julilili42/papers huggingface dataset:
Data from: Effects of plastic fragments on plant performance are mediated by soil properties and drought
2022-10-19

In recent years, the effects of plastic contamination on soil and plants have received growing attention. Plastic can affect soil water content and thus may interact with the effects of drought on soil and plants. However, the effects of plastic on soil are highly context-dependent, and interactions with drought have been hardly tested. We conducted two greenhouse experiments to test the combined effects of plastic fragments (of varying size and concentration), water availability and soil texture, on soil water content and performance of the plant <em>Arabidopsis thaliana</em>. Plastic fragments had stronger negative effects on soil water content in low water availability, and the shape of this response (linear <em>vs.</em> unimodal) was mediated by soil texture. Conversely, increasing concentration of plastic had positive effects on plant growth. We suggest that plastic fragments introduce fracture points within soil aggregates. This increases number and size of soil pores favoring water loss but also facilitating root growth. Our results suggest complex interactive effects of plastic and drought, that may lead to a decoupling of plant and soil response. These processes should be taken into account in ecological studies and agricultural practices.
Data files for Rivollat et al "Extensive pedigrees reveal the social organisation of a Neolithic community"
2022-10-19

&lt;p&gt;Supporting data for&nbsp;Rivollat et al &quot;Extensive pedigrees reveal social organisation of Neolithic communities&quot; &lt;em&gt;Nature&lt;/em&gt;&nbsp;(2023). https://doi.org/10.1038/s41586-023-06350-8&lt;/p&gt; &lt;p&gt;Binomial_distribution_plots.zip &gt; 4371 files&lt;/p&gt; &lt;p&gt;IBD_degrees.zip &gt; 11 files&lt;/p&gt; &lt;p&gt;Strontium_individual_files.zip &gt;&nbsp;56 files&lt;/p&gt;
Data files for Rivollat et al "Extensive pedigrees reveal the social organisation of a Neolithic community"
2022-10-19

Supporting data for Rivollat et al "Extensive pedigrees reveal social organisation of Neolithic communities" <em>Nature</em> (2023). https://doi.org/10.1038/s41586-023-06350-8 Binomial_distribution_plots.zip &gt; 4371 files IBD_degrees.zip &gt; 11 files Strontium_individual_files.zip &gt; 56 files
Biallelic variants in coenzyme Q10 biosynthesis pathway genes cause a retinitis pigmentosa phenotype
2022-10-20

Abstract The aim of this study was to investigate coenzyme Q10 (CoQ 10 ) biosynthesis pathway defects in inherited retinal dystrophy. Individuals affected by inherited retinal dystrophy (IRD) underwent exome or genome sequencing for molecular diagnosis of their condition. Following negative IRD gene panel analysis, patients carrying biallelic variants in CoQ 10 biosynthesis pathway genes were identified. Clinical data were collected from the medical records. Haplotypes harbouring the same missense variant were characterised from family genome sequencing (GS) data and direct Sanger sequencing. Candidate splice variants were characterised using Oxford Nanopore Technologies single molecule sequencing. The CoQ 10 status of the human plasma was determined in some of the study patients. 13 individuals from 12 unrelated families harboured candidate pathogenic genotypes in the genes: PDSS1, COQ2, COQ4 and COQ5 . The PDSS1 variant c.589 A &gt; G was identified in three affected individuals from three unrelated families on a possible ancestral haplotype. Three variants ( PDSS1 c.468-25 A &gt; G, PDSS1 c.722-2 A &gt; G, COQ5 c.682-7 T &gt; G) were shown to lead to cryptic splicing. 6 affected individuals were diagnosed with non-syndromic retinitis pigmentosa and 7 had additional clinical findings. This study provides evidence of CoQ 10 biosynthesis pathway gene defects leading to non-syndromic retinitis pigmentosa in some cases. Intronic variants outside of the canonical splice-sites represent an important cause of disease. RT-PCR nanopore sequencing is effective in characterising these splice defects.
Birding recreation specialization – A test of the factorial invariance in eight languages
2022-10-20

Birding specialization can be measured alongside a continuum from the beginner to the specialist. The structure of birding specialization has three dimensions: (1) skill/knowledge, (2) behavior, and (3) psychological commitment. We tested the factorial structure and factorial invariance of the birding specialization scale in traditional and simplified Chinese, Finnish, German, Italian, Polish, Portuguese, and Spanish birders. A total of 2,913 (32% women) birdwatchers participated in this study. In all languages, the hierarchical factorial structure with three sub-factors and one general factor was satisfactory. We found support for configural invariance in all languages, metric invariance in some language comparisons, but no support for scalar invariance. Therefore, the construct can be applied in all languages, but comparisons of means should be done with caution. Further translation should try to seek the same configural invariance, but also aim for metric and scalar invariance.
The effect of worked material hardness on stone tool wear
2022-10-20

