julilili42/papers huggingface dataset:
Nomad-FAIR North-Remote-Tool Example Dataset Electron Microscopy
2022-08-29

<strong>Dataset.Objective.Aperture.Energy.Slit.cdf.nx5.zip<br> Dataset.Objective.Aperture.Energy.Slit.dm3.cdf.zip<br> parser-focalseries-gatandm-cdf2nx5.py</strong><br> An example dataset for focus-series reconstruction (in-line holography).<br> The dataset supplements/comes from a research study https://doi.org/10.1016/j.ultramic.2021.113264 <strong>em-sprint09-example.zip</strong> This archive contains an example YAML file how metadata to e.g. 1613_Si_HAADF_610_kx.emd<br> (see below) are stored internally in a NOMAD OASIS when saving entries into the customized<br> ELN schema of the EM example that was developed in Sprint09 Area B in the FAIRmat project.<br> This eln_data.yaml file serves as an input to the dataconverter/em reader tool to supplement<br> the numerical data from the 1613_Si_HAADF_610_kx.emd file with metadata during the creation<br> of the emd.nxs file. Furtermore, this archive contains a Bruker BCF, a Velox EMD, and a Digital Micrograph v3 DM3<br> file. These file formats can be used as input to the dataconverter/em reader tool to inject<br> specific numerical data while creating an instance of an NXem-compliant NeXus file. The files have the following SHA256 checksum to verify their integriety: sha256sum eln_data.yaml<br> c0fd230336ce7cd8e2715445ea6af404202b4ab9d7e7186838748bd0559d536f sha256sum 46_ES-LP_L1_brg.bcf<br> bf5ca0f862af49726b848a8a60d73af6f1669990131288ac4b4ca6cb57e58aff sha256sum 1613_Si_HAADF_610_kx.emd<br> 6ed0e8b8c170a0ed307e5c877fd891767a38e636f4680632e9b00c46a2b963b9 sha256sum EELS_map_2_ROI_1_location_4.dm3<br> b97850f6c6b100740813c34d20eda294ef66a6130daa42a6cf975c4572ff599c
Does the emotional design of scaffolds enhance learning and motivational outcomes in game‐based learning?
2022-08-30

Abstract Background In recent years, the importance of emotions in learning has been increasingly recognized. Applying emotional design to induce positive emotions has been considered a means to enhance the instructional effectiveness of digital learning environments. However, only a few studies have examined the specific effects of emotional design in game‐based learning. Objectives This quasi‐experimental study utilized a value‐added research approach to investigate whether emotional design applied to scaffolding in a game‐based learning environment improves learning and motivational outcomes more than emotionally neutral scaffolding. Methods A total of 138 participants, mean age of 11.5 ( SD = 0.73) participated in the study. A total of 68 participants played the base version of a fraction learning game (Number Trace), where scaffolding was provided with emotionally neutral mathematical notations, and 70 participants played the value‐added version of the game using emotionally designed animated scaffolding agents. Pre‐and post‐tests were used to measure conceptual fraction knowledge and self‐reported measures of situational interest and situational self‐efficacy to evaluate motivational outcomes. Results and Conclusions Our results indicate that the emotional design applied to scaffolds can improve the educational value of a game‐based learning environment by enhancing players' situational interest and situational self‐efficacy. However, although the intervention improved the participants' conceptual fraction knowledge, there was no significant difference between the scaffolding conditions in participants' learning outcomes. Takeaways The results suggest that emotional design can increase the educational impact of game‐based learning by promoting the development of interest, as well as improving self‐efficacy.
Modeling dynamic personality theories in a continuous‐time framework: An illustration
2022-08-30

Abstract Objective Personality psychology has traditionally focused on stable between‐person differences. Yet, recent theoretical developments and empirical insights have led to a new conceptualization of personality as a dynamic system (e.g., Cybernetic Big Five Theory). Such dynamic systems comprise several components that need to be conceptually distinguished and mapped to a statistical model for estimation. Method In the current work, we illustrate how common components from these new dynamic personality theories may be implemented in a continuous time‐modeling framework. Results As an empirical example, we reanalyze experience sampling data with N = 180 persons (with on average T = 40 [ SD = 8] measurement occasions) to investigate four different effects between momentary happiness, momentary extraverted behavior, and the perception of a situation as social: (1) between‐person effects, (2) contemporaneous effects, (3) autoregressive effects, and (4) cross‐lagged effects. Conclusion We highlight that these four effects must not necessarily point in the same direction, which is in line with assumptions from dynamic personality theories.
Development of a Hybrid-Imaging-Based Prognostic Index for Metastasized-Melanoma Patients in Whole-Body 18F-FDG PET/CT and PET/MRI Data
2022-08-30

