julilili42/papers huggingface dataset:
Neurophysiology-Driven Parameter Selection in nTMS-Based DTI Tractography: A Multidimensional Mathematical Model
2019-12-18

<b>Object:</b> There is an increasing interest in preoperative diffusion tensor imaging-based fiber tracking (DTI-FT) to preserve function during surgeries in motor eloquent brain regions. However, DTI tractography is challenged by inherent presumptions during particular tracking steps [e.g., deterministic vs. probabilistic DTI, fractional anisotropy (FA) and fiber length (FL) thresholding] and the missing "ground truth" information. In the present study, we intended to establish an objective, neurophysiology-driven approach for parameter selection during DTI-FT of the corticospinal tract integrating both imaging and neurophysiological information. <b>Methods:</b> In ten patients with lesions in eloquent motor areas, preoperative navigated transcranial magnetic stimulation (nTMS) was performed, followed by individual deterministic DTI-FT from a grid of cortical seed points. We investigated over 300 combinations of FA and FL thresholds and applied subsequently a multidimensional mathematical modeling of this empirical data. Optimal DTI parameters were determined by the relationship between DTI-FT (i.e., number of fibers, NoF) and nTMS (i.e., amplitudes of motor-evoked potentials) results. Finally, neurophysiological DTI parameters and the resulting tractography were compared to the current standard approaches of deterministic DTI fiber tracking with a 75% and 50% FA and a FL threshold of 110 mm as well as with intraoperative direct cortical and subcortical stimulation. <b>Results:</b> There was a good goodness-of-fit for the mathematical model (<i>r</i> <sup>2</sup> = 0.68 ± 0 13; range: 0.59-0.97; <i>n</i> = 8) except of two cases. Neurophysiology-driven parameter selection showed a high correlation between DTI-FT and nTMS results (<i>r</i> = 0.73 ± 0.16; range: 0.38-0.93). In comparison to the standard approach, the mathematically calculated thresholds resulted in a higher NoF in 75% of patients. In 50% of patients this approach helped to clarify the exact tract location or to detect additional functional tracts, which were not identified by the standard approach. This was confirmed by direct cortical or subcortical stimulation. <b>Conclusion:</b> The present study evaluates a novel user-independent method to extract objective DTI-FT parameters that were completely based on neurophysiological data. The findings suggest that this method may improve the specificity and sensitivity of DTI-FT and thereby overcome the disadvantages of current approaches.
Referenzielle Kohärenz: Diskrepanz zwischen Theorie und Vermittlung.
2019-12-18

Secondary school graduates are expected to write coherent texts for their respective occupations and other purposes later in life. Schooling should therefore prepare them adequately for this. It is thus paradoxical that textbooks for German provide pupils with very few explicit didactic instructions on how to write coherent texts. This applies in particular to referential coherence.&#x0D; Our article aims to contribute to the appropriate teaching of referential coherence in its complexity. To this end, first, the functions and the actual forms of referential means are examined in detail, from which the requirements for classroom instruction are derived. Next, textbook excerpts are examined to see whether and to what extent they meet these requirements.&#x0D; Our analysis shows that the way coherence is dealt with in textbooks is far from matching either linguistic or didactic demands. Very little attention is paid to form-function relationships. In some cases, tasks are even designed in such a manner that they lead pupils in the wrong direction and are thus counterproductive for the development of suitable writing or text skills.
Gut Peptide Agonism in the Treatment of Obesity and Diabetes
2019-12-18

