julilili42/papers huggingface dataset:
Price Discovery and Learning during the German 5G Auction
2021-06-18

The auctioning of frequency has to comply with a multitude of requirements in order to guarantee a transparent and efficient process. The German Federal Network Agency (Bundesnetzagentur) has opted for a design that provides participants with information on the highest bid after each round for every band along with information on the bidder. We evaluate the price formation efficiency in this setup to see how fast prices become informative about the final auction value. We find that prices are partially informative right from the beginning which allows us to conclude that participants were able to learn fast from their competitors’ bidding behavior and validates the choice of the agency to implement the auction in the present format.
Argyrin F Treatment‐Induced Vulnerabilities Lead to a Novel Combination Therapy in Experimental Glioma
2021-06-19

Abstract Glioblastoma are incurable primary tumors of the central nervous system that frequently harbor molecular alterations in the retinoblastoma pathway with subsequent cell cycle abnormalities. It is aimed to investigate the anti‐glioma activity of the novel cell cycle‐stabilizing compound Argyrin F and its potential treatment‐induced vulnerabilities to exploit possibilities for novel rational combination therapies. Human and murine glioma cells are used, cytotoxicity and clonogenic survival assays, cell cycle analyses, and immunoblots are performed. Residual freshly resected tissue is used for a preclinical glioma model ex vivo, i.e., patient‐derived microtumors (PDMs) for co‐culture experiments with autologous tumor‐infiltrating lymphocytes (TILs). Mass spectrometry‐based immunopeptidomics are performed and the orthotopic syngeneic SMA560/VM/Dk glioma mouse model is used. Argyrin F‐induced cell cycle arrest and reduced clonogenic survival is observed. Argyrin F‐treated experimental glioma in vivo displays 4.6‐fold more glioma‐infiltrating CD8 + T cells. A distinctive treatment‐induced immunopeptidome is discovered. The combination of Argyrin F plus PD‐1 antibody increases cellular toxicity in PDM/TILs co‐cultures ex vivo and prolonged overall survival compared with monotherapies in vivo. Thus, Argyrin F leads to anti‐glioma effects and increases the immunogenicity, paving the way for a novel combination therapy of Argyrin F plus PD‐1 blockade.
Does Respect Foster Tolerance? (Re)analyzing and Synthesizing Data From a Large Research Project Using Meta-Analytic Techniques
2021-06-19

Our own prior research has demonstrated that respect for disapproved others predicts and might foster tolerance toward them. This means that without giving up their disapproval of others’ way of life, people can tolerate others when they respect them as equals (outgroup respect–tolerance hypothesis). Still, there was considerable variation in the study features. Moreover, the studies are part of a larger research project that affords many additional tests of our hypothesis. To achieve integration along with a more robust understanding of the relation between respect and tolerance, we (re)analyzed all existing data from this project, and we synthesized the results with the help of meta-analytic techniques. The average standardized regression coefficient, which describes the relationship between respect and tolerance, was 0.25 (95% confidence interval [CI] = [0.16, 0.34]). In addition to this overall confirmation of our hypothesis, the size of this coefficient varied with a number of variables. It was larger for numerical majorities than for minorities, smaller for high-status than for low-status groups, and larger for religious than for life-style groups. These findings should inspire further theory development and spur growth in the social-psychological literature on tolerance.
Trust in fairness, doping, and the demand for sports: a study on international track and field events
2021-06-19

Research question We investigate empirically the impact of spectators' trust in fairness of the sporting competition on TV demand for sports as well as its role in the doping-demand relation.Research methods We use data from a two-wave panel survey and a sporting event scenario where doping issues are present. The effects are estimated using Zero-Inflated Poisson regressions and radius matching based on the propensity score.Results and findings Results of the panel survey analysis suggest that trust in fairness has no impact on TV demand. Our scenario analysis further reveals that awareness about a major doping case negatively affects trust in the fair conduct and integrity of athletes. However, we again find no general effect on the demand for sports.Implications Results of our study suggest that athletes can be seen as (dis)trust ambassadors promoting the (un)fairness of the sporting competition to consumers. However, in contrast to popular (political) claims, our results question the trust channel as a driver for spectator sports demand and as a mechanism in the doping-demand relation.
Effect of Different Alcoholic Beverages on Human Glioblastoma Cell Lines
2021-06-19

