julilili42/papers huggingface dataset:
Rapid evolution in native plants cultivated for ecological restoration: not a general pattern
2018-08-18

Abstract The growing number of restoration projects worldwide increases the demand for seed material of native species. To meet this demand, seeds are often produced through large‐scale cultivation on specialised farms, using wild‐collected seeds as the original sources. However, during cultivation, plants experience novel environmental conditions compared to those in natural populations, and there is a danger that the plants in cultivation are subject to unintended selection and lose their adaptation to natural habitats. Although the propagation methods are usually designed to maintain as much natural genetic diversity as possible, the effectiveness of these measures have never been tested. We obtained seed of five common grassland species from one of the largest native seed producers in Germany. For each species, the seeds were from multiple generations of seed production. We used AFLP markers and a common garden experiment to test for genetic and phenotypic changes during cultivation of these plants. The molecular markers detected significant evolutionary changes in three out of the five species and we found significant phenotypic changes in two species. The only species that showed substantial genetic and phenotypic changes was the short‐lived and predominantly selfing Medicago lupulina , while in the other, mostly perennial and outcrossing species, the observed changes were mostly minor. Agricultural propagation of native seed material for restoration can cause evolutionary changes, at least in some species. We recommend caution, particularly in selfing and short‐lived species, where evolution may be more rapid and effects may thus be more severe.
Stress-Induced Phosphorylation of Nuclear YB-1 Depends on Nuclear Trafficking of p90 Ribosomal S6 Kinase
2018-08-18

Ionizing radiation (IR) and epidermal growth factor (EGF) stimulate Y-box binding protein-1 (YB-1) phosphorylation at Ser-102 in KRAS wild-type (KRASwt) cells, whereas in KRAS mutated (KRASmut) cells, YB-1 is constitutively phosphorylated, independent of IR or EGF. YB-1 activity stimulates the repair of IR-induced DNA double-strand breaks (DSBs) in the nucleus. Thus far, the YB-1 nuclear translocation pattern after cell exposure to various cellular stressors is not clear. In the present study, we investigated the pattern of YB-1 phosphorylation and its possible translocation to the nucleus in KRASwt cells after exposure to IR, EGF treatment, and conditional expression of mutated KRAS(G12V). IR, EGF, and conditional KRAS(G12V) expression induced YB-1 phosphorylation in both the cytoplasmic and nuclear fractions of KRASwt cells. None of the stimuli induced YB-1 nuclear translocation, while p90 ribosomal s6 kinase (RSK) translocation was enhanced in KRASwt cells after any of the stimuli. EGF-induced RSK translocation to the nucleus and nuclear YB-1 phosphorylation were completely blocked by the EGF receptor kinase inhibitor erlotinib. Likewise, RSK inhibition blocked RSK nuclear translocation and nuclear YB-1 phosphorylation after irradiation and KRAS(G12V) overexpression. In summary, acute stimulation of YB-1 phosphorylation does not lead to YB-1 translocation from the cytoplasm to the nucleus. Rather, irradiation, EGF treatment, or KRAS(G12V) overexpression induces RSK activation, leading to its translocation to the nucleus, where it activates already-existing nuclear YB-1. Our novel finding illuminates the signaling pathways involved in nuclear YB-1 phosphorylation and provides a rationale for designing appropriate targeting strategies to block YB-1 in oncology as well as in radiation oncology.
NAMPT signaling is critical for the proangiogenic activity of tumor‐associated neutrophils
2018-08-19