Obesity is a global healthcare challenge that gives rise to devastating diseases such as the metabolic syndrome, type-2 diabetes (T2D), and a variety of cardiovascular diseases. The escalating prevalence of obesity has led to an increased interest in pharmacological options to counteract excess weight gain. Gastrointestinal hormones such as glucagon, amylin, and glucagon-like peptide-1 (GLP-1) are well recognized for influencing food intake and satiety, but the therapeutic potential of these native peptides is overall limited by a short half-life and an often dose-dependent appearance of unwanted effects. Recent clinical success of chemically optimized GLP-1 mimetics with improved pharmacokinetics and sustained action has propelled pharmacological interest in using bioengineered gut hormones to treat obesity and diabetes. In this article, we summarize the basic biology and signaling mechanisms of selected gut peptides and discuss how they regulate systemic energy and glucose metabolism. Subsequently, we focus on the design and evaluation of unimolecular drugs that combine the beneficial effects of selected gut hormones into a single entity to optimize the beneficial impact on systems metabolism. © 2020 American Physiological Society. Compr Physiol 10:99-124, 2020.
Physical Activity-Related Health Competence, Physical Activity, and Physical Fitness: Analysis of Control Competence for the Self-Directed Exercise of Adolescents
2019-12-19

(1) Background: Individuals have to effectively manage their physical activity in order to optimize the associated physical and psychological health benefits. Control competence allows the individual to structure and pace physical activity in a health-enhancing way. The concept was developed within a model of physical activity-related health competence, and is related to the concepts of health literacy and physical literacy. Therefore, the study firstly aimed to validate a self-report scale to measure the physical and psychological facets of control competence in adolescents. Secondly, relationships between control competence and its basic elements, knowledge and motivation, as well as between control competence, sport activity, and fitness, were investigated. (2) Methods: In two cross-sectional studies, ninth grade adolescents (study A: n = 794, 51% female; study B: n = 860, 52% female) were tested using self-report scales (study A and B), a test for health-related fitness knowledge (study B), and cardiovascular and muscular fitness tests (study B). (3) Results: Confirmatory factor analyses confirmed the two-factor structure of the self-report scale for control competence in studies A and B. In addition, the results of structural equation modeling in study B showed a relationship between motivation (via control competence) and sport activity, and a relationship between control competence and fitness. (4) Conclusion: The questionnaire extends the ability to assess control competence in adolescents. Moreover the findings support the importance of control competence in order to achieve health benefits through physical activity.
UMAP does not preserve global structure any better than t-SNE when using the same initialization
2019-12-19

Abstract One of the most ubiquitous analysis tools employed in single-cell transcriptomics and cytometry is t-distributed stochastic neighbor embedding (t-SNE) [1], used to visualize individual cells as points on a 2D scatter plot such that similar cells are positioned close together. Recently, a related algorithm, called uniform manifold approximation and projection (UMAP) [2] has attracted substantial attention in the single-cell community. In Nature Biotechnology , Becht et al. [3] argued that UMAP is preferable to t-SNE because it better preserves the global structure of the data and is more consistent across runs. Here we show that this alleged superiority of UMAP can be entirely attributed to different choices of initialization in the implementations used by Becht et al.: t-SNE implementations by default used random initialization, while the UMAP implementation used a technique called Laplacian eigenmaps [4] to initialize the embedding. We show that UMAP with random initialization preserves global structure as poorly as t-SNE with random initialization, while t-SNE with informative initialization performs as well as UMAP with informative initialization. Hence, contrary to the claims of Becht et al., their experiments do not demonstrate any advantage of the UMAP algorithm per se , but rather warn against using random initialization.
Effect of wind-driven accretion on planetary migration
2019-12-19

\\nContext. Planetary migration is a key link between planet formation models and observed exoplanet statistics. So far, the theory of planetary migration has focused on the interaction of one or more planets with an inviscid or viscously evolving gaseous disk. Turbulent viscosity is thought to be the main driver of the secular evolution of the disk, and it is known to affect the migration process for intermediate- to high-mass planets. Recently, however, the topic of wind-driven accretion has experienced a renaissance because evidence is mounting that protoplanetary disks may be less turbulent than previously thought, and 3D non-ideal magnetohydrodynamic modeling of the wind-launching process is maturing.\\nAims. We investigate how wind-driven accretion may affect planetary migration. We aim for a qualitative exploration of the main effects and not for a quantitative prediction.\\nMethods. We performed 2D hydrodynamic planet-disk interaction simulations with the FARGO3D code in the (r, φ) plane. The vertical coordinate in the disk and the launching of the wind are not treated explicitly. Instead, the torque caused by the wind onto the disk is treated using a simple two-parameter formula. The parameters are the wind mass-loss rate and the lever arm.\\nResults. We find that the wind-driven accretion process replenishes the co-orbital region in a different way than the viscous accretion process. The former always injects mass from the outer edge of the co-orbital region, and always removes mass from the inner edge, while the latter injects or removes mass from the co-orbital region depending on the radial density gradients in the disk. As a consequence, the migration behavior can differ strongly, and can under certain conditions drive rapid type-III-like outward migration. We derive an analytic expression for the parameters under which this outward migration occurs.\\nConclusions. If wind-driven accretion plays a role in the secular evolution of protoplanetary disks, planetary migration studies have to include this process as well because it can strongly affect the resulting migration rate and migration direction. \\n
Experimental Validation of Mass Balance Models for in Vitro Cell-Based Bioassays
2019-12-19