Background: Anecdotal reports from neurosurgeons have suggested that glioblastoma patients that consumed moderate amounts of alcoholic beverages after glioblastoma surgery presented with improved vitality. Objective: This study aimed to investigate if any evidence for these anecdotal reports can be reproduced experimentally. Furthermore, we studied the effects of different alcoholic beverages on glioblastoma cells. Methods: GOS-3 glioblastoma cells and PC3 prostate carcinoma cells as control were incubated with beer, red wine, white wine, vodka, and whiskey at different concentrations. Membrane disruption by acute cytotoxicity and apoptosis induction was evaluated via Annexin-V-FITC flow cytometry and confocal laser scanning microscopy. Long-term effects on cell proliferation were studied by the XTT test. Results: There was no increased membrane disruption even at physiologically high alcohol concentrations of 1%. Cell proliferation was significantly inhibited by vodka and beer. Among the wines, the white wine caused slight proliferation inhibition in GOS-3 glioblastoma cells while inducing slightly enhanced proliferation in PC3 prostate cancer cells. After these first results, the study was expanded to more different brands of vodka and additional white and red wines from different grapes. While confirming the initial results, no additional differences between the different brands of vodka were observed. In the wine investigations, all the wines showed inhibition of cell proliferation during long-term incubation of three different glioblastoma cell lines. Consistently, the inhibition from red wines was lower than the inhibition from white and rosé wines. Conclusion: In conclusion, alcoholic beverages at concentrations used during the normal ingestion have both cytotoxic and antiproliferative effects on glioblastoma cells in vitro which could not be found in the controls with pure ethanol.
Data for "MorphVAE: Generating Neural Morphologies from 3D-Walks using Variational Autoencoder with Spherical Latent Space"
2021-06-19

The reconstructions and the processed data that accompany the publication <strong>MorphVAE: Generating Neural Morphologies from 3D-Walks using a Variational Autoencoder with Spherical Latent Space</strong> Sophie Laturnus, Philipp Berens https://www.biorxiv.org/content/10.1101/2021.06.14.448271v1 doi: https://doi.org/10.1101/2021.06.14.448271
A Metabolic Choreography of Maize Plants Treated with a Humic Substance-Based Biostimulant under Normal and Starved Conditions
2021-06-20

Humic substance (HS)-based biostimulants show potentials as sustainable strategies for improved crop development and stress resilience. However, cellular and molecular mechanisms governing the agronomically observed effects of HS on plants remain enigmatic. Here, we report a global metabolic reprogramming of maize leaves induced by a humic biostimulant under normal and nutrient starvation conditions. This reconfiguration of the maize metabolism spanned chemical constellations, as revealed by molecular networking approaches. Plant growth and development under normal conditions were characterized by key differential metabolic changes such as increased levels of amino acids, oxylipins and the tricarboxylic acid (TCA) intermediate, isocitric acid. Furthermore, under starvation, the humic biostimulant significantly impacted pathways that are involved in stress-alleviating mechanisms such as redox homeostasis, strengthening of the plant cell wall, osmoregulation, energy production and membrane remodelling. Thus, this study reveals that the humic biostimulant induces a remodelling of inter-compartmental metabolic networks in maize, subsequently readjusting the plant physiology towards growth promotion and stress alleviation. Such insights contribute to ongoing efforts in elucidating modes of action of biostimulants, generating fundamental scientific knowledge that is necessary for development of the biostimulant industry, for sustainable food security.
Stewardship of global collective behavior
2021-06-21

