julilili42/papers huggingface dataset:
The Earliest Tools and Cultures of Hominins
2023-02-23

Abstract This chapter critically discusses the earliest tools and cultures of hominins—the species most closely related to humans. It starts with an inferred organic tool age that would have already existed before the split of hominins from the ape lineage. It then examines the two currently fully established earliest instances of the stone tool age—the Oldowan and Acheulean. Contrary to prevalent assumptions, the cultural status of the Oldowan and most or all of the Acheulean (and the organic tool age) may have been that of ‘minimal culture’. Minimal culture shares with modern human culture and animal culture influences of some social learning types—for example, on frequencies of behaviours and tools—but, unlike human culture, it excludes cultural transmission of novel—supra-individual—behavioural and/or artefact know-how. If true, cumulative cultural transmission of know-how to supra-individual levels would then have started much later than is currently presumed.
Genetics and Justice, Non-Ideal Theory and the Role of Patents: The Case of CRISPR-Cas9
2023-02-23

There are ongoing concerns of social justice regarding inequalities in the distribution of access to potential genome editing technologies. Working within non-ideal theory, Colin Farrelly advances a justification for the use of patents to speed up the arrival of safe and effective interventions for all, including the socially disadvantaged. This chapter argues that such success is less assured when one considers the actual functioning of patents and the practical implications of the patent system in the context of biotechnological innovations. I suggest that non-ideal theoretical approaches risk reverting back to a form of ideal theory if they simply refer to such real-world constraints — e.g. patents — but do not critically assess and fully examine how such constraints manifest themselves in practice. I highlight some considerations that would be important in order to develop and foster a more robust non-ideal approach to justice in biotechnological developments.
Erosion Modelling Indicates a Decrease in Erosion Susceptibility of Historic Ridge and Furrow Fields Near Albershausen, Southern Germany
2023-02-23

Ridge and furrow fields are land-use-related surface structures that are widespread in Europe and represent a geomorphological key signature of the Anthropocene. Previous research has identified various reasons for the intentional and unintentional formation of these structures, such as the use of a mouldboard plough, soil improvement and drainage. We used GIS-based quantitative erosion modelling according to the Universal Soil Loss Equation (USLE) to calculate the erosion susceptibility of a selected study area in Southern Germany. We compared the calculated erosion susceptibility for two scenarios: (1) the present topography with ridges and furrows and (2) the smoothed topography without ridges and furrows. The ridges and furrows for the studied site reduce the erosion susceptibility by more than 50% compared to the smoothed surface. Thus, for the first time, we were able to identify lower soil erosion susceptibility as one of the possible causes for the formation of ridge and furrow fields. Finally, our communication paper points to future perspectives of quantitative analyses of historical soil erosion.
Bayesian Advice Taking: Adaptive Strategy Selection in Sequential Advice Seeking
2023-02-23

In sampling approaches to advice taking, participants can sequentially sample multiple pieces of advice before making a final judgment. To contribute to the understanding of active advice seeking, we develop and compare different strategies for information integration from external sources, including Bayesian belief updating. In a reanalysis of empirical data, we find that participants most frequently compromise between their initial beliefs and the distributions of multiple pieces of advice sampled from others. Moreover, across all participants, compromising predicts their final beliefs better than choosing one of the two sources of information. However, participants’ willingness to integrate external opinions is relatively higher for multiple pieces of reasonably distant as compared to close advice. Nevertheless, egocentrism is as pronounced as in the traditional paradigm where only a single piece of external evidence is provided. Crucially, there are large inter- and intra-individual differences in strategy selection for sequential advice taking. On the one hand, some participants choose their own or others’ judgments more often, and other participants are better described as compromisers between internal and external sources of information. On the other hand, virtually all participants apply different advice taking strategies for different items and trials. Our findings constitute initial evidence of the adaptive utilization of multiple, sequentially sampled external opinions.
Consensus Messaging in Climate Change Communication: Metacognition as Moderator Variable in the Gateway Belief Model
2023-02-23