The freely dissolved concentration in the assay medium (<i>C</i><sub>free</sub>) and the total cellular concentration (<i>C</i><sub>cell</sub>) are essential input parameters for quantitative in vitro-to-in vivo extrapolations (QIVIVE), but available prediction tools for <i>C</i><sub>free</sub> and <i>C</i><sub>cell</sub> have not been sufficiently validated with experimental data. In this study, medium-water distribution ratios (<i>D</i><sub>FBS/w</sub>) and cell-water distribution ratios (<i>D</i><sub>cell/w</sub>) for four different cells lines were determined experimentally for 12 neutral and five ionizable chemicals. Literature data for seven organic acids were added to the dataset, leading to 24 chemicals in total. A mass balance model based on bovine serum albumin-water (<i>D</i><sub>BSA/w</sub>) and liposome-water distribution ratios (<i>D</i><sub>lip/w</sub>) of the chemicals was used to calculate <i>D</i><sub>FBS/w</sub> and <i>D</i><sub>cell/w</sub>. For all neutral and basic test chemicals, the mass balance model predicted <i>D</i><sub>FBS/w</sub> and <i>D</i><sub>cell/w</sub> within a factor of 3 and 3.4, respectively, indicating that existing models can reliably predict <i>C</i><sub>free</sub> and <i>C</i><sub>cell</sub> for these chemicals. For organic acids, a further refinement of the model will be required as large deviations between modeled and measured binding to assay medium and cells of up to a factor of 370 were found. Furthermore, saturation of medium proteins should be further explored for organic acids and neutral chemicals with moderate hydrophobicity.
Simultaneous observations of the blazar PKS 2155−304 from ultra-violet to TeV energies
2019-12-19

Here we report the results of the first ever contemporaneous multi-wavelength observation campaign on the BL Lac object PKS 2155−304 involving Swift , NuSTAR , Fermi -LAT, and H.E.S.S. The use of these instruments allows us to cover a broad energy range, which is important for disentangling the different radiative mechanisms. The source, observed from June 2013 to October 2013, was found in a low flux state with respect to previous observations but exhibited highly significant flux variability in the X-rays. The high-energy end of the synchrotron spectrum can be traced up to 40 keV without significant contamination by high-energy emission. A one-zone synchrotron self-Compton model was used to reproduce the broadband flux of the source for all the observations presented here but failed for previous observations made in April 2013. A lepto-hadronic solution was then explored to explain these earlier observational results.
Methylation of CpG 5962 in L1 of the human papillomavirus 16 genome as a potential predictive marker for viral persistence: A prospective large cohort study using cervical swab samples
2019-12-19

Abstract Several studies have demonstrated that the viral genome can be methylated by the host cell during progression from persistent infection to cervical cancer. The aim of this study was to investigate whether methylation at a specific site could predict the development of viral persistence and whether viral load shows a correlation with specific methylation patterns. HPV16‐positive samples from women aged 20–29 years (n = 99) with a follow‐up time of 13 years, were included from a Danish cohort comprising 11 088 women. Viral load was measured by real‐time PCR and methylation status was determined for 39 CpG sites in the upstream regulatory region (URR), E6/E7, and L1 region of HPV16 by next‐generation sequencing. Participants were divided into two groups according to whether they were persistently (≥ 24 months) or transiently HPV16 infected. The general methylation status was significantly different between women with a persistent and women with a transient infection outcome ( P = .025). One site located in L1 (nt. 5962) was statistically significantly ( P = .00048) different in the methylation status after correction using the Holm‐Sidak method (alpha = 0.05). Correlation analyses of samples from HPV16 persistently infected women suggest that methylation is higher although viral load is lower. This study indicates that methylation at position 5962 of the HPV16 genome within the L1 gene might be a predictive marker for the development of a persistent HPV16 infection.
Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline
2019-12-19

