julilili42/papers huggingface dataset:
Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch–German border region
2021-08-04

Abstract Porcine viruses have been emerging in recent decades, threatening animal and human health, as well as economic stability for pig farmers worldwide. Next‐generation sequencing (NGS) can detect and characterize known and unknown viruses but has limited sensitivity when an unbiased approach, such as shotgun metagenomics sequencing, is used. To increase the sensitivity of NGS for the detection of viruses, we applied and evaluated a broad viral targeted sequence capture (TSC) panel and compared it to an unbiased shotgun metagenomic approach. A cohort of 36 pooled porcine nasal swab and blood serum samples collected from both sides of the Dutch–German border region were evaluated. Overall, we detected 46 different viral species using TSC, compared to 40 viral species with a shotgun metagenomics approach. Furthermore, we performed phylogenetic analysis on recovered influenza A virus (FLUAV) genomes from Germany and revealed a close similarity to a zoonotic influenza strain previously detected in the Netherlands. Although TSC introduced coverage bias within the detected viruses, it improved sensitivity, genome sequence depth and contig length. In‐depth characterization of the swine virome, coupled with developing new enrichment techniques, can play a crucial role in the surveillance of circulating porcine viruses and emerging zoonotic pathogens.
3D Printing of Polyamide to Fabricate a Non-Metal Clasp Removable Partial Denture via Fused Filament Fabrication: A Case Report
2021-08-04

The fabrication of a non-metal clasp removable partial denture (RPD) using polymethylmethacrylate in a fully digital workflow has been reported. According to some studies, the polyamide material may be alternatively used for this purpose. The authors are unaware of any reports concerning the additive manufacturing of polyamide. The current proof-of-concept dental technique describes the pathway to construct the non-metal clasp RPD using intraoral scanning and fused filament fabrication (FFF) printing of gingiva-colored polyamide. The present RPD showed acceptable fit and sufficient retention and was considered a valid temporary treatment option.
What’s in a Like? Motivations for Pressing the Like Button
2021-08-04

Lightweight evaluations of content, such as thumbs-up, Liking, and favoriting, are an important aspect of social media interactions. Although minimal, these acts can carry a variety of meanings and implications. Prior research has revealed various motives and identified some recurring themes, but is often based on small samples or survey procedures prone to memory bias. In the present research, we asked people to view posts they had recently Liked on Facebook and report motives for each concrete post. We offer insights into the prevalence of previously hypothesized motives, and their associations with the content of posts, the relationship between sender and receiver, and the personality of the sender.
LMC N132D: A mature supernova remnant with a power-law gamma-ray spectrum extending beyond 8 TeV
2021-08-04

Context. Supernova remnants (SNRs) are commonly thought to be the dominant sources of Galactic cosmic rays up to the knee of the cosmic-ray spectrum at a few PeV. Imaging Atmospheric Cherenkov Telescopes have revealed young SNRs as very-high-energy (VHE, &gt;100 GeV) gamma-ray sources, but for only a few SNRs the hadronic cosmic-ray origin of their gamma-ray emission is indisputably established. In all these cases, the gamma-ray spectra exhibit a spectral cutoff at energies much below 100 TeV and thus do not reach the PeVatron regime. Aims. The aim of this work was to achieve a firm detection for the oxygen-rich SNR LMC N132D in the VHE gamma-ray domain with an extended set of data, and to clarify the spectral characteristics and the localization of the gamma-ray emission from this exceptionally powerful gamma-ray-emitting SNR. Methods. We analyzed 252 h of High Energy Stereoscopic System (H.E.S.S.) observations towards SNR N132D that were accumulated between December 2004 and March 2016 during a deep survey of the Large Magellanic Cloud, adding 104 h of observations to the previously published data set to ensure a &gt; 5 σ detection. To broaden the gamma-ray spectral coverage required for modeling the spectral energy distribution, an analysis of Fermi -LAT Pass 8 data was also included. Results. We unambiguously detect N132D at VHE with a significance of 5.7 σ . We report the results of a detailed analysis of its spectrum and localization based on the extended H.E.S.S. data set. The joint analysis of the extended H.E.S.S and Fermi -LAT data results in a spectral energy distribution in the energy range from 1.7 GeV to 14.8 TeV, which suggests a high luminosity of N132D at GeV and TeV energies. We set a lower limit on a gamma-ray cutoff energy of 8 TeV with a confidence level of 95%. The new gamma-ray spectrum as well as multiwavelength observations of N132D when compared to physical models suggests a hadronic origin of the VHE gamma-ray emission. Conclusions. SNR N132D is a VHE gamma-ray source that shows a spectrum extending to the VHE domain without a spectral cutoff at a few TeV, unlike the younger oxygen-rich SNR Cassiopeia A. The gamma-ray emission is best explained by a dominant hadronic component formed by diffusive shock acceleration. The gamma-ray properties of N132D may be affected by an interaction with a nearby molecular cloud that partially lies inside the 95% confidence region of the source position.
ADC-Based Stratification of Molecular Glioma Subtypes Using High b-Value Diffusion-Weighted Imaging
2021-08-04

