julilili42/papers huggingface dataset:
Eloquent Lower Grade Gliomas, a Highly Vulnerable Cohort: Assessment of Patients’ Functional Outcome After Surgery Based on the LoG-Glio Registry
2022-03-03

Majority of lower grade glioma (LGG) are located eloquently rendering surgical resection challenging. Aim of our study was to assess rate of permanent deficits and its predisposing risk factors. We retrieved 83 patients harboring an eloquently located LGGs from the prospective LoG-Glio Database. Patients without surgery or incomplete postoperative data were excluded. Sign rank test, explorative correlations by Spearman ρ and multivariable regression for new postoperative deficits were calculated. Eloquent region involved predominantly motor (45%) and language (40%). At first follow up after 3 months permanent neuro-logical deficits (NDs) were noted in 39%. Mild deficits remained in 29% and severe deficits in 10%. Complete tumor removal (CTR) was successfully in 62% of intended cases. Postoperative and 3-month follow up National Institute of Health Stroke Score (NIHSS) showed significantly lower values than preoperatively (p&amp;lt;0.001). 38% cases showed a decreased NIHSS at 3-month, while occurrence was only 14% at 9-12-month follow up. 6/7 patients with mild aphasia recovered after 9-12 months, while motor deficits present at 3-month follow up were persistent in majority of patients. Eastern oncology group functional status (ECOG) significantly decreased by surgery (p &amp;lt; 0.001) in 31% of cases. Between 3-month and 9-12-months follow up no significant improvement was seen. In the multivariable model CTR (p=0.019, OR 31.9), and ECOG&amp;gt;0 (p=0.021, OR 8.5) were independent predictors for permanent postoperative deficit according to NIHSS at 3-month according to multivariable regression model. Patients harboring eloquently located LGG are highly vulnerable for permanent deficits. Almost one third of patients have a permanent reduction of their functional status based on ECOG. Risk of an extended resection has to be balanced with the respective oncological benefit. Especially, patients with impaired pre-operative status are at risk for new permanent deficits. There is a relevant improvement of neurological symptoms in the first year after surgery, especially for patients with slight aphasia.
Identification of three novel homozygous variants in COL9A3 causing autosomal recessive Stickler syndrome
2022-03-03

Abstract Background Stickler syndrome (STL) is a rare, clinically and molecularly heterogeneous connective tissue disorder. Pathogenic variants occurring in a variety of genes cause STL, mainly inherited in an autosomal dominant fashion. Autosomal recessive STL is ultra-rare with only four families with biallelic COL9A3 variants reported to date. Results Here, we report three unrelated families clinically diagnosed with STL carrying different novel biallelic loss of function variants in COL9A3 . Further, we have collected COL9A3 genotype–phenotype associations from the literature. Conclusion Our report substantially expands the molecular genetics and clinical basis of autosomal recessive STL and provides an overview about allelic COL9A3 disorders.
Superhumps linked to X-ray emission. The superoutbursts of SSS J122221.7-311525 and GW Lib
2022-03-03

[Abridged] We present more than 4 years of Swift X-ray observations of the 2013 superoutburst, subsequent decline and quiescence of the WZ Sge-type dwarf nova SSS J122221.7-311525 (SSS122222) from 6 days after discovery. Only a handful of WZ Sge-type dwarf novae have been observed in X-rays, and until recently GW Lib was the only binary of this type with complete coverage of an X-ray light curve throughout a superoutburst. We collected extensive X-ray data of a second such system to understand the extent to which the unexpected properties of GW Lib are common to the WZ Sge class. We analysed the X-ray light curve and compared it with the behaviour of superhumps which were detected in the optical light curve. We also performed spectral analysis of the data. The results were compared with the properties of GW Lib, for which new X-ray observations were also obtained. SSS122222 was variable and around five times brighter in 0.3-10 keV X-rays during the superoutburst than in quiescence, mainly because of a significant strengthening of a high-energy component of the X-ray spectrum. The post-outburst decline of the X-ray flux lasted at least 500 d. The data show no evidence of the expected optically thick boundary layer in the system during the outburst. SSS122222 also exhibited a sudden X-ray flux change in the middle of the superoutburst, which occurred exactly at the time of the superhump stage transition. A similar X-ray behaviour was also detected in GW Lib. This result demonstrates a relationship between the outer disc and the white dwarf boundary layer for the first time, and suggests that models for accretion discs in high mass ratio accreting binaries are currently incomplete. The very long decline to X-ray quiescence is also in strong contrast to the expectation of low viscosity in the disc after outburst.
Transfer, loss and physical processing of water in hit-and-run collisions of planetary embryos
2022-03-03