Besides tremendous treatment success in advanced melanoma patients, the rapid development of oncologic treatment options comes with increasingly high costs and can cause severe life-threatening side effects. For this purpose, predictive baseline biomarkers are becoming increasingly important for risk stratification and personalized treatment planning. Thus, the aim of this pilot study was the development of a prognostic tool for the risk stratification of the treatment response and mortality based on PET/MRI and PET/CT, including a convolutional neural network (CNN) for metastasized-melanoma patients before systemic-treatment initiation. The evaluation was based on 37 patients (19 f, 62 ± 13 y/o) with unresectable metastasized melanomas who underwent whole-body 18F-FDG PET/MRI and PET/CT scans on the same day before the initiation of therapy with checkpoint inhibitors and/or BRAF/MEK inhibitors. The overall survival (OS), therapy response, metastatically involved organs, number of lesions, total lesion glycolysis, total metabolic tumor volume (TMTV), peak standardized uptake value (SULpeak), diameter (Dmlesion) and mean apparent diffusion coefficient (ADCmean) were assessed. For each marker, a Kaplan–Meier analysis and the statistical significance (Wilcoxon test, paired t-test and Bonferroni correction) were assessed. Patients were divided into high- and low-risk groups depending on the OS and treatment response. The CNN segmentation and prediction utilized multimodality imaging data for a complementary in-depth risk analysis per patient. The following parameters correlated with longer OS: a TMTV &lt; 50 mL; no metastases in the brain, bone, liver, spleen or pleura; ≤4 affected organ regions; no metastases; a Dmlesion &gt; 37 mm or SULpeak &lt; 1.3; a range of the ADCmean &lt; 600 mm2/s. However, none of the parameters correlated significantly with the stratification of the patients into the high- or low-risk groups. For the CNN, the sensitivity, specificity, PPV and accuracy were 92%, 96%, 92% and 95%, respectively. Imaging biomarkers such as the metastatic involvement of specific organs, a high tumor burden, the presence of at least one large lesion or a high range of intermetastatic diffusivity were negative predictors for the OS, but the identification of high-risk patients was not feasible with the handcrafted parameters. In contrast, the proposed CNN supplied risk stratification with high specificity and sensitivity.
A new species of Bocchus from upper Eocene Rovno amber (Hymenoptera, Dryinidae)
2022-08-30

A new fossil species of Dryinidae (Hymenoptera, Chrysidoidea) from upper Eocene Rovno amber (Ukraine) is described: Bocchus rex sp. nov. It is compared with two other species of Bocchus known from European amber: B. primaevus Martins &amp; Melo from Baltic amber and B. schmalhauseni Perkovsky, Olmi, Vasilenko, Capradossi &amp; Guglielmino from Rovno amber. A new key to the Cretaceous and Paleogene species of Bocchus is presented. The Dryininae are the most common representatives in all the amber dryinid faunas since the mid-Cretaceous. The Rovno amber fauna is an exception; possible explanations for the abundance of Bocchus species within this amber are presented.
Factors Associated with the COVID-19 Vaccination Status of Higher Education Students: Results of an Online Cross-Sectional Survey at Six Universities in Southwestern Germany
2022-08-30

This cross-sectional study explored factors associated with the corona virus disease 2019 (COVID-19) vaccination acceptance among higher education students in southwestern Germany. We conducted a cross-sectional online survey at six state-approved higher education institutions (HEIs) between July and November 2021. In addition to descriptive analyses, univariate as well as multivariate binary logistic regression analyses were conducted. A total of 6556 higher education students aged 18 years and older participated in our survey; 91.4% of participating students had been vaccinated against COVID-19 at least once. The factors that significantly contributed to the explanation of higher education students’ vaccination status in the multivariate analysis (area under curve—AUC = 0.94) were variables on the perception of the virus SARS-CoV-2 (affective risk perception: Adjusted odds ratio—aOR = 1.2; perception of the outbreak as a media-hype: aOR = 0.8), attitudes towards personal (aOR = 0.7) and study-related (aOR = 0.8) health and safety measures to prevent transmission of SARS-CoV-2, and attitudes towards COVID-19 vaccination (preservation of own health: aOR = 1.3; confidence in vaccine safety: aOR = 1.7; supporting higher education through vaccination: aOR = 1.2; own contribution to the containment of the pandemic: aOR = 1.7). The findings target assisting HEIs in returning to face-to-face teaching after previous semesters of online teaching.
Identification and Current Palaeobiological Understanding of “Keratosa”-Type Nonspicular Demosponge Fossils in Carbonates: With a New Example from the Lowermost Triassic, Armenia
2022-08-30