Purpose: To investigate the diagnostic performance of in vivo ADC-based stratification of integrated molecular glioma grades. Materials and methods: Ninety-seven patients with histopathologically confirmed glioma were evaluated retrospectively. All patients underwent pre-interventional MRI-examination including diffusion-weighted imaging (DWI) with implemented b-values of 500, 1000, 1500, 2000, and 2500 s/mm2. Apparent Diffusion Coefficient (ADC), Mean Kurtosis (MK), and Mean Diffusivity (MD) maps were generated. The average values were compared among the molecular glioma subgroups of IDH-mutant and IDH-wildtype astrocytoma, and 1p/19q-codeleted oligodendroglioma. One-way ANOVA with post-hoc Games-Howell correction compared average ADC, MD, and MK values between molecular glioma groups. A Receiver Operating Characteristic (ROC) analysis determined the area under the curve (AUC). Results: Two b-value-dependent ADC-based evaluations presented statistically significant differences between the three molecular glioma sub-groups (p &lt; 0.001, respectively). Conclusions: High-b-value ADC from preoperative DWI may be used to stratify integrated molecular glioma subgroups and save time compared to diffusion kurtosis imaging. Higher b-values of up to 2500 s/mm2 may present an important step towards increasing diagnostic accuracy compared to standard DWI protocol.
Investigation of a Template‐Based Process Chain for Investment Casting of Open‐Cell Metal Foams
2021-08-04

Herein, a holistic investigation of the process chain of polymer foam template manufacturing for the investment casting of open‐cell metal foams and their evaluation in terms of mechanical response under compressive loading is presented. Polymer foam templates are manufactured using sucrose beads as spaceholders with a body‐centred cubic (bcc) stacking and epoxy resin as matrix material. These templates are used in a modified investment casting process to produce commercial pure open‐cell Al foams (AA 1050 A). The materials used for the polymer foam templates are suitable for the template production and the use in investment casting. The structure of the template can be exactly reproduced by investment casting and no byproducts from the pyrolysis step can be detected within the molds or the Al foams. The mechanical properties under compressive loading are comparable with high‐strength Al‐alloy foams with a structure factor of C 1 of 0.60. The characteristic plastic deformation is dominated by buckling, showing a local plastic failure of the struts within cell layers. Due to a high node‐to‐strut thickness ratio, neither small defects in the microstructure nor stacking errors of the template impact this deformation behavior.
Mitigating the Default? The Influence of Ingroup Diversity on Outgroup Trust
2021-08-04

Maintaining social cohesion in times of increasing diversity is a major challenge of modern societies. Mitigating defaults in group-based trust could be a solution because they are often driven by stereotypes and ingroup favoritism. Ingroup diversity could be a means to achieve such a mitigation given that it increases cognitive flexibility and cognitive flexibility changes defaults in trust – in the sense of increasing low and reducing high trust. We tested whether representing one’s ingroup as high (compared to low) in diversity mitigates defaults in group-based trust using a variety of well-established manipulations of ingroup diversity and measures of trust. None of the four well-powered studies (total 'N' = 885), we conducted provided support for our hypothesis. However, an internal meta-analysis revealed a significant but very small effect in support of our prediction ('r' = 0.07, 95% CI [0.01, 0.14]). Thus, a diverse representation of the ingroup asserts a mitigating impact on group-based trust, but the size of the effect is very small. Thus, real world interventions should not rely on the current effect.
Contrasting Dihydronaphthoquinone Patterns in Closely Related Drosera (Sundew) Species Enable Taxonomic Distinction and Identification
2021-08-04