Collisions between large, similar-sized bodies are believed to shape the final characteristics and composition of terrestrial planets. Their inventories of volatiles such as water, are either delivered or at least significantly modified by such events. Besides the transition from accretion to erosion with increasing impact velocity, similar-sized collisions can also result in hit-and-run outcomes for sufficiently oblique impact angles and large enough projectile-to-target mass ratios. We study volatile transfer and loss focusing on hit-and-run encounters by means of Smooth Particle Hydrodynamics simulations, including all main parameters: impact velocity, impact angle, mass ratio, and also the total colliding mass. We find a broad range of overall water losses, up to 75% in the most energetic hit-and-run events, and confirm the much more severe consequences for the smaller body also for stripping of volatile layers. Transfer of water between projectile and target inventories is found to be mostly rather inefficient, and final water contents are dominated by pre-collision inventories reduced by impact losses, for similar pre-collision water mass fractions. Comparison with our numerical results shows that current collision outcome models are not accurate enough to reliably predict these composition changes in hit-and-run events. To also account for non-mechanical losses we estimate the amount of collisionally vaporized water over a broad range of masses, and find that these contributions are particularly important in collisions of ~Mars-sized bodies, with sufficiently high impact energies, but still relatively low gravity. Our results clearly indicate that the cumulative effect of several (hit-and-run) collisions can efficiently strip protoplanets of their volatile layers, especially the smaller body, as it might be common e.g. for Earth-mass planets in systems with Super-Earths.
Decision-Based Adversarial Attacks: Reliable Attacks Against Black-Box Machine Learning Models
2022-03-03

Many machine learning algorithms are vulnerable to almost imperceptible perturbations of their inputs. So far it was unclear how much risk adversarial perturbations carry for the safety of real-world machine learning applications because most methods used to generate such perturbations rely either on detailed model information (gradient-based attacks) or on confidence scores such as class probabilities (score-based attacks), neither of which are available in most real-world scenarios. In many such cases one currently needs to retreat to transfer-based attacks which rely on cumbersome substitute models, need access to the training data and can be defended against. Here we emphasise the importance of attacks which solely rely on the final model decision. Such decision-based attacks are (1) applicable to real-world black-box models such as autonomous cars, (2) need less knowledge and are easier to apply than transfer-based attacks and (3) are more robust to simple defences than gradient- or score-based attacks. Previous attacks in this category were limited to simple models or simple datasets. Here we introduce the Boundary Attack, a decision-based attack that starts from a large adversarial perturbation and then seeks to reduce the perturbation while staying adversarial. The attack is conceptually simple, requires close to no hyperparameter tuning, does not rely on substitute models and is competitive with the best gradient-based attacks in standard computer vision tasks like ImageNet. We apply the attack on two black-box algorithms from Clarifai.com. The Boundary Attack in particular and the class of decision-based attacks in general open new avenues to study the robustness of machine learning models and raise new questions regarding the safety of deployed machine learning systems. An implementation of the attack is available as part of Foolbox at https://github.com/bethgelab/foolbox .
Flex-Convolution (Million-Scale Point-Cloud Learning Beyond Grid-Worlds)
2022-03-03

Traditional convolution layers are specifically designed to exploit the natural data representation of images -- a fixed and regular grid. However, unstructured data like 3D point clouds containing irregular neighborhoods constantly breaks the grid-based data assumption. Therefore applying best-practices and design choices from 2D-image learning methods towards processing point clouds are not readily possible. In this work, we introduce a natural generalization flex-convolution of the conventional convolution layer along with an efficient GPU implementation. We demonstrate competitive performance on rather small benchmark sets using fewer parameters and lower memory consumption and obtain significant improvements on a million-scale real-world dataset. Ours is the first which allows to efficiently process 7 million points concurrently.
H.E.S.S. highlights
2022-03-03

