julilili42/papers huggingface dataset:
Sentiment Analysis of Comments of American Birders during Two Waves of the COVID-19 Pandemic Reveal More Negative Sentiments in the Context of Birding
2021-12-13

Human–nature relationships are an important aspect of leisure research. Previous studies also reported that nature-related activities have a health benefit. In this study, we surveyed US-American birdwatchers at two time points during the COVID pandemic (independent samples). During the beginning of the COVID pandemic in spring 2020, we analyzed their comments with an AI sentiment analysis. Approximately one year later (winter 2020/21), during the second wave, the study was repeated, and a second data set was analyzed. Here we show that during the ongoing pandemic, the sentiments became more negative. This is an important result because it shows that despite the positive impact of nature on mental health, the sentiments become more negative in the enduring pandemic.
Transnational Network Formation in the Medium of Cultural Magazines
2021-12-13

In this research article, we introduce a methodology we developed in order to collect and analyse data from 42 Spanish-language magazines which were published between 1891 and 1936. The example of the imagery found in these magazines will be used here to illustrate some of the research findings which came out of the project “Blinded for peer review”. In this project, the focus was both on network formation and on the transnational exchanges established by the cultural magazines under scrutiny. Analysis is performed by establishing bimodal networks that enable the examination of transatlantic transfers between Europe and Hispanic America. Beyond the question of transfers, major insights from the project are presented, such as the observation that in the cultural field taste dominates and limits the number of possible connections between contributors and magazines. The limitations of the chosen methodology lie in the explanatory power of centrality measures applied to bimodal networks which provide questionable results with respect to relevant research questions. As a remedy, we propose the use of a ‘cultural transfer rate’ which can easily be calculated from the data established within the project. While the research project had its focus on the cultural exchanges facilitated by Spanish-language magazines, further research avenues which can be explored in the future on the basis of the data provided by the project are also discussed. The first of these avenues consists in transforming the data at hand into one-mode social networks, which would enable the analysis of the social dimensions relevant to the material, especially with regard to groups of artists, and the synergies created within them. The second avenue describes how blockmodeling as an analytic technique can be implemented by the aggregation of further data, thus enabling the differentiation of roles within cultural fields, such as editors, editorial staff, or independent artists.
Differential Proliferative and Cytotoxic Effect of Selected Components ofEssential Oils on Human Glioblastoma Cells
2021-12-13

Background: In the study of bioactive agents from traditional medicine, mono- and sesquiterpenes represent the main ingredients of essential oils. Till now, only thymoquinone and perillyl alcohol have been clinically tested on glioblastoma. Objective: In the present study, we examined the effect of ten different essential oils on three human glioblastoma cell lines and one healthy human cell line. Methods: We used confocal laser scanning microscopy, flow cytometry, and cell growth analysis to evaluate cell morphology changes, membrane disruption effects, acute cytotoxicity and effects on the proliferation rate caused by the essential oils pinene, geraniol, eucalyptol, perillaldehyde, limonene, and linalool, perillyl alcohol, myrcene, bisabolol and valencene on human cells. Caspase 3/7 activity was measured to observe apoptosis induced by the essential oils. Results: We found that the cytotoxicity concentrations varied not only between different essential oils but also among different cell lines. Acute cytotoxicity of essential oils was based on cell membrane disruption and that HEK cells were affected to a much higher degree than the Glioblastoma cells. Vacuoles found in surviving glioblastoma cells appeared to be a factor in this effect. Conclusion: Caspase activity did not correlate with the membrane damage observed in the flow cytometry experiments. This is especially evident in the HEK cells that only showed apoptosis with two out of ten essential oils. Comparison of the effects of other essential oil to perillyl alcohol, which is already used in glioblastoma therapy, revealed perillaldehyde and valencene as two new candidate substances that showed even stronger anti-glioblastoma effects in all experiments.
Platelet ACKR3/CXCR7 favors antiplatelet lipids over an atherothrombotic lipidome and regulates thromboinflammation
2021-12-14