Collective behavior provides a framework for understanding how the actions and properties of groups emerge from the way individuals generate and share information. In humans, information flows were initially shaped by natural selection yet are increasingly structured by emerging communication technologies. Our larger, more complex social networks now transfer high-fidelity information over vast distances at low cost. The digital age and the rise of social media have accelerated changes to our social systems, with poorly understood functional consequences. This gap in our knowledge represents a principal challenge to scientific progress, democracy, and actions to address global crises. We argue that the study of collective behavior must rise to a “crisis discipline” just as medicine, conservation, and climate science have, with a focus on providing actionable insight to policymakers and regulators for the stewardship of social systems.
Prefrontal Theta-Phase Synchronized Brain Stimulation With Real-Time EEG-Triggered TMS
2021-06-21

Background Theta-band neuronal oscillations in the prefrontal cortex are associated with several cognitive functions. Oscillatory phase is an important correlate of excitability and phase synchrony mediates information transfer between neuronal populations oscillating at that frequency. The ability to extract and exploit the prefrontal theta rhythm in real time in humans would facilitate insight into neurophysiological mechanisms of cognitive processes involving the prefrontal cortex, and development of brain-state-dependent stimulation for therapeutic applications. Objectives We investigate individual source-space beamforming-based estimation of the prefrontal theta oscillation as a method to target specific phases of the ongoing theta oscillations in the human dorsomedial prefrontal cortex (DMPFC) with real-time EEG-triggered transcranial magnetic stimulation (TMS). Different spatial filters for extracting the prefrontal theta oscillation from EEG signals are compared and additional signal quality criteria are assessed to take into account the dynamics of this cortical oscillation. Methods Twenty two healthy participants were recruited for anatomical MRI scans and EEG recordings with 18 composing the final analysis. We calculated individual spatial filters based on EEG beamforming in source space. The extracted EEG signal was then used to simulate real-time phase-detection and quantify the accuracy as compared to post-hoc phase estimates. Different spatial filters and triggering parameters were compared. Finally, we validated the feasibility of this approach by actual real-time triggering of TMS pulses at different phases of the prefrontal theta oscillation. Results Higher phase-detection accuracy was achieved using individualized source-based spatial filters, as compared to an average or standard Laplacian filter, and also by detecting and avoiding periods of low theta amplitude and periods containing a phase reset. Using optimized parameters, prefrontal theta-phase synchronized TMS of DMPFC was achieved with an accuracy of ±55°. Conclusion This study demonstrates the feasibility of triggering TMS pulses during different phases of the ongoing prefrontal theta oscillation in real time. This method is relevant for brain state-dependent stimulation in human studies of cognition. It will also enable new personalized therapeutic repetitive TMS protocols for more effective treatment of neuropsychiatric disorders.
DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics
2021-06-21

Data-independent acquisition (DIA) is becoming a leading analysis method in biomedical mass spectrometry. The main advantages include greater reproducibility and sensitivity and a greater dynamic range compared with data-dependent acquisition (DDA). However, the data analysis is complex and often requires expert knowledge when dealing with large-scale data sets. Here we present DIAproteomics, a multifunctional, automated, high-throughput pipeline implemented in the Nextflow workflow management system that allows one to easily process proteomics and peptidomics DIA data sets on diverse compute infrastructures. The central components are well-established tools such as the OpenSwathWorkflow for the DIA spectral library search and PyProphet for the false discovery rate assessment. In addition, it provides options to generate spectral libraries from existing DDA data and to carry out the retention time and chromatogram alignment. The output includes annotated tables and diagnostic visualizations from the statistical postprocessing and computation of fold-changes across pairwise conditions, predefined in an experimental design. DIAproteomics is well documented open-source software and is available under a permissive license to the scientific community at https://www.openms.de/diaproteomics/.
Diversity-aware Recommendations for Social Justice? Exploring User Diversity and Fairness in Recommender Systems
2021-06-21