Tumor‐associated neutrophils (TANs) regulate many processes associated with tumor progression, and depending on the microenvironment, they can exhibit pro‐ or antitumor functions. However, the molecular mechanisms regulating their tumorigenicity are not clear. Using transplantable tumor models, we showed here that nicotinamide phosphoribosyltransferase (NAMPT), a molecule involved in CSF3R downstream signaling, is essential for tumorigenic conversion of TANs and their pro‐angiogenic switch. As a result tumor vascularization and growth are strongly supported by these cells. Inhibition of NAMPT in TANs leads to their antitumor conversion. Adoptive transfer of such TANs into B16F10‐tumor bearing mice attenuates tumor angiogenesis and growth. Of note, we observe that the regulation of NAMPT signaling in TANs, and its effect on the neutrophil tumorigenicity, are analogous in mice and human. NAMPT is up‐regulated in TANs from melanoma and head‐and‐neck tumor patients, and its expression positively correlates with tumor stage. Mechanistically, we found that targeting of NAMPT suppresses neutrophil tumorigenicity by inhibiting SIRT1 signaling, thereby blocking transcription of pro‐angiogenic genes. Based on these results, we propose that NAMPT regulatory axis is important for neutrophils to activate angiogenic switch during early stages of tumorigenesis. Thus, identification of NAMPT as the critical molecule priming protumor functions of neutrophils provides not only mechanistic insight into the regulation of neutrophil tumorigenicity, but also identifies a potential pathway that may be targeted therapeutically in neutrophils. This, in turn, may be utilized as a novel mode of cancer immunotherapy.
Specifying the boundary conditions of the multimedia effect: The influence of content and its distribution between text and pictures
2018-08-19

It was investigated whether the beneficial effect of picture presentation might be influenced by the content conveyed through text and pictures and the way information is distributed between them. Ninety‐nine students learnt in five between‐subjects learning conditions (i.e., text with spatial contents plus pictures, text with visual contents plus pictures, only text with spatial contents, only text with visual contents, only picture) about a tourist centre and a holiday farm. Results showed that pictures (i.e., maps) were beneficial for learning if spatial knowledge had to be acquired, but did not support learning when non‐spatial, visual knowledge had to be acquired. Furthermore, a high overlap of spatial information in text and picture was helpful, which can be explained by the assumption that learning is a text‐guided process. On the other hand, regarding non‐spatial visual information, a high text‐picture overlap did not influence learning, probably because text alone was sufficient for acquiring visual knowledge. The implications of these findings are discussed.
Clinical presentation and natural history of infantile-onset ascending spastic paralysis from three families with an ALS2 founder variant
2018-08-20

Biallelic mutations of the alsin Rho guanine nucleotide exchange factor (ALS2) gene cause a group of overlapping autosomal recessive neurodegenerative disorders including infantile-onset ascending hereditary spastic paralysis (IAHSP), juvenile primary lateral sclerosis (JPLS), and juvenile amyotrophic lateral sclerosis (JALS/ALS2), caused by retrograde degeneration of the upper motor neurons of the pyramidal tracts. Here, we describe 11 individuals with IAHSP, aged 2-48 years, with IAHSP from three unrelated consanguineous Iranian families carrying the homozygous c.1640+1G>A founder mutation in ALS2. Three affected siblings from one family exhibit generalized dystonia which has not been previously described in families with IAHSP and has only been reported in three unrelated consanguineous families with JALS/ALS2. We report the oldest individuals with IAHSP to date and provide evidence that these patients survive well into their late 40s with preserved cognition and normal eye movements. Our study delineates the phenotypic spectrum of IAHSP and ALS2-related disorders and provides valuable insights into the natural disease course.
First‐trimester ductus venosus velocity ratio as a marker of major cardiac defects
2018-08-20

