julilili42/papers huggingface dataset:
Comparison of Target Enrichment Strategies for Ancient Pathogen DNA
2020-11-02

In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods - array-based hybridization capture and in-solution capture using either RNA or DNA baits - have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of <i>Mycobacterium leprae</i> and <i>Treponema pallidum</i> from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits.
The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in Azospirillum brasilense
2020-11-02

The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense . The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors.
Building the Bridge: Outlining Steps Toward an Applied Sleep-and-Memory Research Program
2020-11-02

Sleep’s beneficial role for memory is well documented, yet the translation of such fundamental memory processes into applications for improving memory function is limited so far. Although there are some commercial devices with varying levels of technical complexity that are claimed to improve sleep-dependent memory processing, none of them have been empirically validated. The main issue seems to be that there is basically no applied research in the field of sleep and memory. To change this, we identify the most promising targets for sleep-based memory-improvement applications. We outline the theoretical and technical aspects of the most promising memory-enhancing sleep interventions established in recent years and highlight potential targets of such interventions for different healthy and clinical populations. Finally, we propose a unifying framework that will lay the groundwork for a focused applied-research program in sleep and memory, bridging the gap between basic research and targeted application.
The missing role of gray matter in studying brain controllability
2020-11-02

Brain controllability properties are normally derived from the white matter fiber tracts in which the neural substrate of the actual energy consumption, namely the gray matter, has been widely ignored. Here, we study the relationship between gray matter volume of regions across the whole cortex and their respective control properties derived from the structural architecture of the white matter fiber tracts. The data suggests that the ability of white fiber tracts to exhibit control at specific nodes not only depends on the connection strength of the structural connectome but additionally depends on gray matter volume at the host nodes. Our data indicate that connectivity strength and gray matter volume interact with respect to the brain’s control properties. Disentangling effects of the regional gray matter volume and connectivity strength, we found that frontal and sensory areas play crucial roles in controllability. Together these results suggest that structural and regional properties of the white matter and gray matter provide complementary information in studying the control properties of the intrinsic structural and functional architecture of the brain.
Chemical Space Exploration of Oxetanes
2020-11-02

This paper focuses on new derivatives bearing an oxetane group to extend accessible chemical space for further identification of kinase inhibitors. The ability to modulate kinase activity represents an important therapeutic strategy for the treatment of human illnesses. Known as a nonclassical isoster of the carbonyl group, due to its high polarity and great ability to function as an acceptor of hydrogen bond, oxetane seems to be an attractive and underexplored structural motif in medicinal chemistry.
An R Toolbox for Score-Based Measurement Invariance Tests in IRT Models
2020-11-02

The detection of differential item functioning (DIF) is a central topic in psychometrics and educational measurement. In the past few years, a new family of score-based tests of measurement invariance has been proposed, which allows the detection of DIF along arbitrary person covariates in a variety of item response theory (IRT) models. This paper illustrates the application of these tests within the R system for statistical computing, making them accessible to a broad range of users. This presentation also includes IRT models for which these tests have not previously been investigated, such as the generalized partial credit model. The paper has three goals: First, we review the ideas behind score-based tests of measurement invariance. Second, we describe the implementation of these tests within the R system for statistical computing, which is based on the interaction of the R packages mirt, psychotools and strucchange. Third, we illustrate the application of this software and the interpretation of its output in two empirical datasets. The complete R code for reproducing our results is reported in the paper.
Metabolic Responses of a Phototrophic Co-Culture Enriched from a Freshwater Sediment on Changing Substrate Availability and its Relevance for Biogeochemical Iron Cycling
2020-11-02

Metabolic flexibility controls microbial survival and shapes ecological structures. Although the utilization of a variety of substrates has been studied for individual metabolically versatile microorganisms, only little is known about the response of microbial communities toward substrate fluctuation. Here, we exposed a phototrophic co-culture (Rhodopseudomonas sp. and Chlorobium sp.) that was isolated from a littoral freshwater sediment to a variety of substrates (acetate, Fe(II), or H<sub>2</sub>) and followed the abundance of individual microbial partners based on their characteristic light absorption pattern. Chlorobium sp. dominated the culture when Fe(II) was supplied, whereas Rhodopseudomonas sp. decreased below detection. Rhodopseudomonas sp. dominated when the co-culture was transferred onto acetate (Chlorobium sp. below detection). When grown on H<sub>2</sub>, the dominance pattern depended on pre-culture conditions. Pre-cultures on Fe(II) or acetate resulted in dominance of Chlorobium sp. or Rhodopseudomonas sp., respectively. Although the relative abundance of the two partner strains strictly relies on substrate availability, we were incapable of isolating Chlorobium sp. from the co-culture. Our study shows how substrate fluctuations shape microbial distribution and points toward potential community interactions that enable microbial survival.
Data for "Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics"
2020-11-02