Abstract One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is DNA- or RNA-based 16S rRNA (gene) amplicon sequencing. Subsequent bioinformatics analyses are required to extract valuable information from the high-throughput sequencing approach. However, manifold bioinformatics tools complicate their choice and might cause differences in data interpretation, making the selection of the pipeline a crucial step. Here, we compared the performance of most widely used 16S rRNA gene amplicon sequencing analysis tools (i.e. Mothur, QIIME1, QIIME2, and MEGAN) using mock datasets and environmental samples from contrasting terrestrial and freshwater sites. Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (&gt;10 times less false positives), taxonomic assignments (&gt;22% better F-score) and diversity estimates (&gt;5% better assessment), while there was still room for improvement e.g. imperfect sequence recovery (recall up to 87%) or detection of additional false sequences (precision up to 72%). Furthermore, we found that microbial diversity estimates and highest abundant taxa varied among analysis pipelines (i.e. only one in five genera was shared among all analysis tools) when analyzing environmental samples, which might skew biological conclusions. Our findings were subsequently implemented in a high-performance computing conformant workflow following the FAIR (Findable, Accessible, Interoperable, and Re-usable) principle, allowing reproducible 16S rRNA gene amplicon sequence analysis starting from raw sequence files. Our presented workflow can be utilized for future studies, thereby facilitating the analysis of high-throughput DNA- or RNA-based 16S rRNA (gene) sequencing data substantially. Importance Microorganisms play an essential role in biogeochemical cycling events across the globe. Phylogenetic marker gene analysis is a widely used method to explore microbial community dynamics in space and time, to predict the ecological relevance of microbial populations, or to identify microbial key players in biogeochemical cycles. Several computational analysis methods were developed to aid 16S rRNA gene analysis but choosing the best method is not trivial. In this study, we compared popular analysis methods (i.e. Mothur, QIIME1 and 2, and MEGAN) using samples with known microbial composition (i.e. mock community samples) and environmental samples from contrasting habitats (i.e. groundwater, soil, sediment, and river water). Our findings provide guidance for choosing the currently optimal 16S rRNA gene sequencing analysis method and we implemented our recommended pipeline into a reproducible workflow, which follows highest bioinformatics standards and is open source and free to use.
The Spatial Numerical Association of Response Codes effect and math skills: why related?
2019-12-19

Evidence from multiple studies conducted in the past few decades converges on the conclusion that numerical properties can be associated with specific directions in space. Such Spatial-Numerical Associations (SNAs), as a signature of elementary number processing, seem to be a likely correlate of math skills. Nevertheless, almost three decades of research on the Spatial Numerical Association of Response Codes (SNARC) effect, the hallmark of SNAs, has not provided conclusive results on whether there is a relation with math skills. Here, going beyond reviewing the existing literature on the topic, we try to answer a more fundamental question about WHY the SNARC effect should (and should not) be related to math skills. We propose a multi-route model framework for a SNARC-math skills relationship. We conclude that the relationship is not straightforward and that several other factors should be considered, which under certain circumstances or in certain groups, can cause effects of opposite directions. The model can account for conflicting results, and thus may be helpful for deriving predictions in future studies.
Objects, Events, and Property-Instances
2019-12-19

The theory of events as property-instances has been considered one of the most widely accepted metaphysical theories of events. On the other hand, several philosophers claim that if both events and objects perdure, then objects must be identified with events. In this work, I investigate whether these two views can be held together. I shall argue that if they can, it depends on the particular theory of instantiation one is to adopt. In particular, I shall conclude that the theory of events as property-instances and the view that identifies objects with events can be held together only if instances of eventive universals are temporal parts of objects – namely, those temporal parts that have the universals in question.
Some generalized characters associated to a transitive permutation group
2019-12-19