ABSTRACT Objectives To examine ductus venosus (DV) flow in fetuses with and those without a cardiac defect and to evaluate different phases of DV flow in addition to the standard assessment of DV pulsatility index for veins (PIV) and the a‐wave. Methods This was a retrospective study of singleton pregnancies that underwent first‐trimester ultrasound screening, which included DV flow assessment, at the University of Tübingen (between 2010 and 2017) or the University of Cologne (between 2013 and 2016). The study population comprised normal fetuses and fetuses with major cardiac defects at a ratio of 10:1. For each fetus, the following parameters of the DV waveform were evaluated: qualitative assessment of the a‐wave, PIV measurement and ratios of flow velocities during the S‐wave (S) or D‐wave (D) and the a‐wave (a) or v‐wave (v). Reproducibility of DV‐PIV and DV flow ratios was evaluated in 30 fetuses in which the DV flow was assessed twice. Results Our study population included 480 anatomically normal fetuses and 48 with a cardiac defect. Median fetal nuchal translucency (NT) in the normal and in the affected group was 1.9 mm and 2.6 mm, respectively. In five (1.0%) of the normal and 18 (37.5%) of the affected cases, fetal NT thickness was above the 99 th centile. In the normal group, the DV a‐wave was reversed in 15 (3.1%) cases and the DV‐PIV was above the 95 th centile in 25 (5.2%). In the cases with cardiac defects, the a‐wave was reversed and the DV‐PIV measurement was above the 95 th centile in 26 (54.2%). The reproducibility of measurement of the ratios of DV flow velocities was similar to that of the DV‐PIV. Most cardiac defects were associated with an abnormal a/S or a/D ratio. If the cut‐off for these two ratios was set at the 5 th centile of the normal distribution, the detection rate of fetal cardiac anomalies would be 62.5%. This compares favorably with the DV‐PIV, which detects 26 (54.2%) of the affected fetuses for the same threshold. Conclusion In the first trimester, the a/S ratio has the potential to detect approximately 60% of congenital cardiac defects for a false‐positive rate of 5%. Copyright © 2018 ISUOG. Published by John Wiley &amp; Sons Ltd.
Fear of cancer progression in patients with stage IA malignant melanoma
2018-08-20

We aimed to determine the prevalence and importance of fear of cancer progression (FoP) in melanoma patients with stage IA tumours to assess psychosocial and demographic factors associated with severity of FoP and to determine the relationship of FoP and quality of life (QoL). One hundred and thirty-six patients with stage IA melanoma completed the short version of the Fear of Progression Questionnaire (FoP-Q-SF), the Hospital Anxiety and Depression Scale (HADS) and the EORTC-QLQ-C30. We found a mean FoP-Q-SF sum score of 30.2 points (±8.4 points SD). In this study, 33% of patients reported high FoP at or above the cutoff-value of 34 points. Higher FoP was found in women (p < 0.01), young (p = 0.03) and employed (p = 0.02) patients. Being confronted with a cancer diagnosis in closely related persons predicted higher FoP (p < 0.01). FoP correlated positively with the HADS anxiety (r = 0.50, p < 0.01) and depression scales (r = 0.26, p < 0.01) and negatively with the EORTC-QLQ-C30 global health state (r = -0.32, p < 0.01). FoP is considerably prevalent in low-risk melanoma patients and associated with reduced QoL, cancer in related persons, women sex and participation in working life. Considerably high levels of FoP, even in patients with low-risk malignancies, underline the need for psychosocial support and psychotherapeutic interventions for melanoma patients.
Lewis‐Acid Stabilized Organoimide Complexes of Divalent Samarium, Europium, and Ytterbium
2018-08-20

Abstract Discrete organoimide complexes of the divalent rare‐earth metals samarium, europium, and ytterbium are reported. Tandem salt metathesis‐protonolysis reactions using Ln II bis(tetramethylaluminate) precursors [Ln(AlMe 4 ) 2 ] n and monopotassium salts of 2,6‐diisopropylaniline (H 2 NDipp) and triphenylsilylamine prove viable and efficient protocols. Depending on the ionic radius of the Ln II metal centers and the steric demand of the imido carbon backbone, mono‐ and dilanthanide arrangements of general composition [(thf) x Ln(NR)(AlMe 3 )] y (Ln=Sm, Eu, Yb; R=Dipp, SiPh 3 ) are found in the solid state. Complex formation and stabilization is achieved by coordination of the Lewis acid AlMe 3 , which also prevents formation of higher aggregated species. The feasibility of redox chemistry is shown with the plumbocene derivative Cp* 2 Pb, providing access to the corresponding monomeric Ln III half‐sandwich complexes [Cp*Ln(NR)(AlMe 3 )(thf) 2 ] (Ln=Sm, Yb).
Controlled experiment contradicts the apparent benefits of the Fenton reaction during anaerobic digestion at a municipal wastewater treatment plant
2018-08-20