The issue of anthropogenic climate change is one of the most pressing challenges for society. Thus, the development of efficient strategies to increase the public's awareness of climate change is essential. Previous research has shown that one such strategy, consensus messaging, can correct peoples' misconceptions about their estimation of scientific consensus concerning climate change and increase, for example, their support for measures against global warming. Given the importanceof developing reliable strategies, understanding the circumstances under which consensus messaging does and does not work is crucial. Thus, the present study investigated confidence in perceived scientific consensus (PSC) as a moderator variable in the consensus messaging process, using a national representative US sample (N = 898). More specifically, we investigated the role of confidence in PSC for (i) the debiasing process, i.e., the integration of the consensus message into theestimation of scientific consensus, and (ii) the updating process of climate change attitudes (belief in climate change, worry about climate change, and human causation of climate change). Results showed that confidence in PSC significantly predicts how much participants updated their PSC toward the consensus. We replicated those results for a high-consensus country (N = 1110,representative German sample). Furthermore, confidence in PSC played a moderating role in updating participants’ beliefs in the human causation of climate change. Our findings suggest climate change related metacognition to be an important factor explaining the formation and updating of corresponding beliefs and highlight the importance of considering metacognitive aspects of climatechange communication strategies.
The 3D Digital Documentation of Shaft K24 in Saqqara
2023-02-23

In our contribution we discuss in detail the three-dimensional digital documentation strategy of the intact burial chambers of Shaft K24 of the recently discovered mummification workshop complex by the Saqqara Saite Tombs Project (SSTP). This 30 m deep shaft served as a communal burial site. In six tombs dug into the walls of the shaft at different depths, a large number of significant archaeological materials were found in situ. After an introduction to the project, we discuss the different 3D technologies, which we used to document the site and the excavation process, highlighting their advantages and disadvantages. Besides the technical description, a main focus of the paper will be the influence of 3D documentation on the research and conservation processes.
Extensive re-modelling of the cell wall during the development ofStaphylococcus aureusbacteraemia
2023-02-23

Introductory Paragraph / Abstract The bloodstream represents a hostile environment that bacteria must overcome to cause bacteraemia. To understand how the major human pathogen Staphylococcus aureus manages this we have utilised a functional genomics approach to identify a number of new loci that affect the ability of the bacteria to survive exposure to serum, the critical first step in the development of bacteraemia. The expression of one of these genes, tcaA, was found to be induced upon exposure to serum, and we show that it is involved in the elaboration of a critical virulence factor, the wall teichoic acids (WTA), within the cell envelope. The activity of the TcaA protein alters the sensitivity of the bacteria to cell wall attacking agents, including antimicrobial peptides, human defence fatty acids, and several antibiotics. This protein also affects the autolytic activity and lysostaphin sensitivity of the bacteria, suggesting that in addition to changing WTA abundance in the cell envelope, it also plays a role in peptidoglycan crosslinking. With TcaA rendering the bacteria more susceptible to serum killing, while simultaneously increasing the abundance of WTA in the cell envelope, it was unclear what effect this protein may have during infection. To explore this, we examined human data and performed murine experimental infections. Collectively, our data suggests that whilst mutations in tcaA are selected for during bacteraemia, this protein positively contributes to the virulence of S. aureus through its involvement in altering the cell wall architecture of the bacteria, a process that appears to play a key role in the development of bacteraemia.
HilE represses the activity of HilD via a mechanism distinct from that of intestinal long-chain fatty acids
2023-02-23

Abstract The expression of virulence factors essential for the invasion of host cells by Salmonella enterica is tightly controlled by a network of transcription regulators. The AraC/XylS transcription factor HilD is the main integration point of environmental signals into this regulatory network, with many factors affecting HilD activity. Long chain fatty acids (LCFAs), which are highly abundant throughout the host intestine directly bind to, and repress HilD, acting as environmental cues to coordinate virulence gene expression. The regulatory protein HilE also negatively regulates HilD activity, through a protein-protein interaction. Both of these regulators inhibit HilD dimerisation, preventing HilD from binding to target DNA. We investigated the structural basis of these mechanisms of HilD repression. LCFAs bind to a conserved pocket in HilD, in a comparable manner to that reported for other AraC/XylS regulators, whereas HilE forms a stable heterodimer with HilD by binding to the HilD dimerisation interface. Our results highlight two distinct mechanisms by which HilD activity is repressed, which could be exploited for the development of new antivirulence leads.
A fluid inclusion and stable-isotope study of hydrothermal vein mineralization, Schwarzwald district, Germany
2023-02-23

