empirically show that changing the balance between the attractive and the repulsive forces in t-SNE yields a spectrum of embeddings, which is characterized by a simple trade-off: stronger attraction can better represent continuous manifold structures, while stronger repulsion can better represent discrete cluster structures. We find that UMAP embeddings correspond to t-SNE with increased attraction; mathematical analysis shows that this is because the negative sampling optimisation strategy employed by UMAP strongly lowers the effective repulsion. Likewise, ForceAtlas2, commonly used for visualizing developmental single-cell transcriptomic data, yields embeddings corresponding to t-SNE with the attraction increased even more. At the extreme of this spectrum lies Laplacian Eigenmaps, corresponding to zero repulsion. Our results demonstrate that many prominent neighbor embedding algorithms can be placed onto this attraction-repulsion spectrum, and highlight the inherent trade-offs between them.
Closing the Generalization Gap in One-Shot Object Detection
2021-05-04

Despite substantial progress in object detection and few-shot learning, detecting objects based on a single example - one-shot object detection - remains a challenge. A central problem is the generalization gap: Object categories used during training are detected much more reliably than novel ones. We here show that this generalization gap can be nearly closed by increasing the number of object categories used during training. Doing so allows us to beat the state-of-the-art on COCO by 5.4 %AP50 (from 22.0 to 27.5) and improve generalization from seen to unseen classes from 45% to 89%. We verify that the effect is caused by the number of categories and not the amount of data and that it holds for different models, backbones and datasets. This result suggests that the key to strong few-shot detection models may not lie in sophisticated metric learning approaches, but instead simply in scaling the number of categories. We hope that our findings will help to better understand the challenges of few-shot learning and encourage future data annotation efforts to focus on wider datasets with a broader set of categories rather than gathering more samples per category.
Active Tuning
2021-05-04

We introduce Active Tuning, a novel paradigm for optimizing the internal dynamics of recurrent neural networks (RNNs) on the fly. In contrast to the conventional sequence-to-sequence mapping scheme, Active Tuning decouples the RNN's recurrent neural activities from the input stream, using the unfolding temporal gradient signal to tune the internal dynamics into the data stream. As a consequence, the model output depends only on its internal hidden dynamics and the closed-loop feedback of its own predictions; its hidden state is continuously adapted by means of the temporal gradient resulting from backpropagating the discrepancy between the signal observations and the model outputs through time. In this way, Active Tuning infers the signal actively but indirectly based on the originally learned temporal patterns, fitting the most plausible hidden state sequence into the observations. We demonstrate the effectiveness of Active Tuning on several time series prediction benchmarks, including multiple super-imposed sine waves, a chaotic double pendulum, and spatiotemporal wave dynamics. Active Tuning consistently improves the robustness, accuracy, and generalization abilities of all evaluated models. Moreover, networks trained for signal prediction and denoising can be successfully applied to a much larger range of noise conditions with the help of Active Tuning. Thus, given a capable time series predictor, Active Tuning enhances its online signal filtering, denoising, and reconstruction abilities without the need for additional training.
Fixing Asymptotic Uncertainty of Bayesian Neural Networks with Infinite ReLU Features
2021-05-04

Approximate Bayesian methods can mitigate overconfidence in ReLU networks. However, far away from the training data, even Bayesian neural networks (BNNs) can still underestimate uncertainty and thus be overconfident. We suggest to fix this by considering an infinite number of ReLU features over the input domain that are never part of the training process and thus remain at prior values. Perhaps surprisingly, we show that this model leads to a tractable Gaussian process (GP) term that can be added to a pre-trained BNN's posterior at test time with negligible cost overhead. The BNN then yields structured uncertainty in the proximity of training data, while the GP prior calibrates uncertainty far away from them. As a key contribution, we prove that the added uncertainty yields cubic predictive variance growth, and thus the ideal uniform (maximum entropy) confidence in multi-class classification far from the training data.
Semantic object-scene inconsistencies affect eye movements, but not in the way predicted by contextualized meaning maps
2021-05-04