Abstract Platelet ACKR3/CXCR7 surface expression is enhanced and influences prognosis in coronary artery disease (CAD) patients, who exhibit a distinct atherothrombotic platelet lipidome. Current investigation validates the potential of ACKR3/CXCR7 in regulating thromboinflammatory response through its impact on the platelet lipidome. CAD patients with enhanced platelet ACKR3/CXCR7 expression exhibited reduced aggregation. Pharmacological CXCR7 agonist (VUF11207) significantly reduced prothrombotic platelet response in blood from acute coronary syndrome patients ex vivo. CXCR7 agonist administration reduced thrombotic functions and thromboinflammatory plateletleukocyte interactions post–myocardial infarction and arterial injury in vivo. ACKR3/CXCR7 ligation did not affect surface availability of surface receptors, coagulation profile, bleeding time, plasma-dependent thrombin generation (thrombinoscopy), or clot formation (thromboelastography) but counteracted activation-induced phosphatidylserine exposure and procoagulant platelet-assisted thrombin generation. Targeted (micro-UHPLC-ESI-QTrap-MS/MS) and untargeted (UHPLCESI-QTOF-MS/MS) lipidomics analysis revealed that ACKR3/CXCR7 ligation favored generation of antithrombotic lipids (dihomo-γ-linolenic acid [DGLA], 12-hydroxyeicosatrienoic acid [12-HETrE]) over cyclooxygenase-1 (COX-1) or 12-lipoxygenase (12-LOX) metabolized prothrombotic and phospholipase-derived atherogenic lipids in healthy subjects and CAD patients, contrary to antiplatelet therapy. Through 12-HETrE, ACKR3/CXCR7 ligation coordinated with Gαs-coupled prostacyclin receptor to trigger cyclic adenosine monophosphate/protein kinase A–mediated platelet inhibition. ACKR3/CXCR7 ligation reduced generation of lipid agonists and lipid signaling intermediates, which affected calcium mobilization, intracellular signaling, and consequently platelet interaction with physiological matrices and thromboinflammatory secretome. This emphasized its functional dichotomy from prothrombotic CXCR4. Moreover, CXCR7 agonist regulated heparin-induced thrombocytopenia–sera/immunoglobulin G–triggered platelet and neutrophil activation, heparin-induced platelet aggregation, generation of thromboinflammatory lipids, platelet-neutrophil aggregate formation, and thromboinflammatory secretion ex vivo. Therefore, ACKR3/CXCR7 may offer a novel therapeutic strategy in acute/chronic thromboinflammation exaggerated cardiovascular pathologies and CAD.
Fungal–Mineral Interactions Modulating Intrinsic Peroxidase-like Activity of Iron Nanoparticles: Implications for the Biogeochemical Cycles of Nutrient Elements and Attenuation of Contaminants
2021-12-14

Fungal-mediated extracellular reactive oxygen species (ROS) are essential for biogeochemical cycles of carbon, nitrogen, and contaminants in terrestrial environments. These ROS levels may be modulated by iron nanoparticles that possess intrinsic peroxidase (POD)-like activity (nanozymes). However, it remains largely undescribed how fungi modulate the POD-like activity of the iron nanoparticles with various crystallinities and crystal facets. Using well-controlled fungal-mineral cultivation experiments, here, we showed that fungi possessed a robust defect engineering strategy to modulate the POD-like activity of the attached iron minerals by decreasing the catalytic activity of poorly ordered ferrihydrite but enhancing that of well-crystallized hematite. The dynamics of POD-like activity were found to reside in molecular trade-offs between lattice oxygen and oxygen vacancies in the iron nanoparticles, which may be located in a cytoprotective fungal exoskeleton. Together, our findings unveil coupled POD-like activity and oxygen redox dynamics during fungal-mineral interactions, which increase the understanding of the catalytic mechanisms of POD-like nanozymes and microbial-mediated biogeochemical cycles of nutrient elements as well as the attenuation of contaminants in terrestrial environments.
Transcriptional Active Parvovirus B19 Infection Predicts Adverse Long-Term Outcome in Patients with Non-Ischemic Cardiomyopathy
2021-12-14