Structures similar to fossilized nonspicular demosponges have been reported in carbonates throughout the Phanerozoic and recently in rocks dating back to 890 Ma ago. Interpretation of these records is increasingly influential to our understanding of metazoans in multiple aspects, including their early evolution, the ecology in fossil reefs, and recovery after mass extinction events. Here, we propose six identification criteria of “Keratosa”-type nonspicular demosponge fossils based on the well-established taphonomical models and their biological characteristics. Besides, sponge fossils of this kind from the lowermost Triassic of Chanakhchi (Armenia) are described with a 3-D reconstruction to exemplify the application of these criteria in recognition of such organisms. Subsequently, the state-of-the-art understanding of the taxonomy and evolution of these fossil sponges, a previously poorly addressed topic, is summarized. The morphology of the Triassic Chanakhchi fossils indicates an affinity with verongimorphs, a group that may have evolved by Cambrian Age 3. Other than that, further efforts are encouraged to forge quantitative criteria based on the here proposed descriptive version and to explore the taxonomic diversity and evolutionary details of these fossil nonspicular demosponges.
Comprehensive Cardiac Magnetic Resonance to Detect Subacute Myocarditis
2022-08-30

(1) Background: Compared to acute myocarditis in the initial phase, detection of subacute myocarditis with cardiac magnetic resonance (CMR) parameters can be challenging due to a lower degree of myocardial inflammation compared to the acute phase. (2) Objectives: To systematically evaluate non-invasive CMR imaging parameters in acute and subacute myocarditis. (3) Methods: 48 patients (age 37 (IQR 28–55) years; 52% female) with clinically suspected myocarditis were consecutively included. Patients with onset of symptoms ≤2 weeks prior to 1.5T CMR were assigned to the acute group (n = 25, 52%), patients with symptom duration &gt;2 to 6 weeks were assigned to the subacute group (n = 23, 48%). CMR protocol comprised morphology, function, 3D-strain, late gadolinium enhancement (LGE) imaging and mapping (T1, ECV, T2). (4) Results: Highest diagnostic performance in the detection of subacute myocarditis was achieved by ECV evaluation either as single parameter or in combination with T1 mapping (applying a segmental or global increase of native T1 &gt; 1015 ms and ECV &gt; 28%), sensitivity 96% and accuracy 91%. Compared to subacute myocarditis, acute myocarditis demonstrated higher prevalence and extent of LGE (AUC 0.76) and increased T2 (AUC 0.66). (5) Conclusions: A comprehensive CMR approach allows reliable diagnosis of clinically suspected subacute myocarditis. Thereby, ECV alone or in combination with native T1 mapping indicated the best performance for diagnosing subacute myocarditis. Acute vs. subacute myocarditis is difficult to discriminate by CMR alone, due to chronological connection and overlap of pathologic findings.
Prediction of estimated risk for bipolar disorder using machine learning and structural MRI features
2022-08-30

<title>Abstract</title> Individuals with bipolar disorder are commonly correctly diagnosed a decade after the onset of first symptoms. Machine learning techniques may aid in early recognition and reduce the disease burden. As both individuals at risk and those with a manifest disease display structural brain markers, structural magnetic resonance imaging (MRI) may provide relevant classification features. Following a pre-registered protocol, we trained linear support vector machine (SVM) to classify individuals according to their estimated risk for bipolar disorder using regional cortical thickness values of help-seeking individuals from 7 study sites (N = 276). We estimated the risk using three state-of-the-art assessment instruments (BPSS-P, BARS and EPI<italic>bipolar</italic>). For BPSS-P, SVM achieved a fair performance of Cohen's kappa of 0.235 (95% CI 0.11–0.361) and a balanced accuracy of 63.1% (95% CI 55.9–70.3) in the 10-fold crossvalidation. In the leave-one-site-out crossvalidation, the model performed with a Cohen's kappa of 0.128 (95% CI -0.069-0.325) and a balanced accuracy of 56.2% (95% CI 44.6–67.8). BARS and EPI<italic>bipolar</italic> could not be predicted. In post hoc analyses, regional surface area, subcortical volumes as well as hyperparameter optimization did not improve the performance. Individuals at risk for bipolar disorder, as assessed by BPSS-P, display brain structural alterations that can be detected using machine learning. The achieved performance is comparable to previous studies which attempted to classify patients with manifest disease and healthy controls. Unlike previous studies of bipolar risk, our multicenter design permitted a leave-one-site-out crossvalidation. Whole brain cortical thickness seem to be superior to other structural brain features.
Quantitative immunopeptidomics reveals a tumor stroma–specific target for T cell therapy
2022-08-31