The H.E.S.S. collaboration continues to run an array of five Imaging Atmospheric Cherenkov Telescopes to observe the Southern sky in very high energy gamma-rays. In this presentation, recent highlight results obtained with H.E.S.S. are briefly reviewed, with references to the relevant publications.
Arbitrary-order functionally fitted energy-diminishing methods for gradient systems
2022-03-03

It is well known that for gradient systems in Euclidean space or on a Riemannian manifold, the energy decreases monotonically along solutions. In this letter we derive and analyse functionally fitted energy-diminishing methods to preserve this key property of gradient systems. It is proved that the novel methods are unconditionally energy-diminishing and can achieve damping for very stiff gradient systems. We also show that the methods can be of arbitrarily high order and discuss their implementations. A numerical test is reported to illustrate the efficiency of the new methods in comparison with three existing numerical methods in the literature.
Direct fluorescent labeling of NF186 and NaV1.6 in living primary neurons using bioorthogonal click chemistry
2022-03-03

Abstract The axon initial segment (AIS) is a highly specialized neuronal compartment that regulates the generation of action potentials and maintenance of neuronal polarity. Despite its importance, live imaging of the AIS is challenging due to the limited number of suitable labeling methods. To overcome this limitation, we established a novel approach for live labeling of the AIS using unnatural amino acids (UAAs) and bioorthogonal click chemistry. The small size of the UAAs and the possibility of introducing them virtually anywhere into the target proteins make this method particularly suitable for live labeling and imaging of complex and spatially restricted proteins. With this approach, we labeled two large AIS components, the 186 kDa isoform of neurofascin (NF186) and the 260 kDa voltage-gated sodium channel (Na V 1.6), and performed widefield and confocal microscopy in fixed and living neurons. Moreover, we demonstrated the applicability of this method by studying the localization of two epilepsy-causing Na V 1.6 variants with a loss-of-function effect. Finally, to further improve the efficiency of the UAA incorporation, we developed adeno-associated viral (AAV) vectors for click labeling in primary neurons. The use of AAV vectors will facilitate the transfer of UAA-based click labeling technology to more complex biological systems, such as organotypic slice cultures, organoids, and animal models.
Spatiotemporal Assessment of Soil Organic Carbon Change Using Machine-Learning in Arid Regions
2022-03-04

Soil organic carbon (SOC) is an essential property of soil, and understanding its spatial patterns is critical to understanding vegetation management, soil degradation, and environmental issues. This study applies a framework using remote sensing data and digital soil mapping techniques to examine the spatiotemporal dynamics of SOC for the Yazd-Ardakan Plain, Iran, from 1986 to 2016. Here, a conditioned Latin hypercube sampling method was used to select 201 sampling sites. A set of 37 environmental predictors were obtained from Landsat imagery taken in 1986, 1999, 2010 and 2016. Here, SOC was modeled for 2016 using the Random Forest (RF), support vector regression (SVR), and artificial neural networks (ANN) machine-learners by correlating environmental predictors with soil data. The results showed that RF yielded the highest accuracy (R2 = 0.53), compared to the other two learners. By performing a variable importance analysis of the RF model, normalized difference vegetation index, modified vegetation index, and ground-adjusted vegetation index were determined to be the most important environmental predictors. By applying the model calibrated from 2016 data to 1986, 1999 and 2010, the results showed a substantial decrease in SOC; these decreases in SOC were mainly attributed to land use changes and agricultural activities.
Vegetation and vertebrate abundance as drivers of bioturbation patterns along a climate gradient
2022-03-04