Dihydronaphthoquinones are described as constituents of sundews (Drosera), Venus flytraps (Dionaea), and dewy pines (Drosophyllum) for the first time. As in the corresponding naphthoquinones, these reduced derivatives may occur in two regio-isomeric series distinguished by the relative position of a methyl group (at position 2 or 7 in the naphthalene skeleton), depending on the taxon. Species producing plumbagin (2-methyljuglone, 1) do commonly contain the corresponding dihydroplumbagin (5), while species containing ramentaceone (7-methyljuglone, 2) also contain dihydroramentaceone (7-methyl-β-dihydrojuglone, 6). So far, only few species containing plumbagin (1) and dihydroplumbagin (5) additionally form dihydroramentaceone (6) but not ramentaceone (2). Thus, subtle but constant differences in the chemism of closely related and morphologically similar species reliably define and distinguish taxa within D. sect. Arachnopus, which is taken to exemplify their chemotaxonomic utility. The joint presence of quinones and hydroquinones allows observations and predictions on the chemical structures and the reactions of these intriguing natural products.
The Information Geometry of Sensor Configuration
2021-08-04

In problems of parameter estimation from sensor data, the Fisher information provides a measure of the performance of the sensor; effectively, in an infinitesimal sense, how much information about the parameters can be obtained from the measurements. From the geometric viewpoint, it is a Riemannian metric on the manifold of parameters of the observed system. In this paper, we consider the case of parameterized sensors and answer the question, “How best to reconfigure a sensor (vary the parameters of the sensor) to optimize the information collected?” A change in the sensor parameters results in a corresponding change to the metric. We show that the change in information due to reconfiguration exactly corresponds to the natural metric on the infinite-dimensional space of Riemannian metrics on the parameter manifold, restricted to finite-dimensional sub-manifold determined by the sensor parameters. The distance measure on this configuration manifold is shown to provide optimal, dynamic sensor reconfiguration based on an information criterion. Geodesics on the configuration manifold are shown to optimize the information gain but only if the change is made at a certain rate. An example of configuring two bearings-only sensors to optimally locate a target is developed in detail to illustrate the mathematical machinery, with Fast Marching methods employed to efficiently calculate the geodesics and illustrate the practicality of using this approach.
The association of basic numerical abilities and math achievement: The mediating role of visuospatial and arithmetical abilities
2021-08-04

Basic numerical abilities such as number line estimation have been observed repeatedly to be associated with mathematical achievement. Recently, it was argued that the association between basic numerical abilities and mathematical achievement is fully mediated by visuospatial abilities. However, arithmetical abilities have not yet been considered as influencing this association, even though solution strategies in number line estimation as well as mathematical achievement often involve arithmetical procedures. Therefore, we investigated the mediating role of arithmetical and visuospatial abilities on the association between number line estimation and mathematical achievement in a sample of n = 599 German elementary school students. The results indicated that arithmetical abilities as well as visuospatial abilities mediated the association between number line estimation and mathematical achievement. However, neither visuospatial nor arithmetical abilities fully mediated the association between number line estimation and mathematical achievement when considered in isolation. This substantiates the relevance of the intertwined development of visuospatial and arithmetical abilities as well as basic numerical abilities such as number line estimation (i.e., the combination of domain-specific numerical and domain-general abilities) driving mathematical achievement.
Sleep and conditioning of the siphon withdrawal reflex in Aplysia
2021-08-04

ABSTRACT Sleep is essential for memory consolidation after learning as shown in mammals and invertebrates such as bees and flies. Aplysia californica displays sleep, and sleep in this mollusk was also found to support memory for an operant conditioning task. Here, we investigated whether sleep in Aplysia is also required for memory consolidation in a simpler type of learning, i.e. the conditioning of the siphon withdrawal reflex. Two groups of animals (Wake, Sleep, each n=11) were conditioned on the siphon withdrawal reflex, with the training following a classical conditioning procedure where an electrical tail shock served as the unconditioned stimulus (US) and a tactile stimulus to the siphon as the conditioned stimulus (CS). Responses to the CS were tested before (pre-test), and 24 and 48 h after training. While Wake animals remained awake for 6 h after training, Sleep animals had undisturbed sleep. The 24 h test in both groups was combined with extinction training, i.e. the extended presentation of the CS alone over two blocks. At the 24 h test, siphon withdrawal duration in response to the CS was distinctly enhanced in both Sleep and Wake groups with no significant difference between groups, consistent with the view that consolidation of a simple conditioned reflex response does not require post-training sleep. Surprisingly, extinction training did not reverse the enhancement of responses to the CS. On the contrary, at the 48 h test, withdrawal duration in response to the CS was even further enhanced across both groups. This suggests that processes of sensitization, an even simpler non-associative type of learning, contributed to the withdrawal responses. Our study provides evidence for the hypothesis that sleep preferentially benefits consolidation of more complex learning paradigms than conditioning of simple reflexes.
Improved Multigram Route to a Tricyclic Key Intermediate for Dibenzosuberone-Based p38 Inhibitors via an Optimized Early-Stage Heck Coupling
2021-08-04