&lt;p&gt;Experimental and precomputed data for the paper &quot;Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics&quot;&nbsp;by Oesterle et al. 2020 (DOI:&nbsp;&lt;a href="https://doi.org/10.7554/eLife.54997"&gt;10.7554/eLife.54997&lt;/a&gt;).&lt;/p&gt; &lt;p&gt;The cone bipolar cell data has been described and&nbsp;published in the paper &quot;Inhibition decorrelates visual feature representations in the inner retina&quot; by&nbsp;Franke et al. 2017 (DOI:&nbsp;&lt;a href="https://doi.org/10.1038/nature21394"&gt;10.1038/nature21394&lt;/a&gt;).&nbsp;&lt;/p&gt; &lt;p&gt;This data is both a supplement to the Oesterle et al. paper and the code for this paper.&lt;/p&gt; &lt;p&gt;The code&nbsp;is available in this&nbsp;&lt;a href="http://github.com/berenslab/CBC_inference"&gt;GitHub repository&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;We recommend&nbsp;downloading the GitHub repository&nbsp;and to follow the instructions there.&lt;/p&gt;
Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome
2020-11-03

To understand and treat immunology-related diseases, a comprehensive, unbiased characterization of major histocompatibility complex (MHC) peptide ligands is of key importance. Preceding the analysis by mass spectrometry, MHC class I peptide ligands are typically isolated by MHC immunoaffinity chromatography (MHC-IAC) and less often by mild acid elution (MAE). MAE may provide a cheap alternative to MHC-IAC for suspension cells but has been hampered by the high number of contaminating, MHC-unrelated peptides. Here, we optimized MAE, yielding MHC peptide ligand purities of more than 80%. When compared with MHC-IAC, obtained peptides were similar in numbers, identities, and to a large extent intensities, while the percentage of cysteinylated peptides was 5 times higher in MAE. The latter benefitted the discovery of MHC-allotype-specific, distinct cysteinylation frequencies at individual positions of MHC peptide ligands. MAE revealed many MHC ligands with unmodified, N-terminal cysteine residues which get lost in MHC-IAC workflows. The results support the idea that MAE might be particularly valuable for the high-confidence analysis of post-translational modifications by avoiding the exposure of the investigated peptides to enzymes and reactive molecules in the cell lysate. Our improved and carefully documented MAE workflow represents a high-quality, cost-effective alternative to MHC-IAC for suspension cells.
Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes
2020-11-03

The capacity for achieving immense specificity and resolution in science increases day to day. Fluorescence-activated nuclear sorting (FANS) offers this great precision, enabling one to count and separate distinct types of nuclei from specific cells of heterogeneous mixtures. We developed a workflow to collect nuclei from Arabidopsis thaliana by FANS according to cell lineage and endopolyploidy level with high efficiency. We sorted GFP-labeled nuclei with different ploidy levels from the epidermal tissue layer of three-day, dark-grown hypocotyls followed by a shift to light for one day and compared them to plants left in the dark. We then accessed early chromatin accessibility patterns associated with skotomorphogenesis and photomorphogenesis by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) within primarily stomatal 2C and fully endoreduplicated 16C nuclei. Our quantitative analysis shows that dark- and light-treated samples in 2C nuclei do not exhibit any different chromatin accessibility landscapes, whereas changes in 16C can be linked to transcriptional changes involved in light response.
Highly Stable and Fine-Textured Hybrid Microspheres for Entrapment of Cosmetic Active Ingredients
2020-11-03

This study details the preparation and application of supramolecular host-guest inclusion complexes entrapping biomineralized microspheres for long-term storage and their pH-responsive behavior. The microspheres were assembled using a CaCO<sub>3</sub> synthesis process coupled with cyclodextrin-tetrahydrocurcumin (CD-THC) inclusion complexes, forming fine-textured and mechanically stable hybrid materials. The products were successfully characterized using field-emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDS), Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), and particle size analysis (PSA). Various parameters such as the Brunauer-Emmett-Teller (BET) surface area, single point total pore volume, and pore size via adsorption/desorption analysis were also determined. The obtained THC-entrapped hybrid microspheres contained as high as 20 wt % THC loading and were very stable, preserving 90% of the initial concentration over four weeks of storage at different temperatures, largely limiting THC leaching and indicating high stability in a physiological environment. In addition, the pH-responsive release of THC from the hybrid microspheres was observed, showing potential use for application to weakly acidic skin surfaces. To our knowledge, this is the first demonstration of antiaging cosmetic formulation technology using biomineralization based on the co-synthesis of CaCO<sub>3</sub> and CD-THC complexes.
Intravascular BOLD signal characterization of balanced SSFP experiments in human blood at high to ultrahigh fields
2020-11-03