Bioturbators shape their environment with considerable consequences for ecosystem processes. However, both the composition and the impact of bioturbator communities may change along climatic gradients. For burrowing animals, their abundance and composition depend on climatic and other abiotic components, with ants and mammals dominating in arid and semiarid areas, and earthworms in humid areas. Moreover, the activity of burrowing animals is often positively associated with vegetation cover (biotic component). These observations highlight the need to understand the relative contributions of abiotic and biotic components in bioturbation in order to predict soil-shaping processes along broad climatic gradients. In this study, we estimated the activity of animal bioturbation by counting the density of holes and the quantity of bioturbation based on the volume of soil excavated by bioturbators along a gradient ranging from arid to humid in Chile. We distinguished between invertebrates and vertebrates. Overall, hole density (no/ 100 m 2 ) decreased from arid (raw mean and standard deviation for invertebrates: 14 ± 7.8, vertebrates: 2.8 ± 2.9) to humid (invertebrates: 2.8 ± 3.1, vertebrates: 2.2 ± 2.1) environments. However, excavated soil volume did not follow the same clear geographic trend and was 300-fold larger for vertebrates than for invertebrates. The relationship between bioturbating invertebrates and vegetation cover was consistently negative whereas for vertebrates both, positive and negative relationships were determined along the gradient. Our study demonstrates complex relationships between climate, vegetation and the contribution of bioturbating invertebrates and vertebrates, which will be reflected in their impact on ecosystem functions.
Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate
2022-03-04

Despite the widespread use of antiseptics such as chlorhexidine digluconate (CHX) in dental practice and oral care, the risks of potential resistance toward these antimicrobial compounds in oral bacteria have only been highlighted very recently. Since the molecular mechanisms behind antiseptic resistance or adaptation are not entirely clear and the bacterial stress response has not been investigated systematically so far, the aim of the present study was to investigate the transcriptomic stress response in Streptococcus mutans after treatment with CHX using RNA sequencing (RNA-seq). Planktonic cultures of stationary-phase S. mutans were treated with a sublethal dose of CHX (125 μg/mL) for 5 min. After treatment, RNA was extracted, and RNA-seq was performed on an Illumina NextSeq 500. Differentially expressed genes were analyzed and validated by qRT-PCR. Analysis of differential gene expression following pathway analysis revealed a considerable number of genes and pathways significantly up- or downregulated in S. mutans after sublethal treatment with CHX. In summary, the expression of 404 genes was upregulated, and that of 271 genes was downregulated after sublethal CHX treatment. Analysis of differentially expressed genes and significantly regulated pathways showed regulation of genes involved in purine nucleotide synthesis, biofilm formation, transport systems and stress responses. In conclusion, the results show a transcriptomic stress response in S. mutans upon exposure to CHX and offer insight into potential mechanisms that may result in development of resistances.
Stellar laboratories. IX. New Se V, Sr IV - VII, Te VI, and I VI oscillator strengths and the Se, Sr, Te, and I abundances in the hot white dwarfs G191-B2B and RE 0503-289
2022-03-04

To analyze spectra of hot stars, advanced non-local thermodynamic equilibrium (NLTE) model-atmosphere techniques are mandatory. Reliable atomic data is for the calculation of such model atmospheres. We aim to calculate new Sr IV - VII oscillator strengths to identify for the first time Sr spectral lines in hot white dwarf (WD) stars and to determine the photospheric Sr abundances. o measure the abundances of Se, Te, and I in hot WDs, we aim to compute new Se V, Te VI, and I VI oscillator strengths. To consider radiative and collisional bound-bound transitions of Se V, Sr IV - VII, Te VI, and I VI in our NLTE atmosphere models, we calculated oscillator strengths for these ions. We newly identified four Se V, 23 Sr V, 1 Te VI, and three I VI lines in the ultraviolet (UV) spectrum of RE0503-289. We measured a photospheric Sr abundance of 6.5 +3.8/-2.4 x 10**-4 (mass fraction, 9500 - 23800 times solar). We determined the abundances of Se (1.6 +0.9/-0.6 x 10**-3, 8000 - 20000), Te (2.5 +1.5/-0.9 x 10**-4, 11000 - 28000), and I (1.4 +0.8/-0.5 x 10**-5, 2700 - 6700). No Se, Sr, Te, and I line was found in the UV spectra of G191-B2B and we could determine only upper abundance limits of approximately 100 times solar. All identified Se V, Sr V, Te VI, and I VI lines in the UV spectrum of RE0503-289 were simultaneously well reproduced with our newly calculated oscillator strengths.
Heterogeneous workers, trade, and migration
2022-03-04

