julilili42/papers huggingface dataset:
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
2023-05-23

Abstract Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework &lt;monospace&gt;stdpopsim&lt;/monospace&gt; seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of &lt;monospace&gt;stdpopsim&lt;/monospace&gt; focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of &lt;monospace&gt;stdpopsim&lt;/monospace&gt; (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than three-fold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to &lt;monospace&gt;stdpopsim&lt;/monospace&gt; aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.
An enigma of Przybylski's star: Is there promethium on its surface?
2023-05-23

Abstract We carried out a new attempt to check for the presence of promethium lines in the spectrum of HD 101065 (Przybylski's star). The neutron capture element promethium does not have stable isotopes, and the maximum half‐life time is about 18 years. Thus, its presence in this peculiar star would indicate an ongoing process of irradiation of its surface layers with free neutrons. Unfortunately, almost all promethium lines are heavily blended with lines of other neutron capture elements and other species. We selected and analyzed three lines of promethium (Pm I and Pm II) and came to the conclusion that at present it is impossible to definitely claim the presence of this element in Przybylski's star atmosphere.
Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
2023-05-23

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species . Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than three-fold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.
Nerve Ultrasound of Peripheral Nerves in Patients Treated with Immune Checkpoint Inhibitors
2023-05-23

Background and Objectives: Immune checkpoint inhibitors (ICIs) have enriched tumor therapy, improving overall survival. Immunotherapy adverse events (irAEs) occur in up to 50% of patients and also affect the peripheral nervous system. The exact pathomechanism is unclear; however, an autoimmune process is implicated. Thus, the clinical evaluation of irAEs in the peripheral nervous system is still demanding. We retrospectively analyzed nerve ultrasound (NU) data of polyneuropathies (PNPs) secondary to checkpoint inhibitors. Materials and Methods: NU data of patients with PNP symptoms secondary to ICI therapy were retrospectively analyzed using the Ultrasound Pattern Sum Score (UPSS) as a quantitative marker. Our findings were compared with a propensity score match analysis (1:1 ratio) to NU findings in patients with chronic inflammatory demyelinating polyneuropathy (CIDP) and chemotherapy-associated PNP patients. Results: In total, 10 patients were included (4 female, mean age 66 ± 10.5, IQR 60–77), where NU was performed in 80%. The UPSS obtained ranged from 0 to 5 (mean 2 ± 1.6, IQR 1–2.5). The morphological changes seen in the NUs resembled sonographic changes seen in chemotherapy-associated PNP (n = 10, mean UPSS 1 ± 1, IQR 0–2) with little to no nerve swelling. In contrast, CIDP patients had a significantly higher UPSS (n = 10, mean UPSS 11 ± 4, IQR 8–13, p &lt; 0.0001). Conclusions: Although an autoimmune process is hypothesized to cause peripheral neurological irAEs, NU showed no increased swelling as seen in CIDP. The nerve swelling observed was mild and comparable to ultrasound findings seen in chemotherapy-associated PNP.
Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere‐associated bacteria
2023-05-24

Summary Biotic and abiotic interactions shape natural microbial communities. The mechanisms behind microbe–microbe interactions, particularly those protein based, are not well understood. We hypothesize that released proteins with antimicrobial activity are a powerful and highly specific toolset to shape and defend plant niches. We have studied Albugo candida , an obligate plant parasite from the protist Oomycota phylum, for its potential to modulate the growth of bacteria through release of antimicrobial proteins into the apoplast. Amplicon sequencing and network analysis of Albugo ‐infected and uninfected wild Arabidopsis thaliana samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the apoplastic proteome of Albugo‐ colonized leaves combined with machine learning predictors enabled the selection of antimicrobial candidates for heterologous expression and study of their inhibitory function. We found for three candidate proteins selective antimicrobial activity against Gram‐positive bacteria isolated from A. thaliana and demonstrate that these inhibited bacteria are precisely important for the stability of the community structure. We could ascribe the antibacterial activity of the candidates to intrinsically disordered regions and positively correlate it with their net charge. This is the first report of protist proteins with antimicrobial activity under apoplastic conditions that therefore are potential biocontrol tools for targeted manipulation of the microbiome.
Genotype–phenotype correlation and treatment effects in young patients withGNAO1-associated disorders
2023-05-24