Purpose To investigate the intravascular contribution to the overall balanced SSFP (bSSFP) BOLD effect in human blood at high to ultrahigh field strengths (3 T, 9.4 T, and 14.1 T). Methods Venous blood prepared at two different oxygenation levels (deoxygenated: Y ≈ 71%, oxygenated: Y ≈ 94%) was measured with phase‐cycled bSSFP for varying TRs/flip angles at 3 T, 9.4 T, and 14.1 T. The oxygen sensitivity was analyzed by intrinsic MIRACLE (motion‐insensitive rapid configuration relaxometry)‐R 2 estimation and passband signal differences. The intravascular BOLD‐related signal change was extracted from the measured data for microvasculature and macrovasculature, and compared with the extravascular contribution obtained by Monte Carlo simulations. Results The MIRACLE‐R 2 values showed a characteristic increase with longer TRs in deoxygenated blood, corroborating that SE‐R 2 data cannot be used to assess the intravascular bSSFP BOLD effect. Passband bSSFP signal differences measured at optimal flip angles of 30° at 3 T and 20° at 9.4 T/14.1 T revealed considerable relative intravascular contributions of 95%/70% at 3 T, 74%/43% at 9.4 T, 66%/46% at 14.1 T for TR = 5 ms, and 90%/65% at 3 T, 36%/27% at 9.4 T, 13%/15% at 14.1 T for TR = 10 ms in macrovascular/microvascular regimes. Conclusion The results indicate that intravascular effects have to be considered to better understand the origin of bSSFP BOLD contrast in functional MRI experiments, especially at short TRs. The MIRACLE‐R 2 method demonstrated the ability to quantify the apparent decrease in R 2 due to rapid RF refocusing.
Fine mapping of the HLA locus in Parkinson’s disease in Europeans
2020-11-03

Abstract Objective To fine map the association between human leukocyte antigen ( HLA) genes and Parkinson’s disease (PD) that was discovered using genome-wide association studies (GWASs). Methods We performed a thorough analysis of the HLA locus in 13,770 PD patients, 20,214 proxy-cases and 490,861 controls of European origin. We used GWAS data to impute HLA types and performed multiple regression models to examine the association of specific HLA types, different haplotypes and specific amino acid changes. We further performed conditional analyzes to identify specific alleles or genetic variants that drive the association with PD. Results Four HLA types were associated with PD after correction for multiple comparisons, HLA-DQA1 *03:01, HLA-DQB1 *03:02, HLA-DRB1 *04:01 and HLA-DRB1 *04:04. Haplotype analyzes followed by amino-acid analysis and conditional analyzes suggested that the association is protective and primarily driven by three specific amino acid polymorphisms present in most HLA-DRB1 *04 subtypes - 11V, 13H and 33H (OR=0.87 95%CI=0.83-0.90, p &lt;8.23×10 −9 for all three variants). No other effects were present after adjustment for these amino acids. Conclusions Our results suggest that specific variants in the HLA-DRB1 gene are associated with reduced risk of PD, providing additional evidence for the role of the immune system in PD. Although effect size is small and has no diagnostic significance, understanding the mechanism underlying this association may lead to identification of new targets for therapeutics development.
Free Choice Items and Modal Indefinites
2020-11-03

This chapter discusses a class of determiner phrases with one or more of the following properties: (i) they have a restricted distribution; (ii) in combination with (some) modals, they convey, roughly, that all the individuals in their domain are possibilities (a “free choice effect”); and (iii) they can express modality in the absence of an overt modal. The chapter has two main parts: the first deals with free choice items , like English free choice any , Spanish cualquiera , or Italian qualsiasi , which have properties (i) and (ii); the second surveys modal indefinites , existential items with property (iii), like German irgendein , Spanish algún , or Italian un qualche .
Problems in measuring the JTC-bias in patients with psychotic disorders with the fish task: A secondary analysis of a baseline assessment of a randomized controlled trial&nbsp;
2020-11-03