Semantic information is important in eye-movement control. An important semantic influence on gaze guidance relates to object-scene relationships: objects that are semantically inconsistent with the scene attract more fixations than consistent objects. One interpretation of this effect is that fixations are driven towards inconsistent objects because they are semantically more informative. We tested this explanation using contextualized meaning maps, a method that is based on crowd-sourced ratings to quantify the spatial distribution of context-sensitive ‘meaning’ in images. In Experiment 1, we compared gaze data and contextualized meaning maps for images, in which objects-scene consistency was manipulated. Observers fixated more on inconsistent vs. consistent objects. However, contextualized meaning maps did not assigned higher meaning to image regions that contained semantic inconsistencies. In Experiment 2, a large number of raters evaluated the meaningfulness of a set of carefully selected image-regions. The results suggest that the same scene locations were experienced as slightly less meaningful when they contained inconsistent compared to consistent objects. In summary, we demonstrated that – in the context of our rating task – semantically inconsistent objects are experienced as less meaningful than their consistent counterparts, and that contextualized meaning maps do not capture prototypical influences of image meaning on gaze guidance.
Cerebellar control of saccadic adaptation using a spiking neural network model integrated into the Neurorobotics platform
2021-05-04

The cerebellum is essential for motor learning and adaptation since it can change the relationship between sensory input and motor output. Cerebellar activity contributes to the motor execution with the aim of optimizing the resulting performance. This optimization is driven by the error information, that the cerebellum receives through the sensory feedback. In this study, we aim at studying the cerebellar contribution in the saccadic adaptation, fine and rapid control of eye movements. We set up a virtual experiment where an iCub robot, controlled by a cerebellar-inspired spiking neural network, was challenged in a saccadic adaptation task. The virtual robot, at first, made inaccurate saccades and therefore attempted to adjust them, trial after trial, based on sensory error feedback. The spiking neural network model was equipped with plasticity mechanisms, that allowed the robot to change and adapt the amplitude of the saccade movement after a few trials. Interestingly, we observed that for this task a single plasticity mechanism was sufficient to produce a fast adaptation, while in other cerebellar-driven tasks, the addition of more plasticities granted an improvement of the adaptation performances.
Comment on esurf-2021-22
2021-05-04

<strong class="journal-contentHeaderColor">Abstract.</strong> Weathering of bedrock to produce regolith is essential for sustaining life on Earth and global biogeochemical cycles. The rate of this process is influenced not only by tectonics, but also by climate and biota. We present new data on soil production, chemical weathering, and physical erosion rates from the large climate and ecological gradient of the Chilean Coastal Cordillera (26Â to 38<span class="inline-formula"><sup>â</sup></span>âS). Four Chilean study areas are investigated and span (from north to south) arid (Pan de AzÃocar), semi-arid (Santa Gracia), Mediterranean (LaÂ Campana), and temperate humid (Nahuelbuta) climate zones. Observed soil production rates in granitoid soil-mantled hillslopes range from <span class="inline-formula">â1⁄47</span>Â to 290âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span> and are lowest in the sparsely vegetated and arid north and highest in the Mediterranean setting. Calculated chemical weathering rates range from zero in the arid north to a high of 211âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span> in the Mediterranean zone. Chemical weathering rates are moderate in the semi-arid and temperate humid zones (<span class="inline-formula">â1⁄420</span>Â to 50âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span>). Similarly, physical erosion rates are lowest in the arid zone (<span class="inline-formula">â1⁄411</span>âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span>) and highest in the Mediterranean climate zone (<span class="inline-formula">â1⁄491</span>âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span>). The contribution of chemical weathering to total denudation rates is lower in the arid north than further south. However, due to heterogeneities in lithologies and ZrÂ concentrations, reported chemical weathering rates and chemical depletion fractions are affected by large uncertainties. Comparison of Chilean results to published global data collected from hillslope settings underlain by granitoid lithologies documents similar patterns in soil production, chemical weathering, and total denudation rates for varying mean annual precipitation and vegetation cover amounts. We discuss the Chilean and global data in the light of contending model frameworks in the literature and find that observed variations in soil production rates bear the closest resemblance to models explicitly accounting for variations in soil thickness and biomass.