Diversity and fairness are increasingly linked in the field of personalized recommendations. For instance, the diversification of items ("item diversity") is considered key to fairness. Less attention has been paid to "user diversity" and its implications for fairness. In this paper, I problematize the conceptualization and application of user diversity in recommender systems. I argue that the widespread understanding of user diversity as natural, value-neutral, and individual-level categories may accidentally compound historical injustice. To mitigate emerging biases, diversity dimensions need to be contextualized by mapping structural inequalities between users. The paper thus stresses the importance of paying attention to the structural context of diversity, whereas the context refers to political and social circumstances surrounding the user's life. The paper makes three contributions: 1) It connects fairness to diversity literature in the field of recommender system, 2) it specifies the tension between item-side and user-side fairness by revealing a bias in the treatment of user diversity, 3) it proposes solutions to mitigate the bias by drawing on Black feminist and critical race theory.
Evolution of (Bio‐)Geochemical Processes and Diagenetic Alteration of Sediments Along the Tectonic Migration of Ocean Floor in the Shikoku Basin off Japan
2021-06-21

Abstract Biogeochemical processes in subseafloor sediments are closely coupled to global element cycles. To improve the understanding of changes in biogeochemical conditions on geological timescales, we investigate sediment cores from a 1,180 m deep hole in the Nankai Trough offshore Japan (Site C0023) drilled during International Ocean Discovery Program Expedition 370. During its tectonic migration from the Shikoku Basin to the Nankai Trough over the past 15 Ma, Site C0023 has experienced significant changes in depositional, thermal, and geochemical conditions. By combining pore‐water, solid‐phase, and rock magnetic data, we demonstrate that a transition from organic carbon‐starved conditions with predominantly aerobic respiration to an elevated carbon burial environment with increased sedimentation occurred at ∼2.5 Ma. Higher rates of organic carbon burial in consequence of increased nutrient supply and productivity likely stimulated the onset of anaerobic electron‐accepting processes during organic carbon degradation. A significant temperature increase by ∼50°C across the sediment column associated with trench‐style sedimentation since ∼0.5 Ma could increase the bioavailability of organic matter and enhance biogenic methanogenesis. The resulting shifts in reaction fronts led to diagenetic transformation of iron (oxyhydr)oxides into pyrite in the organic carbon‐starved sediments several millions of years after burial. We also show that high amounts of reducible iron(III) which can serve as electron acceptor for microbial iron(III) reduction are preserved and still available as phyllosilicate‐bound iron. This is the first study that shows the evolution of long‐term variations of (bio‐)geochemical processes along tectonic migration of ocean floor, thereby altering the primary sediment composition long after deposition.
Robust LFA Protection for Software-Defined Networks (RoLPS)
2021-06-21

In software-defined networks, forwarding entries on switches are configured by a controller. In case of an unreachable next-hop, traffic is dropped until forwarding entries are updated, which takes significant time. Therefore, fast reroute (FRR) mechanisms are needed to forward affected traffic over alternate paths in the meantime. Loop-free alternates (LFAs) and remote LFAs (rLFAs) have been proposed for FRR in IP networks. However, they cannot protect traffic for all destinations and some LFAs may create loops under challenging conditions. This paper proposes robust LFA protection for software-defined networks (RoLPS). RoLPS augments the coverage of (r)LFAs with novel explicit LFAs (eLFAs). RoLPS ranks available LFAs according to protection quality and complexity for selection of the best available LFA. Furthermore, we introduce advanced loop detection (ALD) so that RoLPS stops loops caused by LFAs. We evaluate RoLPS-based protection variants on a large set of representative networks with unit and non-unit link costs. We study their protection coverage, additional forwarding entries, and path extensions for rerouted traffic, and compare them with MPLS facility backup. Results show that RoLPS can protect traffic against all single link or node failures, and against most double failures while inducing only little overhead. We implement FRR on the P4-programmable switch ASIC Tofino and provide a control plane logic based on RoLPS. Measurement results show that the prototype achieves a throughput of 100 Gb/s, reroutes traffic within less than a millisecond, and reliably detects and drops looping traffic.
Voretigene neparvovec in patients with RPE65 mutation-associated inherited retinal dystrophy: Baseline characteristics from the real-world, prospective, observational PERCEIVE study
2021-06-21