Parvovirus B19 (B19V) is the predominant cardiotropic virus currently found in endomyocardial biopsies (EMBs). However, direct evidence showing a causal relationship between B19V and progression of inflammatory cardiomyopathy are still missing. The aim of this study was to analyze the impact of transcriptionally active cardiotropic B19V infection determined by viral RNA expression upon long-term outcomes in a large cohort of adult patients with non-ischemic cardiomyopathy in a retrospective analysis from a prospective observational cohort. In total, the analyzed study group comprised 871 consecutive B19V-positive patients (mean age 50.0 ± 15.0 years) with non-ischemic cardiomyopathy who underwent EMB. B19V-positivity was ascertained by routine diagnosis of viral genomes in EMBs. Molecular analysis of EMB revealed positive B19V transcriptional activity in n = 165 patients (18.9%). Primary endpoint was all-cause mortality in the overall cohort. The patients were followed up to 60 months. On the Cox regression analysis, B19V transcriptional activity was predictive of a worse prognosis compared to those without actively replicating B19V (p = 0.01). Moreover, multivariable analysis revealed transcriptional active B19V combined with inflammation [hazard ratio 4.013, 95% confidence interval 1.515–10.629 (p = 0.005)] as the strongest predictor of impaired survival even after adjustment for age and baseline LVEF (p = 0.005) and independently of viral load. The study demonstrates for the first time the pathogenic clinical importance of B19V with transcriptional activity in a large cohort of patients. Transcriptionally active B19V infection is an unfavourable prognostic trigger of adverse outcome. Our findings are of high clinical relevance, indicating that advanced diagnostic differentiation of B19V positive patients is of high prognostic importance.
Neural processing associated with cognitive empathy in pedophilia and child sexual offending
2021-12-14

Abstract Behavioral studies found evidence for superior cognitive empathy (CE) in pedophilic men without a history of child sexual offending (P − CSO) compared to pedophilic men with a history of child sexual offending (P + CSO). Functional magnetic resonance imaging (fMRI) studies also point to differences between P − CSO and P + CSO. Neural processing associated with CE has not yet been investigated. Therefore, the present study aimed to explore the neural correlates of CE in subjects with pedophilia with (P + CSO) and without (P − CSO) child sexual offending. 15 P + CSO, 15 P − CSO and 24 teleiophilic male controls (TC) performed a CE task during fMRI. We observed reduced activation in the left precuneus (Pcu) and increased activation in the left anterior cingulate cortex (ACC) in P − CSO compared to P + CSO. P − CSO also showed stronger connectivity between these regions, which might reflect a top-down modulation of the Pcu by the ACC toward an increased self-focused emotional reaction in social situations. There was also evidence for increased right superior temporal gyrus activation in P − CSO that might constitute a potentially compensatory recruitment due to the dampened Pcu activation. These findings provide first evidence for altered neural processing of CE in P − CSO and underline the importance of addressing CE in pedophilia and CSO in order to uncover processes relevant to effective prevention of child sexual abuse.
Socio-Emotional Skills and the Socioeconomic Achievement Gap
2021-12-14

Empirical evidence suggests that children's socio-emotional skills—an important determinant of school achievement—vary by socio-economic family background. In this study, we assessed the degree to which differences in socio-emotional skills contribute to the achievement gap between socioeconomically advantaged and disadvantaged children. We used data on 74 countries from the 2018 Programme for International Student Assessment (PISA), which contains an extensive set of psychological measures, including growth mindset, self-efficacy, and work mastery. We developed three conceptual scenarios to analyze the role of socio-emotional skills in learning inequality: simple accumulation, multiplicative accumulation, and compensatory accumulation. Our findings are in line with the simple accumulation scenario: socioeconomically advantaged children have somewhat higher levels of socio-emotional skills than their disadvantaged peers, but the effect of these skills on academic performance is largely similar for both groups. Using a counterfactual decomposition method, we show that the measured socio-emotional skills explain no more than 8.8% of the socioeconomic achievement gap. Based on these findings, we argue that initiatives to promote social and emotional learning (SEL) are unlikely to substantially reduce educational inequalities.
Pitfalls in Sleep and Memory Research and How to Avoid Them: A Consensus Paper
2021-12-14