T cell receptor (TCR)–based immunotherapy has emerged as a promising therapeutic approach for the treatment of patients with solid cancers. Identifying peptide–human leukocyte antigen (pHLA) complexes highly presented on tumors and rarely expressed on healthy tissue in combination with high-affinity TCRs that when introduced into T cells can redirect T cells to eliminate tumor but not healthy tissue is a key requirement for safe and efficacious TCR-based therapies. To discover promising shared tumor antigens that could be targeted via TCR-based adoptive T cell therapy, we employed population-scale immunopeptidomics using quantitative mass spectrometry across ~1500 tumor and normal tissue samples. We identified an HLA-A*02:01-restricted pan-cancer epitope within the collagen type VI α-3 ( COL6A3 ) gene that is highly presented on tumor stroma across multiple solid cancers due to a tumor-specific alternative splicing event that rarely occurs outside the tumor microenvironment. T cells expressing natural COL6A3-specific TCRs demonstrated only modest activity against cells presenting high copy numbers of COL6A3 pHLAs. One of these TCRs was affinity-enhanced, enabling transduced T cells to specifically eliminate tumors in vivo that expressed similar copy numbers of pHLAs as primary tumor specimens. The enhanced TCR variants exhibited a favorable safety profile with no detectable off-target reactivity, paving the way to initiate clinical trials using COL6A3-specific TCRs to target an array of solid tumors.
Increase in coercive measures in psychiatric hospitals in Germany during the COVID-19 pandemic
2022-08-31

Objective To examine whether the pandemic in 2020 caused changes in psychiatric hospital cases, the percentage of patients exposed to coercive interventions, and aggressive incidents. Methods We used the case registry for coercive measures of the State of Baden-Wuerttemberg, comprising case-related data on mechanical restraint, seclusion, physical restraint, and forced medication in each of the State’s 31 licensed hospitals treating adults, to compare data from 2019 and 2020. Results The number of cases in adult psychiatry decreased by 7.6% from 105,782 to 97,761. The percentage of involuntary cases increased from 12.3 to 14.1%, and the absolute number of coercive measures increased by 4.7% from 26,269 to 27,514. The percentage of cases exposed to any kind of coercive measure increased by 24.6% from 6.5 to 8.1%, and the median cumulative duration per affected case increased by 13.1% from 12.2 to 13.8 hrs, where seclusion increased more than mechanical restraint. The percentage of patients with aggressive incidents, collected in 10 hospitals, remained unchanged. Conclusions While voluntary cases decreased considerably during the pandemic, involuntary cases increased slightly. However, the increased percentage of patients exposed to coercion is not only due to a decreased percentage of voluntary patients, as the duration of coercive measures per case also increased. The changes that indicate deterioration in treatment quality were probably caused by the multitude of measures to manage the pandemic. The focus of attention and internal rules as well have shifted from prevention of coercion to prevention of infection.
The Arabidopsis SAC9 enzyme is enriched in a cortical population of early endosomes and restricts PI(4,5)P2 at the plasma membrane
2022-08-31