Purpose : Voretigene neparvovec (VN) is the first ocular gene therapy approved in multiple countries including the USA and Europe for treating patients (pts) with visual impairment due to confirmed biallelic RPE65 mutation-associated inherited retinal dystrophy having sufficient viable retinal cells. PERCEIVE, a registry-based post-authorization safety study, is designed to assess long-term safety of VN in a real-world (RW) setting. Here, baseline characteristics of participating pts treated with VN up to August 2020 are reported. Methods : PERCEIVE is an ongoing, prospective, longitudinal, multicenter (ex-US), observational, safety study, which commenced December 2019 with the aim to enroll a minimum of 40 pts. All VN-treated pts are encouraged to participate in the study to maximize data collection, including those treated prior to study inception. After receiving VN as per local prescribing information, pts are followed-up as per the routine medical care for 5 years. The objectives are to characterize the long-term safety profile of VN via systematic collection of adverse event data, to follow pregnancy outcomes and assess visual function over time. Results : Until data cut-off (Aug 2020), of the 15 pts enrolled, 10 pts (16 eyes) have received VN (6 bilateral;4 unilateral). All treated pts are from Europe (Germany: 6;France: 3;Austria: 1). At the time of enrollment, the mean (standard deviation [SD]) age was 27.6 (9.81) years with a range of 15-51 years (1 adolescent;9 adults). The majority of treated pts are female (n=7;70%). For the treated eyes (n=16), baseline mean (SD) visual acuity was 0.96 (0.37) logMAR (n=14;range: 0.5-1.6 logMAR) and full-field stimulus threshold (white light) was -4.32 (9.40) dB (n=15;range: -34.9 to 3.2 dB). Optical coherence tomography (OCT) revealed a mean foveal thickness of 150.5 (41.07) μm (n=15;range: 76- 216 μm). Central OCT showed that 11 eyes had an outer nuclear layer with a thickness range of 36-74 μm (n=9), while it was absent in 4 eyes. The ellipsoid zone line was disrupted in 9 eyes and was undetected in 6. Conclusions : While enrollment and in person follow-up of VN-treated pts has been impacted due to COVID-19, PERCEIVE has started to provide valuable information on baseline characteristics of this vision-impaired population, and effect of VN therapy in a RW setting.
Loss of Gap Junction Delta-2 (GJD2) gene orthologs leads to refractive error in zebrafish
2021-06-21

Myopia is the most common developmental disorder of juvenile eyes, and it has become an increasing cause of severe visual impairment. The GJD2 locus has been consistently associated with myopia in multiple independent genome-wide association studies. However, despite the strong genetic evidence, little is known about the functional role of GJD2 in refractive error development. Here, we find that depletion of gjd2a (Cx35.5) or gjd2b (Cx35.1) orthologs in zebrafish, cause changes in the biometry and refractive status of the eye. Our immunohistological and scRNA sequencing studies show that Cx35.5 (gjd2a) is a retinal connexin and its depletion leads to hyperopia and electrophysiological changes in the retina. These findings support a role for Cx35.5 (gjd2a) in the regulation of ocular biometry. Cx35.1 (gjd2b) has previously been identified in the retina, however, we found an additional lenticular role. Lack of Cx35.1 (gjd2b) led to a nuclear cataract that triggered axial elongation. Our results provide functional evidence of a link between gjd2 and refractive error.