The p38α MAP kinase has been a heavily investigated target in the last two decades. The structural class of dibenzosuberone-based p38 inhibitors, exemplified by the promising candidate skepinone-L, was already successfully validated in several in vivo models of inflammatory as well as oncologic indications. The increasing demand of key intermediates and final compounds caused by the ongoing development of this inhibitor class urged the conception of an optimized route for the preparation of the core dibenzosuberone scaffold in multigram quantities. Rerouting of the initial discovery route resulted in an almost 4-fold increase of overall yield to 46%, the elimination of chromatographic purification, and the substitution of two critical reaction steps, which hindered a feasible scale-up. The key modification was the introduction and optimization of an early-stage Heck coupling based on Buchwald precatalysts allowing consistently high yields (ca. 90%) at multigram scales with a favorably low Pd loading of 0.1 mol %. This newly developed synthetic access to the dibenzosuberone intermediate 2-chloro-7-hydroxy-10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-one is capable of ensuring the supply of skepinone-L and other candidates during further development.
Oscillatory brain activity associated with skin conductance responses in the context of risk
2021-08-04

We studied neural oscillations associated with risk-sensitive skin conductance responses. Going beyond previous studies, we applied methods with high-temporal resolution to account for the temporal properties of the sympathetic activity. Preceding skin conductance peaks, we observed decreased occipital cortex oscillatory power and a relationship between the oscillatory power decrease and the skin conductance peak amplitude. Our study suggests an interaction between attention and emotion such as threat perception reflected in skin conductance responses.
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes
2021-08-04

Bacterial specialized metabolites are a proven source of antibiotics and cancer therapeutics, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~ 170,000 bacterial genomes and ~ 47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We found that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation of secondary metabolite biosynthetic diversity drops significantly on a genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on Relative Evolutionary Distance revealed that <em>Streptomyces</em> bacteria encode the largest biosynthetic diversity by far, with <em>Amycolatopsis</em>, <em>Kutzneria</em> and <em>Micromonospora</em> also encoding substantial chemical diversity. Finally we find that several less-well-studied taxa such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), <em>Pleurocapsa</em> and Nostocaceae (Cyanobacteria) have potential to produce highly diverse secondary metabolites that warrant further investigation.
CAMISIM hybrid time series data
2021-08-04

CAMISIM was used to simulate Illumina and Nanopore reads for a time series based on the genome sources from the “CAMI II challenge toy mouse gut dataset” (Meyer et al., 2021), containing 791 genomes. For this, the most recent development version of CAMISIM at the time of preparing this data was used (available at https://doi.org/10.5281/zenodo.5137751). Two groups of samples were generated by using different CAMISIM seeds, each comprising a time series of four samples. The sample sheet file (samplesheet.CAMISIM_hybrid.csv) can be used as direct input for the nf-core/mag pipeline, e.g. with the command: &gt; nextflow run nf-core/mag -r 2.1.0 -profile &lt;docker/singularity/podman/shifter/charliecloud/conda/institute&gt; --input https://zenodo.org/record/5155395/files/samplesheet.CAMISIM_hybrid.csv --coassemble_group Note, in case of download problems, restarting the pipeline run with `-resume` or downloading the files beforehand and adjusting the paths in the sample sheet file should help. See https://nf-co.re/mag for a comprehensive usage documentation.
A global survey of specialized metabolic diversity encoded in bacterial genomes
2021-08-04

Bacterial secondary metabolites have been studied for decades for their usefulness as drugs, such as antibiotics. However, the identification of new structures has been decelerating, in part due to rediscovery of known compounds. Meanwhile, multi-resistant pathogens continue to emerge, urging the need for new antibiotics. It is unclear how much chemical diversity exists in Nature and whether discovery efforts should be focused on established antibiotic producers or rather on understudied taxa. Here, we surveyed around 170,000 bacterial genomes as well as several thousands of Metagenome Assembled Genomes (MAGs) for their diversity in Biosynthetic Gene Clusters (BGCs) known to encode the biosynthetic machinery for producing secondary metabolites. We used two distinct algorithms to provide a global overview of the biosynthetic diversity present in the sequenced part of the bacterial kingdom. Our results indicate that only 3% of genomic potential for natural products has been experimentally discovered. We connect the emergence of most biosynthetic diversity in evolutionary history close to the taxonomic rank of genus. Despite enormous differences in potential among taxa, we identify <em>Streptomyces</em> as by far the most biosynthetically diverse based on currently available data. Simultaneously, our analysis highlights multiple promising high-producing taxas that have thus far escaped investigation.