The identification of ancient worked materials is one of the fundamental goals of lithic use wear analysis and one of the most important parts of understanding how stone tools were used in the past. Given the documented overlaps in wear patterns generated by different materials, it is imperative to understand how individual materials’ mechanical properties might influence wear formation. Because isolating physical parameters and measuring their change is necessary for such an endeavor, controlled (rather than replicative) experiments combined with objective measurements of surface topography are necessary to better grasp how surface modifications formed on stone tools. Therefore, we used a tribometer to wear natural flint surfaces against five materials (bone, antler, beech wood, spruce wood, and ivory) under the same force, and speed, over one, three, and five hours. The study aimed to test if there is a correlation between surface modifications and the hardness of the worked material. We measured each raw material’s hardness using a nano-indentation test, and we compared the surface texture of the flint bits using a 3D optical profilometer. The interfacial detritus powder was analyzed with a scanning electron microscope to look for abraded flint particles. We demonstrate that, contrary to expectation, softer materials, such as wood, create a smoother surface than hard ones, such as ivory.
Weber’s Law for Timing and Time Perception: Reconciling the Poisson Clock with Scalar Expectancy Theory (SET)
2022-10-20

Abstract The pacemaker-counter model is the most prominent psychological account of timing and time perception. It has been often assumed that an internal pacemaker generates pulses according to a Poisson process and that these pulses are accumulated over time. According to Scalar Expectancy Theory (SET), the number of accumulated pulses represents the elapsed duration to be timed. Although the Poisson process provides a plausible cognitive and physiological mechanism for timing and time perception, its implementation into the framework of SET remains a theoretical challenge. The present contribution shows that a merger of Creelman’s (1962) and Treisman’s (1963) counting models enables such an implementation, which can account for Weber’s law and scalar timing. We demonstrate this for the fundamental principles of counting and timing, as well as for a temporal bisection task.
Spatial prediction of soil properties through hybridized random forest model and combination of reflectance spectroscopy and environmental covariates
2022-10-20

Spatial information on land and soil resources are critical towards addressing land degradation for ensuring sustainable soil and crop management. To address these needs, digital soil mapping techniques have emerged as an efficient and low-cost solution. Although digital soil mapping has typically leveraged geospatial environmental variables (e.g. remote sensing), the application and integration of spectroscopic data with those environmental variables remain limited. Hence, this study combines visible and near-infrared (Vis-NIR) spectroscopy, remote sensing, and topographic data and applies random forests, hybridized with particle swarm optimization algorithm (RF + PSO), to predict the spatial variability of soil clay content, electrical conductivity (EC), and calcium carbonate equivalent (CCE) for 370 km2 of agricultural land in western Iran. Using a conditioned Latin hypercube approach, 220 soil samples at the 0–20 cm depth increment were acquired throughout the study area. Three sets of environmental covariates were tested: Scenario A (Vis-NIR spectroscopy data), Scenario B (environmental data), and Scenario C (Vis-NIR spectroscopy + environmental data). According to the 10-fold cross-validation procedure with 100 replications, the RF + PSO model showed an acceptable level accuracy for all scenarios, although the accuracy of the RF + PSO model using the Scenario C data was higher than all other scenarios: the Lin's Concordance Correlation Coefficient values were 0.77, 0.83, and 0.74 for the clay contents, EC, and CCE, respectively. The results demonstrated that the combination of Vis-NIR spectroscopic data and commonly available environmental covariates provided the best input data for the hybridized model and enhanced its performance.
Reduction or de-escalation of dual antiplatelet therapy intensity or duration in patients with acute coronary syndromes undergoing percutaneous coronary intervention: A mini-review
2022-10-20

Current guidelines for patients with acute coronary syndrome (ACS) recommend dual antiplatelet therapy (DAPT) for 12 months. Since bleeding is the main Achilles' heel of DAPT, in recent years several randomized controlled trials have evaluated the safety and efficacy of de-escalation of DAPT with respect to ischaemic and bleeding endpoints. These trials can be broadly divided into studies evaluating a shorter duration of DAPT, and those studies in which DAPT that includes a potent P2Y 12 inhibitor, such as prasugrel or ticagrelor, is compared to less intense DAPT, mainly clopidogrel or reduced-dose prasugrel. We sought to evaluate the studies assessing de-escalation of DAPT in patients with ACS undergoing PCI. We review the studies evaluating the strategies of de-escalation of DAPT intensity and those evaluating a strategy of de-escalation of DAPT duration in ACS patients undergoing PCI. We summarize the limitations of studies to date, gaps in evidence and make recommendations for future studies.
Bromoditerpenes from the Red Seaweed Sphaerococcus coronopifolius as Potential Cytotoxic Agents and Proteasome Inhibitors and Related Mechanisms of Action
2022-10-20