Background Patients carrying pathogenic variants in GNAO1 often present with early-onset central hypotonia and global developmental delay, with or without epilepsy. As the disorder progresses, a complex hypertonic and hyperkinetic movement disorder is a common phenotype. A genotype–phenotype correlation has not yet been described and there are no evidence-based therapeutic recommendations. Methods To improve understanding of the clinical course and pathophysiology of this ultra-rare disorder, we built up a registry for GNAO1 patients in Germany. In this retrospective, multicentre cohort study, we collected detailed clinical data, treatment effects and genetic data for 25 affected patients. Results The main clinical features were symptom onset within the first months of life, with central hypotonia or seizures. Within the first year of life, nearly all patients developed a movement disorder comprising dystonia (84%) and choreoathetosis (52%). Twelve (48%) patients suffered life-threatening hyperkinetic crises. Fifteen (60%) patients had epilepsy with poor treatment response. Two patients showed an atypical phenotype and seven novel pathogenic variants in GNAO1 were identified. Nine (38%) patients were treated with bilateral deep brain stimulation of the globus pallidus internus. Deep brain stimulation reduced hyperkinetic symptoms and prevented further hyperkinetic crises. The in silico prediction programmes did not predict the phenotype by the genotype. Conclusion The broad clinical spectrum and genetic findings expand the phenotypical spectrum of GNAO1 -associated disorder and therefore disprove the assumption that there are only two main phenotypes. No specific overall genotype–phenotype correlation was identified. We highlight deep brain stimulation as a useful treatment option in this disorder.
European Union’s Regulating of Social Media: A Discourse Analysis of the Digital Services Act
2023-05-24

Traditional conceptions of democratic publics are changing due to the rise of social media as a global communication tool. While social media brings people together globally and creates new spaces for creativity and resistance, it is also a space of harassment, discrimination, and violence. As recent debates about hate speech and the distribution of “fake news” have shown, the political responsibilities and consequences of regulating online content remain unclear. More recently, the EU is increasingly paying attention to platform providers. How is the EU legitimizing its new approach to social media platform regulation and how will this legislation shape transnational publics? This article contributes to ongoing debates on platform regulation by governments and other political authorities (especially the EU as a transnational legislator) and discussions about the shape of online publics. By applying a discourse analytical perspective, key legitimation narratives can be explored. I argue that the EU claims political authority over corporate interests by introducing new legislation to regulate social media platforms with the Digital Services Act. On the one hand, the EU imagines an idealized democratic online public without harmful and illegal content. On the other hand, the new legislation serves the EU’s agenda on digital sovereignty, taking back control from big and US-based enterprises. There is a strong consensus about four legitimation narratives: (a) “What is illegal offline has to be illegal online”; (b) the EU is “taking back control”; (c) the EU is “protecting small businesses, consumers, and our citizens against big tech”; (d) the EU is developing “a golden standard and rulebook beyond the EU.” Held together by the idea of democratic procedures, authority, and sovereignty, these narratives are demanding more action from social media providers to act on harmful and illegal content.
Long-term mental health consequences of female- versus male-perpetrated child sexual abuse
2023-05-24

The differences may be due to stigmatization leading to dysfunctional coping mechanisms. Societal gender stereotypes must be reduced, especially within the professional helping system to ensure support for people who have experienced sexual abuse, regardless of gender.
The ethics of sustainable AI: Why animals (should) matter for a sustainable use of AI
2023-05-24