Abstract Let G be a finite transitive permutation group of degree n , with point stabilizer <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>H</m:mi> <m:mo>≠</m:mo> <m:mn>1</m:mn> </m:mrow> </m:math> {H\\neq 1} and permutation character π. For every positive integer t , we consider the generalized character <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:msub> <m:mi>ψ</m:mi> <m:mi>t</m:mi> </m:msub> <m:mo>=</m:mo> <m:mrow> <m:msub> <m:mi>ρ</m:mi> <m:mi>G</m:mi> </m:msub> <m:mo>-</m:mo> <m:mrow> <m:mi>t</m:mi> <m:mo>⁢</m:mo> <m:mrow> <m:mo>(</m:mo> <m:mrow> <m:mi>π</m:mi> <m:mo>-</m:mo> <m:msub> <m:mn>1</m:mn> <m:mi>G</m:mi> </m:msub> </m:mrow> <m:mo>)</m:mo> </m:mrow> </m:mrow> </m:mrow> </m:mrow> </m:math> {\\psi_{t}=\\rho_{G}-t(\\pi-1_{G})} , where <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msub> <m:mi>ρ</m:mi> <m:mi>G</m:mi> </m:msub> </m:math> {\\rho_{G}} is the regular character of G and <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msub> <m:mn>1</m:mn> <m:mi>G</m:mi> </m:msub> </m:math> {1_{G}} the 1-character. We give necessary and sufficient conditions on t (and G ) which guarantee that <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msub> <m:mi>ψ</m:mi> <m:mi>t</m:mi> </m:msub> </m:math> {\\psi_{t}} is a character of G . A necessary condition is that <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>t</m:mi> <m:mo>≤</m:mo> <m:mrow> <m:mi>min</m:mi> <m:mo>⁡</m:mo> <m:mrow> <m:mo>{</m:mo> <m:mrow> <m:mi>n</m:mi> <m:mo>-</m:mo> <m:mn>1</m:mn> </m:mrow> <m:mo>,</m:mo> <m:mrow> <m:mo>|</m:mo> <m:mi>H</m:mi> <m:mo>|</m:mo> </m:mrow> <m:mo>}</m:mo> </m:mrow> </m:mrow> </m:mrow> </m:math> {t\\leq\\min\\{n-1,\\lvert H\\rvert\\}} , and it turns out that <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msub> <m:mi>ψ</m:mi> <m:mi>t</m:mi> </m:msub> </m:math> {\\psi_{t}} is a character of G for <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>t</m:mi> <m:mo>=</m:mo> <m:mrow> <m:mi>n</m:mi> <m:mo>-</m:mo> <m:mn>1</m:mn> </m:mrow> </m:mrow> </m:math> {t=n-1} resp. <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>t</m:mi> <m:mo>=</m:mo> <m:mrow> <m:mo>|</m:mo> <m:mi>H</m:mi> <m:mo>|</m:mo> </m:mrow> </m:mrow> </m:math> {t=\\lvert H\\rvert} precisely when G is 2-transitive resp. a Frobenius group.
Christian and Jewish Readers of the Bible. Rosenzweig’s Contribution to a Theological Hermeneutics of the Scriptures – a Protestant Perspective
2019-12-19

How can the Christian reader regard the Old Testament as a canonical part of the Bible? The article argues that not only in the late essays of Franz Rosenzweig, dealing with questions of hermeneutics, but also in the Star of Redemption we find arguments to read the whole Bible in a Christian and a Jewish perspective. There is good news of Gods grace in the Christian Old Testament already. Rosenzweig of- fers a hermeneutic of the conjunction and which presupposes a dialogical experience and prepares the way of further dialogue between Christian, Jewish and possibly also Muslim or “religious unmusical” readers of the Bible. This book gives witness of a common human experience in three dimensions, including the experience not only of man and the world, but also of God who is one in the Old and the New Testament.