We analyze the welfare effects of trade and migration, focusing on two-sided horizontal heterogeneity among workers and firms. Horizontal (skill-type) heterogeneity among workers generates monopsonistic labor markets as well as within-firm wage inequality and an endogenous quality of worker–firm matches. In a model combining horizontal worker heterogeneity with monopolistic competition on goods markets, trade liberalization causes firm exit which raises wage markdowns and worsens the average quality of worker–firm matches. It also increases the degree of income inequality. Yet, aggregate welfare is higher under free trade than under autarky. Integration of labor markets leads to two-way migration between symmetric countries. Liberalizing migration has an ambiguous effect on the quality of worker–firm matches and income inequality, but it leads to lower wage markdowns and lower goods prices and thus to higher welfare in both countries. Our model advocates opening up labor markets simultaneously with trade liberalization.
What Does the General Public Know (or Not) About Neuroscience? Effects of Age, Region and Profession in Brazil
2022-03-04

The field of Neuroscience has experienced a growing interest in recent decades, which has led to an exponential growth in the amount of related information made available online as well as the market for Neuroscience-related courses. While this type of knowledge can be greatly beneficial to people working in science, health and education, it can also benefit individuals in other areas. For example, neuroscience knowledge can help people from all fields better understand and critique information about new discoveries or products, and even make better education- and health-related decisions. Online platforms are fertile ground for the creation and spread of fake information, including misrepresentations of scientific knowledge or new discoveries (e.g., neuromyths). These types of false information, once spread, can be difficult to tear down and may have widespread negative effects. For example, even scientists are less likely to access retractions of peer-reviewed articles than the original discredited articles. In this study we surveyed general knowledge about neuroscience and the brain among volunteers in Brazil, Latin America’s largest country. We were interested in evaluating the prevalence of neuromyths in this region, and test whether knowledge/neuromyth endorsement differs by age, region, and/or profession. To that end, we created a 30-item survey that was anonymously answered online by 1128 individuals. While younger people (20–29-year-olds) generally responded more accurately than people 60 and older, people in the North responded significantly worse than those in the South and Southeast. Most interestingly, people in the biological sciences consistently responded best, but people in the health sciences responded no better than people in the exact sciences or humanities. Furthermore, years of schooling did not correlate with performance, suggesting that quantity may surpass quality when it comes to extension or graduate-level course offerings. We discuss how our findings can help guide efforts toward improving access to quality information and training in the region.
The tail domain of neurofilament light chain accumulates in neuronal nuclei during oxidative injury
2022-03-04

Abstract Neurofilament light chain (NFL), one of the major subunits of neuron-specific intermediate filaments, is an important component of the neuronal cytoskeleton. Mutations in the NEFL gene and disturbances of NFL turnover or transport are associated with the pathophysiology of various diseases of the nervous system. Also, NFL is released from neurons as a result of neuroaxonal damage and NFL levels in cerebrospinal fluid and blood have emerged as a biomarker of the progression of numerous neurological diseases. One common underlying factor in these diseases is oxidative stress. Although both NFL and oxidative injury play a role in the development of neurological diseases, the effect of oxidative stress on NFL at the cellular level has not been extensively studied. Here, by investigating the response of neurofilaments to in vitro oxidative injury, we discovered that NFL localizes in the nuclei of primary neurons. We show that this depends on calpain activity and determine that a proteolytic fragment of the tail domain, not the full-length NFL, is that which accumulates in the nuclei. Furthermore, we demonstrate that the recombinant NFL tail domain accumulates in the nuclei of neurons and neuroblastoma cells, even in the absence of oxidative injury. Finally, we show that the tail domain of NFL interacts with the DNA in the nuclei of living cells, suggesting that NFL plays a role in the regulation of gene expression in response to oxidative injury.