Understanding the complex relationship between sleep and memory is a major challenge in neuroscience. Thousands of studies on memory consolidation in humans suggest that sleep triggers offline memory processes, resulting in less forgetting of declarative memory and performance stabilization in non-declarative memory. However, an increasing number of contradictory findings reveal potential issues with how research is conducted in this field and call into question the reliability and interpretation of the results. In this consensus paper, we describe four sets of prevalent methodological pitfalls in human sleep and memory research: (i) non-optimal experimental designs, (ii) task complexity, (iii) fatigue effects in repetitive tasks, and (iv) inappropriate data analysis practices. We then offer solutions to each of these pitfalls. We believe that implementing these solutions in future research of sleep and memory will lead to more reliable results and significantly advance our understanding in this field.
Diversity, Identity, Oppression: The Construction of “Blackness” in Dear White People
2021-12-14

Abstract In the series Dear White People (DWP), students at the fictional University of Winchester struggle for racial justice. We analyze how the series treats “race” and racism and how this relates to contemporary debates in the United States. While the series presents an imaginary environment, we recognize strong similarities to actual student life and students grappling with various experiences of oppression including sexual violence. We draw on theories of identity formation (Margalit and Raz; Vondermaßen; Young) and intersectionality (Crenshaw; Collins) to uncover how the series portrays and complicates “Blackness” as an identity-forming experience and as an experience shaped by converging forms of structural discrimination. While we highlight the merit of combining two theoretical approaches (one of identity formation and one of oppression), we note that especially intersectionality helped uncover a major blind spot of the series. Although Black women are at the center of the series and the struggle for racial equality at Winchester, their particular experiences of violence are marginalized in seasons 1–3. This tendency to overlook the experiences of Black women reflects the larger debate around race, racism, and movements for social justice.
The Transmembrane Receptor TIRC7 Identifies a Distinct Subset of Immune Cells with Prognostic Implications in Cholangiocarcinoma
2021-12-14

Cholangiocarcinoma (CCA) is a heterogeneous malignancy with a dismal prognosis. Therapeutic options are largely limited to surgery and conventional chemotherapy offers limited benefit. As immunotherapy has proven highly effective in various cancer types, we have undertaken a quantitative immunohistopathological assessment of immune cells expressing the immunoinhibitory T cell immune response cDNA 7 receptor (TIRC7), an emerging immunoinhibitory receptor, in a cohort of 135 CCA patients. TIRC7+ immune cells were present in both the tumor epithelia and stroma in the majority of CCA cases with the highest levels found in intrahepatic CCA. While intraepithelial density of TIRC7+ immune cells was decreased compared to matched non-neoplastic bile ducts, stromal quantity was higher in the tumor samples. Tumors exhibiting signet ring cell or adenosquamous morphology were exclusively associated with an intraepithelial TIRC7+ phenotype. Survival analysis showed intraepithelial TIRC7+ immune cell density to be a highly significant favorable prognosticator in intrahepatic but not proximal or distal CCA. Furthermore, intraepithelial TIRC7+ immune cell density correlated with the number of intraepithelial CD8+ immune cells and with the total number of CD4+ immune cells. Our results suggest the presence and prognostic relevance of TIRC7+ immune cells in CCA and warrant further functional studies on its pharmacological modulation.
A unified model for the biogenesis of mitochondrial outer membrane multi-span proteins
2021-12-14