Abstract Technologies equipped with artificial intelligence (AI) influence our everyday lives in a variety of ways. Due to their contribution to greenhouse gas emissions, their high use of energy, but also their impact on fairness issues, these technologies are increasingly discussed in the “sustainable AI” discourse. However, current “sustainable AI” approaches remain anthropocentric. In this article, we argue from the perspective of applied ethics that such anthropocentric outlook falls short. We present a sentientist approach, arguing that the normative foundation of sustainability and sustainable development—that is, theories of intra‐ and intergenerational justice—should include sentient animals. Consequently, theories of sustainable AI must also be non‐anthropocentric. Moreover, we investigate consequences of our approach for applying AI technologies in a sustainable way.
Skeletal Muscle MicroRNA Patterns in Response to a Single Bout of Exercise in Females: Biomarkers for Subsequent Training Adaptation?
2023-05-24

microRNAs (miRs) have been proposed as a promising new class of biomarkers in the context of training adaptation. Using microarray analysis, we studied skeletal muscle miR patterns in sedentary young healthy females (n = 6) before and after a single submaximal bout of endurance exercise (‘reference training’). Subsequently, participants were subjected to a structured training program, consisting of six weeks of moderate-intensity continuous endurance training (MICT) and six weeks of high-intensity interval training (HIIT) in randomized order. In vastus lateralis muscle, we found significant downregulation of myomiRs, specifically miR-1, 133a-3p, and -5p, -133b, and -499a-5p. Similarly, exercise-associated miRs-23a-3p, -378a-5p, -128-3p, -21-5p, -107, -27a-3p, -126-3p, and -152-3p were significantly downregulated, whereas miR-23a-5p was upregulated. Furthermore, in an untargeted approach for differential expression in response to acute exercise, we identified n = 35 miRs that were downregulated and n = 20 miRs that were upregulated by factor 4.5 or more. Remarkably, KEGG pathway analysis indicated central involvement of this set of miRs in fatty acid metabolism. To reproduce these data in a larger cohort of all-female subjects (n = 29), qPCR analysis was carried out on n = 15 miRs selected from the microarray, which confirmed their differential expression. Furthermore, the acute response, i.e., the difference between miR concentrations before and after the reference training, was correlated with changes in maximum oxygen uptake (V̇O2max) in response to the training program. Here, we found that miRs-199a-3p and -19b-3p might be suitable acute-response candidates that correlate with individual degrees of training adaptation in females.
The Tiny Eye Movement Transformer
2023-05-24

In this paper, we evaluate different small neural network models for eye movement classification and show our so far developed improved model architecture. For evaluation, we used a subset (1.5 million sequences) of the TEyeDS annotations since it contains in the wild recordings and has the most eye movement annotations to our knowledge. We classified fixations, saccades, and smooth pursuits with four different network architectures and the proposed model improves the equally weighted accuracy by 3.8% to the best competitor while only using 6% of the amount of learnable weights.
Loss or gain of function? Effects of ion channel mutations on neuronal firing depend on the neuron type
2023-05-24

Introduction Clinically relevant mutations to voltage-gated ion channels, called channelopathies, alter ion channel function, properties of ionic currents, and neuronal firing. The effects of ion channel mutations are routinely assessed and characterized as loss of function (LOF) or gain of function (GOF) at the level of ionic currents. However, emerging personalized medicine approaches based on LOF/GOF characterization have limited therapeutic success. Potential reasons are among others that the translation from this binary characterization to neuronal firing is currently not well-understood—especially when considering different neuronal cell types. In this study, we investigate the impact of neuronal cell type on the firing outcome of ion channel mutations. Methods To this end, we simulated a diverse collection of single-compartment, conductance-based neuron models that differed in their composition of ionic currents. We systematically analyzed the effects of changes in ion current properties on firing in different neuronal types. Additionally, we simulated the effects of known mutations in KCNA1 gene encoding the K V 1.1 potassium channel subtype associated with episodic ataxia type 1 (EA1). Results These simulations revealed that the outcome of a given change in ion channel properties on neuronal excitability depends on neuron type, i.e., the properties and expression levels of the unaffected ionic currents. Discussion Consequently, neuron-type specific effects are vital to a full understanding of the effects of channelopathies on neuronal excitability and are an important step toward improving the efficacy and precision of personalized medicine approaches.
One step closer to EEG based eye tracking
2023-05-24