Membrane lipids, and especially phosphoinositides, are differentially enriched within the eukaryotic endomembrane system. This generates a landmark code by modulating the properties of each membrane. Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ] specifically accumulates at the plasma membrane in yeast, animal, and plant cells, where it regulates a wide range of cellular processes including endocytic trafficking. However, the functional consequences of mispatterning PI(4,5)P 2 in plants are unknown. Here, we functionally characterized the putative phosphoinositide phosphatase SUPPRESSOR OF ACTIN9 (SAC9) in Arabidopsis thaliana ( Arabidopsis ). We found that SAC9 depletion led to the ectopic localization of PI(4,5)P 2 on cortical intracellular compartments, which depends on PI4P and PI(4,5)P 2 production at the plasma membrane. SAC9 localizes to a subpopulation of trans -Golgi Network/early endosomes that are enriched in a region close to the cell cortex and that are coated with clathrin. Furthermore, it interacts and colocalizes with Src Homology 3 Domain Protein 2 (SH3P2), a protein involved in endocytic trafficking. In the absence of SAC9, SH3P2 localization is altered and the clathrin-mediated endocytosis rate is reduced. Together, our results highlight the importance of restricting PI(4,5)P 2 at the plasma membrane and illustrate that one of the consequences of PI(4,5)P 2 misspatterning in plants is to impact the endocytic trafficking.
Source-based artifact-rejection techniques for TMS–EEG
2022-08-31

Neuronal electroencephalography (EEG) signals arise from the cortical postsynaptic currents. Due to the conductive properties of the head, these neuronal sources produce relatively smeared spatial patterns in EEG. We can model these topographies to deduce which signals reflect genuine TMS-evoked cortical activity and which data components are merely noise and artifacts. This review will concentrate on two source-based artifact-rejection techniques developed for TMS-EEG data analysis, signal-space-projection-source-informed reconstruction (SSP-SIR), and the source-estimate-utilizing noise-discarding algorithm (SOUND). The former method was designed for rejecting TMS-evoked muscle artifacts, while the latter was developed to suppress noise signals from EEG and magnetoencephalography (MEG) in general. We shall cover the theoretical background for both methods, but most importantly, we will describe some essential practical perspectives for using these techniques effectively. We demonstrate and explain what approaches produce the most reliable inverse estimates after cleaning the data or how to perform non-biased comparisons between cleaned datasets. All noise-cleaning algorithms compromise the signals of interest to a degree. We elaborate on how the source-based methods allow objective quantification of the overcorrection. Finally, we consider possible future directions. While this article concentrates on TMS-EEG data analysis, many theoretical and practical aspects, presented here, can be readily applied in other EEG/MEG applications. Overall, the source-based cleaning methods provide a valuable set of TMS-EEG preprocessing tools. We can objectively evaluate their performance regarding possible overcorrection. Furthermore, the overcorrection can always be taken into account to compare cleaned datasets reliably. The described methods are based on current electrophysiological and anatomical understanding of the head and the EEG generators; strong assumptions of the statistical properties of the noise and artifact signals, such as independence, are not needed.
High-resolution sediment analysis reveals Middle Bronze Age byre-houses at the site of Oppeano (Verona province, NE Italy)
2022-08-31

High-resolution sediment analysis allowed us to identify two Middle Bronze Age (MBA 1, 1650–1550 cal a BCE) byre-houses at the waterlogged site of Oppeano “4D”, south of Verona (Veneto region, NE Italy). The site lies in a low-lying valley incised by the Adige River in its LGM alluvial fan. In this fluvio-palustrine environment burial and taphonomic conditions were such that the archaeological record was extremely well preserved. The wooden elements making up basal parts of nine ‘huts’ were in fact exposed at Oppeano, and so were their internal accretion deposits. These featured finely laminated dung units deriving from the stalling of small herbivores, possibly ovicaprids, intercalated with repeated accumulations of wood ash. This was produced in large and multi-stratified hearths that were exposed within each hut. Organic petrology provided evidence of the production of wood tar inside one of the studied structures. At Oppeano 4D it was thus demonstrated that these structures were not just byres or stables, but spaces that housed humans together with animals at least during some periods of the year, hence byre-houses. The identification of byre-houses in a Middle Bronze Age settlement is key for the reconstruction of socio-economic aspects of Bronze Age economy and production systems.
A new ornithopod dinosaur, Transylvanosaurus platycephalus gen. et sp. nov. (Dinosauria: Ornithischia), from the Upper Cretaceous of the Haţeg Basin, Romania
2022-08-31

Augustin, Felix J., Bastiaans, Dylan, Dumbravă, Mihai D., Csiki-Sava, Zoltán (2022): A new ornithopod dinosaur, &lt;i&gt;Transylvanosaurus platycephalus&lt;/i&gt; gen. et sp. nov. (Dinosauria: Ornithischia), from the Upper Cretaceous of the Haţeg Basin, Romania. Journal of Vertebrate Paleontology (e2133610) 42 (2): 1-23, DOI: 10.1080/02724634.2022.2133610, URL: http://dx.doi.org/10.1080/02724634.2022.2133610