A combined fluid inclusion and stable isotope study has been carried out on over 180 individual samples from 89 post-Variscan hydrothermal veins (Pb-Zn-Cu-bearing fluorite-barite-quartz veins, Co-Ni-Ag-Bi-U-bearing barite-fluorite-quartz veins and barren barite-fluorite-quartz veins) from the Schwarzwald district, Germany. The salinities of fluid inclusions in post-Variscan primary fluorite, calcite, barite and quartz are in the range of 22–25 wt.% equivalent (eqv.) NaCl, and the eutectic temperatures range between –57 and –45°C, indicating the presence of H2O-NaCl-CaCl2 fluids. Homogenization temperatures vary from 130 to 180°C. A low-salinity fluid (0 to 15 wt.% eqv. NaCl) was observed in some late stage fluorite, calcite and quartz samples, which were trapped similar temperature, range of high salinity fluids.&#x0D; Raman microprobe analyses show that the only detectable volatile in the vapour is CO2. Almost all δ18O (n=86) measurements of quartz from the fluorite-bearing post-Variscan veins range between +11.1 and +20.9 ‰. The calculated δ18OH2O values are between –11.0 and +4.4 ‰, using known quartz-water fractionation and fluid inclusion homogenization temperatures. The δ18OH2O values of directly extracted fluid inclusion water of fluorites range from –11.6 to +1.1 ‰, very consistent with the calculated values. The δD values of fluid inclusion water in calcites (extracted from primary and late calcite samples) lie in a narrower range between –26 and –15 ‰. The extracted fluid inclusion water from quartz samples has significantly more variable δD values between –63 and +9 ‰. The δ13C and δ18O values of fluid inclusion gas (CO2) range between –21.4 and –6.7 ‰ and between –16.3 to –7.1 ‰, respectively.&#x0D; Calculations for fluorite-barite-quartz veins combining oxygen isotope equilibria with microthermometric data result in quartz precipitation temperatures of 120–170°C at pressures between 0.3 to 0.5 kbar. The δ18OH2O and δD data, particularly the observed wide range in hydrogen isotopic compositions, indicate that the hydrothermal mineralization formed through large-scale mixing of a basement-derived saline NaCl-CaCl2 brine with meteoric water.
Manipulation of plant metabolism by pathogen effectors: more than just food
2023-02-24

Abstract To successfully infect plants, pathogens secrete effector proteins to the plant apoplast or inside plant cells, where they suppress plant immunity or interfere with other cellular processes to facilitate infection. Plant metabolism is crucial for most cellular processes and plays a key role in defense against pathogens, making it a major target for pathogen effectors. Effector proteins manipulate host metabolism to provide the pathogen with nutrients or to indirectly suppress plant chemical defense responses. Recent studies have shown that pathogens also utilize effectors to shape the microbiota composition by altering the concentration of certain plant metabolites. Here, we summarize current knowledge on the manipulation of plant metabolism by pathogen effectors. We also discuss what remains unknown regarding the manipulation of host metabolism by pathogen effectors.
Mesenchymal stem cell-released oncolytic virus: an innovative strategy for cancer treatment
2023-02-24

Abstract Oncolytic viruses (OVs) infect, multiply, and finally remove tumor cells selectively, causing no damage to normal cells in the process. Because of their specific features, such as, the ability to induce immunogenic cell death and to contain curative transgenes in their genomes, OVs have attracted attention as candidates to be utilized in cooperation with immunotherapies for cancer treatment. This treatment takes advantage of most tumor cells' inherent tendency to be infected by certain OVs and both innate and adaptive immune responses are elicited by OV infection and oncolysis. OVs can also modulate tumor microenvironment and boost anti-tumor immune responses. Mesenchymal stem cells (MSC) are gathering interest as promising anti-cancer treatments with the ability to address a wide range of cancers. MSCs exhibit tumor-trophic migration characteristics, allowing them to be used as delivery vehicles for successful, targeted treatment of isolated tumors and metastatic malignancies. Preclinical and clinical research were reviewed in this study to discuss using MSC-released OVs as a novel method for the treatment of cancer.
MEK inhibitors as novel host-targeted antivirals with a dual-benefit mode of action against hyperinflammatory respiratory viral diseases
2023-02-24

Acute hyperinflammatory virus infections, such as influenza or coronavirus disease-19, are still a major health burden worldwide. In these diseases, a massive overproduction of pro-inflammatory cytokines and chemokines (cytokine storm syndrome) determine the severity of the disease, especially in late stages. Direct-acting antivirals against these pathogens have to be administered very early after infection to be effective and may induce viral resistance. Here, we summarize data on a host-targeted strategy using inhibitors of the cellular Raf/MEK/ERK kinase cascade that not only block replication of different RNA viruses but also suppress the hyperinflammatory cytokine response upon infection. In the first phase-II clinical trial of that approach, the MEK inhibitor Zapnometinib shows evidence of clinical benefit.
State of the Art of Molecular Visualization in Immersive Virtual Environments
2023-02-24

Abstract Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head‐mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.
Efficient PFAS prioritization in non-target HRMS data: systematic evaluation of the novel MD/C-m/C approach
2023-02-24