In this paper, we present two approaches and algorithms that adapt areas of interest. We present a new deep neural network (DNN) that can be used to directly determine gaze position using EEG data. EEG-based eye tracking is a new and difficult research topic in the field of eye tracking, but it provides an alternative to image-based eye tracking with an input data set comparable to conventional image processing. The presented DNN exploits spatial dependencies of the EEG signal and uses convolutions similar to spatial filtering, which is used for preprocessing EEG signals. By this, we improve the direct gaze determination from the EEG signal compared to the state of the art by 3.5 cm MAE (Mean absolute error), but unfortunately still do not achieve a directly applicable system, since the inaccuracy is still significantly higher compared to image-based eye trackers.
ZERO: A Generic Open-Source Extended Reality Eye-Tracking Controller Interface for Scientists
2023-05-24

Virtual reality and eye-tracking technologies are nowadays standard research tools. A growing number of researchers from different disciplines are utilizing these technologies. Currently, access to eye-tracking hardware in virtual reality glasses is usually provided as APIs to call functions of the eye-tracking device. Proper implementation is device-specific and left to the user. Especially non-computer scientists are left alone with this problem, which impedes eye-tracking research in virtual reality for many scientists. This paper describes a generic open-source interface for everyone to efficiently and easily utilize common eye trackers in virtual reality. The interface is published under a friendly CC BY 4.0 license that allows for integration, modification, and extension of the code. It includes a standardized interface for several eye-tracking devices in virtual reality, is ready to be used out of the box, and allows easy addition of APIs from other manufacturers. The code is available at https://bitbucket.org/benediktwhosp/zvsl-zero
Area of interest adaption using feature importance
2023-05-24

In this paper, we present two approaches and algorithms that adapt areas of interest (AOI) or regions of interest (ROI), respectively, to the eye tracking data quality and classification task. The first approach uses feature importance in a greedy way and grows or shrinks AOIs in all directions. The second approach is an extension of the first approach, which divides the AOIs into areas and calculates a direction of growth, i.e. a gradient. Both approaches improve the classification results considerably in the case of generalized AOIs, but can also be used for qualitative analysis. In qualitative analysis, the algorithms presented allow the AOIs to be adapted to the data, which means that errors and inaccuracies in eye tracking data can be better compensated for. A good application example is abstract art, where manual AOIs annotation is hardly possible, and data-driven approaches are mainly used for initial AOIs.
Leveraging Eye Tracking in Digital Classrooms: A Step Towards Multimodal Model for Learning Assistance
2023-05-24

Instructors who teach digital literacy skills are increasingly faced with the challenges that come with larger student populations and online courses. We asked an educator how we could support student learning and better assist instructors both online and in the classroom. To address these challenges, we discuss how behavioral signals collected from eye tracking and mouse tracking can be combined to offer predictions of student performance. In our preliminary study, participants completed two image masking tasks in Adobe Photoshop based on real college-level course content. We then trained a machine learning model to predict student performance in each task based on data from other students, as a step towards offering automated student assistance and feedback to instructors. We reflect on the challenges and scalability issues to deploying such a system in-the-wild, and present some guidelines for future work.
Watch out for those bananas! Gaze Based Mario Kart Performance Classification
2023-05-24

This paper is about a small eye tracking study for scan path classification. Seven participants played Mario Kart while wearing a head mounted eye tracker. In total, we had 64 recordings, but one had to be removed (Only 79 gaze samples were recorded). We compared different scan path classification features to estimate the performance of the participants based on the ranking they achieved. The best performing feature was ENCODJI which incooperates saccades and the heatmap in one feature. HOV, which uses saccade angles, performed well for all tasks but was outperformed by the heatmap (HEAT) for the last two groups.
A temporally quantized distribution of pupil diameters as a new feature for cognitive load classification
2023-05-24

In this paper, we present a new feature that can be used to classify cognitive load based on pupil information. The feature consists of a temporal segmentation of the eye tracking recordings. For each segment of the temporal partition, a probability distribution of pupil size is computed and stored. These probability distributions can then be used to classify the cognitive load. The presented feature significantly improves the classification accuracy of the cognitive load compared to other statistical values obtained from eye tracking data, which represent the state of the art in this field. The applications of determining Cognitive Load from pupil data are numerous and could lead, for example, to pre-warning systems for burnouts.