<title>Abstract</title> Background: The jumping to conclusions bias (JTC) is considered to be an important causal factor in theoretical models for the formation and maintenance of delusions. However, recent meta-analytic findings show a rather equivocal pattern of results regarding associations between JTC and delusions. Thus, the present study aims to investigate in a large sample whether the JTC-bias is more pronounced in patients with psychotic disorders in comparison to controls and whether the JTC bias is associated with a more severe delusional conviction, persecutory delusions, and positive symptoms in general.Methods: Patients with psychotic disorders (<italic>n</italic> = 300) enrolled in a therapy trial and healthy controls (<italic>n</italic> = 51) conducted a variant of the beads task (fish task) as a measure for the JTC-bias at the start of the trial. Further, clinical interviews were used to assess patients’ delusional severity and delusional conviction. Results: There were no statistically significant differences between patients with psychotic disorders (with 53% displaying the JTC-bias) and controls (41%). Furthermore, there were no statistically significant correlations between JTC measures and persecutory delusions, delusional conviction, and positive symptoms.Conclusions: We found no differences in JTC between patients with psychotic disorders and healthy controls, which is in part in line with meta-analytic findings using a wide range of JTC task variants. Interestingly, patients with psychotic disorders displayed JTC rates commonly found in the literature, while healthy control subjects showed an unexpectedly high level of JTC. The task variant we used in the present study (fish task) is discussed as a potential reason for our results, as it may induce a more deliberative reasoning style in controls as compared to the traditional beads task. Furthermore, possible implications for the measurement of the JTC-bias, in general, are discussed.Trial Registration: ISRCTN29242879 (isrctn.com), date of registration: April 12<sup>th</sup> 2006
Adversarial vulnerabilities of human decision-making
2020-11-04

Significance “What I cannot efficiently break, I cannot understand.” Understanding the vulnerabilities of human choice processes allows us to detect and potentially avoid adversarial attacks. We develop a general framework for creating adversaries for human decision-making. The framework is based on recent developments in deep reinforcement learning models and recurrent neural networks and can in principle be applied to any decision-making task and adversarial objective. We show the performance of the framework in three tasks involving choice, response inhibition, and social decision-making. In all of the cases the framework was successful in its adversarial attack. Furthermore, we show various ways to interpret the models to provide insights into the exploitability of human choice.
The Multifactorial Nature of Early Numeracy and Its Stability
2020-11-04

Early numeracy is a robust predictor of later mathematical abilities. So far, early numeracy has typically been presented as a unitary or two-factorial construct. Nevertheless, there is recent evidence suggesting that it may also be reflected by more basic numerical competences. However, the structure and stability of such a multifactorial model of early numeracy over time has not been investigated yet. In the present study, we used data from a large, longitudinal sample (<i>N</i> = 1292) in the United States with assessments of math ability in prekindergarten and kindergarten to evaluate both the factorial structure of early numeracy and its stability over time. Confirmatory factor analysis identified four distinct basic numerical competences making up early numeracy in prekindergarten: patterning/geometry, number sense, arithmetic, and data analysis/statistics. Stability as tested by means of measurement invariance indicated configural invariance of these four factors from prekindergarten to kindergarten. This reflected that early numeracy in kindergarten was made up by the same four basic numerical competences as in prekindergarten and thus seemed rather stable over the course of preschool. These findings may not only have implications for research on numerical cognition but particularly for diagnostic processes or the development of interventions in educational practice.
Plant Broth- (Not Bovine-) Based Culture Media Provide the Most Compatible Vegan Nutrition for In Vitro Culturing and In Situ Probing of Plant Microbiota
2020-11-04

Plant microbiota support the diversity and productivity of plants. Thus, cultivation-dependent approaches are indispensable for in vitro manipulation of hub taxa. Despite recent advances in high-throughput methods, cultivability is lagging behind other environmental microbiomes, notably the human microbiome. As a plant-based culturing strategy, we developed culture media based on a broth of cooked aqueous mixtures of host plants. This improved the in vitro growth of representative isolates of plant microbiota and extended the in situ recovery of plant microbiota. With clover, 16S rRNA gene sequencing of representative isolates confirmed the predominance of Firmicutes, Alphaproteobacteria and Gammaproteobacteria, and less frequently Bacteroidetes and Actinobacteria. Whereas bovine-based culture media (modified R2A) confined the diversity to Firmicutes, the plant broth-based culture media revealed a wider scope of endophytes beyond rhizobia, i.e., multiple genera such as Chryseobacterium, Cronobacter, Kosakonia, Tsukamurella, and a potentially/presumptive novel species. Matrix-assisted laser desorption/ionization time-of-flight (MADI-TOF) analysis clustered isolates according to their plant niches, the endo-phyllosphere/endo-rhizosphere. We recommend the plant broth for simplicity, reproducibility and perdurable storage, supporting future culturomics applications, good laboratory practice (GLP) and good manufacturing practice (GMP). The strategy creates an “in-situ-similis” vegan nutritional matrix to analyze microbial diversity and reveal novel microbial resources pertinent to biotechnological and environmental applications.