Abstract The mitochondrial outer membrane (MOM) harbors proteins that traverse the membrane via several helical segments, so-called multi-span proteins. Two contradicting mechanisms were suggested to describe their integration into the MOM. The first proposes that the m itochondrial im port (MIM) complex facilitates this process and functions as an insertase, whereas the second suggests that such proteins can integrate into the lipid phase without the assistance of import factors in a process that is enhanced by phosphatidic acid. To resolve this discrepancy and obtain new insights on the biogenesis of these proteins, we addressed this issue using yeast mitochondria and the multi-span protein Om14. Testing different truncation variants, we show that only the full-length protein contains all the required information that assure targeting specificity. Employing a specific insertion assay and several single and double deletion strains, we show that neither the import receptor Tom70 nor any other protein with a cytosolically exposed domain have a crucial contribution to the biogenesis process. We further demonstrate that Mim1 and Porin are required for optimal membrane integration of Om14 but none of them is absolutely required. Unfolding of the newly synthesized protein, its optimal hydrophobicity, as well as higher fluidity of the membrane dramatically enhanced the import capacity of Om14. Collectively, our findings suggest that MOM multi-span proteins can follow different biogenesis pathways in which proteinaceous elements and membrane behavior contribute to a variable extent to the combined efficiency. Summary Zhou et al. provide new insights to the biogenesis of mitochondrial outer membrane proteins. They demonstrate that such proteins can follow various routes where both proteinaceous elements and membrane behavior regulate the efficiency and specificity of this process.
PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
2021-12-15

ABSTRACT Plant-beneficial microorganisms are gaining importance for sustainable plant production and phytosanitary practices. Yet there is a lack of computational approaches targeting bacterial traits associated with plant growth-promotion (PGP), which hinders the in-silico identification, comparison, and selection of phytostimulatory bacterial strains. To address this problem, we have developed the new web resource PLaBAse (v1.01, http://plabase.informatik.uni-tuebingen.de/pb/plabase.php ), which provides a number of services, including (i) a database for screening 5,565 plant-associated bacteria (PLaBA-db), (ii) a tool for predicting plant growth-promoting traits (PGPTs) of single bacterial genomes (PGPT-Pred), and (iii) a tool for the prediction of bacterial plant-association by marker gene identification (PIFAR-Pred). The latter was developed by Martínez-García et al. and is now hosted at University of Tuebingen. The PGPT-Pred tool is based on our new PGPT ontology, a literature- and OMICs-curated, comprehensive, and hierarchical collection of ∼6,900 PGPTs that are associated with 6,965,955 protein sequences. To study the distribution of the PGPTs across different environments, we applied it to 70,540 bacterial strains associated with (i) seven different environments (including plants), (iii) five different plant spheres (organs), and (iii) two bacteria-induced plant phenotypes. This analysis revealed that plant-symbiotic bacteria generally have a larger genome size and a higher count of PGPT-annotated protein encoding genes. Obviously, not all reported PGPTs are restricted to -or only enriched in-plant-associated and plant symbiotic bacteria. Some also occur in human- and animal-associated bacteria, perhaps due to the transmission of PGP bacteria (PGPBs) between environments, or because some functions are involved in adaption processes to various environments. Here we provide an easy-to-use approach for screening of PGPTs in bacterial genomes across various phyla and isolation sites, using PLaBA-db, and for standardized annotation, using PGPT-Pred. We believe that this resource will improve our understanding about the entire PGP processes and facilitate the prediction of PGPB as bio-inoculants and for biosafety strategies, so as to help to establish sustainable and targeted bacteria-incorporated plant production systems in the future.
Thick toroidal configurations around scalarized Kerr black holes
2021-12-15

In this work we aim to investigate thick tori configurations around Kerr black holes with scalar hair (KBHsSH). For that goal, we provide a first approach using constant specific angular momentum non-self-gravitating Polish doughnuts. Through a series of examples, we show the feasibility of new topologies, such as double-centered tori with two cusps as well as similar structures as the ones found for rotating boson stars (BSs), namely, tori endowed with two centers and a single cusp. These KBHsSH solutions are also shown to possibly house static surfaces, associated with the static rings present in these spacetimes. Through this paper we highlight the differences between these fluid configurations when housed by some KBHsSH examples, standard Kerr black holes and rotating BSs.
Biogeochemical Niches of Fe-Cycling Communities Influencing Heavy Metal Transport along the Rio Tinto, Spain
2021-12-15

The estuary of the Rio Tinto is a unique environment in which extremely acidic, heavy metal-rich, and especially iron-rich river water is mixed with seawater. Due to the mixing events, the estuarine water is characterized by a low pH, almost seawater salinity, and high concentrations of bioavailable iron.