Seaweeds are a great source of compounds with cytotoxic properties with the potential to be used as anticancer agents. This study evaluated the cytotoxic and proteasome inhibitory activities of 12R-hydroxy-bromosphaerol, 12S-hydroxy-bromosphaerol, and bromosphaerol isolated from Sphaerococcus coronopifolius. The cytotoxicity was evaluated on malignant cell lines (A549, CACO-2, HCT-15, MCF-7, NCI-H226, PC-3, SH-SY5Y, and SK-MEL-28) using the MTT and LDH assays. The ability of compounds to stimulate the production of hydrogen peroxide (H2O2) and to induce mitochondrial dysfunction, the externalization of phosphatidylserine, Caspase-9 activity, and changes in nuclear morphology was also studied on MCF-7 cells. The ability to induce DNA damage was also studied on L929 fibroblasts. The proteasome inhibitory activity was estimated through molecular docking studies. The compounds exhibited IC50 values between 15.35 and 53.34 μM. 12R-hydroxy-bromosphaerol and 12S-hydroxy-bromosphaerol increased the H2O2 levels on MCF-7 cells, and bromosphaerol induced DNA damage on fibroblasts. All compounds promoted a depolarization of mitochondrial membrane potential, Caspase-9 activity, and nuclear condensation and fragmentation. The compounds have been shown to interact with the chymotrypsin-like catalytic site through molecular docking studies; however, only 12S-hydroxy-bromosphaerol evidenced interaction with ALA20 and SER169, key residues of the proteasome catalytic mechanism. Further studies should be outlined to deeply characterize and understand the potential of those bromoditerpenes for anticancer therapeutics.
Electroweak renormalization based on gauge-invariant vacuum expectation values
2022-10-20

We briefly review a recently proposed scheme for a gauge-invariant treatment of tadpole corrections in spontaneously broken gauge theories called Gauge-Invariant Vacuum expectation value Scheme (GIVS). The tadpole scheme matters in higher-order predictions of observables if not all free parameters are fixed by renormalization conditions based on S-matrix elements, such as in MSbar renormalization. In contrast to previously used tadpole schemes, the GIVS unifies the properties of gauge invariance and perturbative stability. The application of the GIVS to the Standard Model, for instance, leads to very moderate electroweak corrections in the conversion of on-shell-renormalized to MSbar-renormalized masses. Moreover, in models with extended Higgs sectors, the GIVS is less prone to perturbative instabilities in the MSbar renormalization of Higgs mixing angles than observed for the traditional gauge-independent tadpole treatment. We illustrate this by considering the next-to-leading-order (electroweak and QCD) corrections to the decay processes fermions of the CP-even neutral Higgs bosons~h and H in a singlet Higgs extension of the Standard Model and in the Two-Higgs-Doublet Model.
UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysis
2022-10-20

Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for untargeted metabolomics that combines algorithms for data pre-processing, spectral matching, molecular formula and structural predictions, and an integration to the GNPS workflows Feature-Based Molecular Networking and Ion Identity Molecular Networking for downstream analysis. UmetaFlow is implemented as a Snakemake workflow, making it easy to use, scalable, and reproducible. For more interactive computing, visualization, as well as development, the workflow is also implemented in Jupyter notebooks using the Python programming language and a set of Python bindings to the OpenMS algorithms (pyOpenMS). UmetaFlow was validated with in-house LC-MS/MS datasets of actinomycetes producing known secondary metabolites, as well as commercial standards, and it detected all expected features and accurately annotated 76% of the molecular formulas and 65% of the structures. As a more generic validation, the publicly available MTBLS733 dataset was used for benchmarking, and UmetaFlow detected 797 out of the 836 (~95.3%) ground truth features and accurately quantified 94.9% of these. We anticipate that UmetaFlow will provide a universal platform for the interpretation of large metabolomics datasets.
Overview on Strategies and Assays for Antibiotic Discovery
2022-10-21