Abstract Non-target screening (NTS) based on high-resolution mass spectrometry (HRMS) is necessary to comprehensively characterize per- and polyfluoroalkyl substances (PFAS) in environmental, biological, and technical samples due to the very limited availability of authentic PFAS reference standards. Since in trace analysis, MS/MS information is not always achievable and only selected PFAS are present in homologous series, further techniques to prioritize measured HRMS data (features) according to their likelihood of being PFAS are highly desired due to the importance of efficient data reduction during NTS. Kaufmann et al. ( J AOAC Int , 2022) presented a very promising approach to separate selected PFAS from sample matrix features by plotting the mass defect (MD) normalized to the number of carbons (MD/C) vs. mass normalized to the number of C (m/C). We systematically evaluated the advantages and limitations of this approach by using ~ 490,000 chemical formulas of organic chemicals (~ 210,000 PFAS, ~ 160,000 organic contaminants, and 125,000 natural organic matter compounds) and calculating how efficiently, and especially which, PFAS can be prioritized. While PFAS with high fluorine content (approximately: F/C &gt; 0.8, H/F &lt; 0.8, mass percent of fluorine &gt; 55%) can be separated well, partially fluorinated PFAS with a high hydrogen content are more difficult to prioritize, which we discuss for selected PFAS. In the MD/C-m/C approach, even compounds with highly positive MDs above 0.5 Da and hence incorrectly assigned to negative MDs can still be separated from true negative mass defect features by the normalized mass (m/C). Furthermore, based on the position in the MD/C-m/C plot, we propose the estimation of the fluorine fraction in molecules for selected PFAS classes. The promising MD/C-m/C approach can be widely used in PFAS research and routine analysis. The concept is also applicable to other compound classes like iodinated compounds. Graphical Abstract
MeganServer: facilitating interactive access to metagenomic data on a server
2023-02-24

Abstract Motivation Metagenomic projects often involve large numbers of large sequencing datasets (totaling hundreds of gigabytes of data). Thus, computational preprocessing and analysis are usually performed on a server. The results of such analyses are then usually explored interactively. One approach is to use MEGAN, an interactive program that allows analysis and comparison of metagenomic datasets. Previous releases have required that the user first download the computed data from the server, an increasingly time-consuming process. Here, we present MeganServer, a stand-alone program that serves MEGAN files to the web, using a RESTful API, facilitating interactive analysis in MEGAN, without requiring prior download of the data. We describe a number of different application scenarios. Availability and implementation MeganServer is provided as a stand-alone program tools/megan-server in the MEGAN software suite, available at https://software-ab.cs.uni-tuebingen.de/download/megan6. Source is available at: https://github.com/husonlab/megan-ce/tree/master/src/megan/ms. Supplementary information Supplementary data are available at Bioinformatics online.
Is learning a logographic script easier than reading an alphabetic script for German children with dyslexia?
2023-02-24

Purpose Developmental dyslexia in alphabetic languages (DD) is characterized by a phonological deficit. Since logographic scripts rely predominantly on visual and morphological processing, reading performance in DD can be assumed to be less impaired when reading logographic scripts. Methods 40 German-speaking children (18 with DD, 22 not reading-impaired—group C; 9–11 years) received Chinese lessons. Eye movements (EM) were recorded during naming single alphabetic words, pictures (confrontational) and Chinese characters to be named in German and Chinese. The main outcome variables were: Articulation latency, numbers and durations of fixations. Quality of life (QoL) was assessed by questionnaires. Results While reading alphabetic words, articulation latencies and numbers of fixations were significantly higher for group DD than for group C (AL-DD = 1.13, AL-C = 0.84, p&lt; .001; FN-DD = 3.50; FN-C = 2.00, p&lt; .001). For naming pictures and Chinese characters in German and in Chinese, no significant group differences were found for any of the EM variables. The percentage of correct answers was high for German naming (DD = 86.67%, C = 95.24%; p = .015) and lower for Chinese naming in both groups, but significantly lower in group DD, especially for Chinese naming (DD = 56.67%, C: 83.77%; p = .003). QoL differed between groups from the children’s perspective only at posttest. Parents of group DD perceived their children`s QoL to be lower compared with parents of group C at pre- and posttest. Conclusions Children with dyslexia performed as well as group C during naming Chinese characters in German and in Chinese regarding their EM variables, presumably because they processed Chinese characters by the visuo-spatial pathway with direct access to the semantic system. However, the significantly lower percentage of correct answers especially during Chinese naming showed that group DD had more difficulties naming Chinese characters than group C, which could be attributed to their phonological deficit, among other factors. Trial registration German clinical trials register ( DRKS00015697 ).