The increase in antibiotic resistance poses a major threat to global health. Actinomycetes, the Gram-positive bacteria of the order Actinomycetales, are fertile producers of bioactive secondary metabolites, including antibiotics. Nearly two-thirds of antibiotics that are used for the treatment of bacterial infections were originally isolated from actinomycetes strains belonging to the genus Streptomyces. This emphasizes the importance of actinomycetes in antibiotic discovery. However, the identification of a new antimicrobial compound and the exploration of its mode of action are very challenging tasks. Therefore, different approaches that enable the “detection” of an antibiotic and the characterization of the mechanisms leading to the biological activity are indispensable. Beyond bioinformatics tools facilitating the identification of biosynthetic gene clusters (BGCs), whole cell-screenings—in which cells are exposed to actinomycete-derived compounds—are a common strategy applied at the very early stage in antibiotic drug development. More recently, target-based approaches have been established. In this case, the drug candidates were tested for interactions with usually validated targets. This review focuses on the bioactivity-based screening methods and provides the readers with an overview on the most relevant assays for the identification of antibiotic activity and investigation of mechanisms of action. Moreover, the article includes examples of the successful application of these methods and suggestions for improvement.
Trait-trait relationships and tradeoffs vary with genome size in prokaryotes
2022-10-21

We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait–trait variations of 11 genomic traits from ~18,000 sequenced genomes. The studied trait–trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an oligotrophic-copiotrophic axis. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from traits associated with resource availability. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. Genome size distributions differ across habitats and our findings therefore point to habitat dependent tradeoffs between resistance and resilience. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.
Frontal sinuses and human evolution
2022-10-21

The frontal sinuses are cavities inside the frontal bone located at the junction between the face and the cranial vault and close to the brain. Despite a long history of study, understanding of their origin and variation through evolution is limited. This work compares most hominin species’ holotypes and other key individuals with extant hominids. It provides a unique and valuable perspective of the variation in sinuses position, shape, and dimensions based on a simple and reproducible methodology. We also observed a covariation between the size and shape of the sinuses and the underlying frontal lobes in hominin species from at least the appearance of Homo erectus . Our results additionally undermine hypotheses stating that hominin frontal sinuses were directly affected by biomechanical constraints resulting from either chewing or adaptation to climate. Last, we demonstrate their substantial potential for discussions of the evolutionary relationships between hominin species.
A Novel Method to Achieve Precision and Reproducibility in Exposure Parameters for Low-Frequency Pulsed Magnetic Fields in Human Cell Cultures
2022-10-21

The effects of extremely low-frequency electromagnetic field (ELF-MF) exposure on living systems have been widely studied at the fundamental level and also claimed as beneficial for the treatment of diseases for over 50 years. However, the underlying mechanisms and cellular targets of ELF-MF exposure remain poorly understood and the field has been plagued with controversy stemming from an endemic lack of reproducibility of published findings. To address this problem, we here demonstrate a technically simple and reproducible EMF exposure protocol to achieve a standardized experimental approach which can be readily adopted in any lab. As an assay system, we chose a commercially available inflammatory model human cell line; its response to magnetic fields involves changes in gene expression which can be monitored by a simple colorimetric reporter gene assay. The cells were seeded and cultured in microplates and inserted into a custom-built, semi-automated incubation and exposure system which accurately controls the incubation (temperature, humidity, CO2) and magnetic-field exposure conditions. A specific alternating magnetic field (&lt;1.0% spatial variance) including far-field reduction provided defined exposure conditions at the position of each well of the microplate. To avoid artifacts, all environmental and magnetic-field exposure parameters were logged in real time throughout the duration of the experiment. Under these extensively controlled conditions, the effect of the magnetic field on the cell cultures as assayed by the standardized operating procedure was highly reproducible between experiments. As we could fully define the characteristics (frequency, intensity, duration) of the pulsed magnetic field signals at the position of the sample well, we were, for the first time, able to accurately determine the effect of changing single ELF-MF parameters such as signal shape, frequency, intensity and duty cycle on the biological response. One signal in particular (10 Hz, 50% duty cycle, rectangular, bipolar, 39.6μT) provided a significant reduction in cytokine reporter gene expression by 37% in our model cell culture line. In sum, the accuracy, environmental control and data-logging capacity of the semi-automated exposure system should greatly facilitate research into fundamental cellular response mechanisms and achieve the consistency necessary to bring ELF-MF/PEMF research results into the scientific mainstream.
Chitotriosidase is a biomarker for adult‐onset leukoencephalopathy with axonal spheroids and pigmented glia
2022-10-21

Abstract Adult‐onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) leads to rapidly progressive dementia and is caused by mutations in the gene CSF1R . Neurodegeneration is driven by dysfunction of microglia, the predominant cell type expressing CSF1R in the brain. We assessed chitotriosidase, an enzyme secreted by microglia, in serum and cerebrospinal fluid of patients with ALSP. Chitotriosidase activity was highly increased in cerebrospinal fluid of patients and correlated inversely with disease duration. Of interest, presymptomatic CSF1R mutation carriers did not show elevated chitotriosidase levels. This makes chitotriosidase a promising new biomarker of disease activity for this rare disease.