Abstract A previous study had reported that the Fenton reaction at full scale increased the digestibility of thickened sludge in a digester. The authors of the study had observed a positive effect on biogas productivity, but without a control. Here, we evaluated this result by investigating the anaerobic treatment characteristics of fresh, thickened sludge in an experimental design with a control. To accomplish this, two identical continuously stirred anaerobic digesters (CSADs) were operated in parallel at mesophilic conditions. We also included anaerobic settlers to mimic the full-scale plant and to accomplish sludge recycling. We fed fresh, thickened sludge to both setups once every other day, but performed the Fenton reaction with only the experimental system by adding H2O2 to the recycled biosolids from the anaerobic settler. We observed very large fluctuations in biogas production due to ever-changing characteristics of the thickened sludge both on a daily and seasonal basis. Regardless, the two setups performed almost identically with: 1) chemical oxygen demand removal efficiencies of 63.8 ± 2.9% and 62.1 ± 3.2%; and 2) biogas productivities of 0.280 and 0.279 L CH4·g−1 volatile solids for the experimental (with Fenton) and control (without Fenton) CSADs, respectively. These results indicate that the use of a Fenton reaction did not affect biogas productivities.
Elastic to Plastic Deformation in Uniaxially Stressed Polylelectrolyte Multilayer Films
2018-08-20

Polyelectrolyte multilayer (PEM) are thin polymeric films produced by alternating adsorption of positively and negatively charged polyelectrolytes (PE) on a substrate. These films are considered drug delivery agents as well as coating material for implants, due to their antibiofouling and biologically benign properties. For these reasons the film mechanical properties as well as response to mechanical stress are important measurement parameters. Especially intriguing is the correlation of the mechanical properties of PEM on macroscopic level with the structure of PEM on molecular level, which is addressed here for the first time. This study investigates PEM from PDADMA/PSS produced by spraying technique with neutron and X-ray reflectometry. Reflectometry technique provides precise information on thickness and density (i.e., electron density or scattering length density, respectively), and, this way, allows to conclude on changes in film composition. Thus, neutron and X-ray reflectometry technique is suitable to investigate the overall and the internal transformations, which PEM films might undergo upon exposure to mechanical load. During uniaxial elongation two regimes of PEM-deformation can be observed: An elastic regime at small elongations (below ca. 0.2%), which is characterized by a reversible change of film thickness, and a plastic regime with a permanent change above this limit. Both regimes have in common, that the mechanical load induces an increase of the film thickness, which is accompanied by an uptake of water from the surrounding atmosphere. The strain causes a molecular rearrangement within the PEM-structure of stratified layers, which, even in elastic regime, is permanent, although the thickness change remains reversible.
What do speaker judgments tell us about theories of quantifier scope in German?
2018-08-20

In this paper we use German data to evaluate configurational and multi-factor approaches to quantifier scope. Configurational theories derive scope relations syntactically at the level of Logical Form; semantic and pragmatic factors are either built into the syntactic representation or ignored, at least during the first derivational step. By contrast, multi-factor approaches consider syntactic, semantic and pragmatic properties of quantifiers as multiple constraints affecting quantifier scope. We examined predictions for quantifier scope in German of the configurational theory by Frey (1993) and of the multi-factor account by Pafel (2005). These fundamentally different approaches were tested in a series of picture verification experiments to assess scope preferences in doubly quantified German sentences. The results show that at least three factors affect the preferred scope. Our findings are neither fully consistent with Frey’s configurational theory nor with Pafel’s multi-factor approach; both theories made incorrect predictions for German doubly quantified sentences with a subject-before-object word order. For object-before-subject sentences, however, the experimental data by and large support the predictions of Pafel’s (2005) multi-factor approach.
DeepLabCut: markerless pose estimation of user-defined body parts with deep learning
2018-08-20

&amp;lt;p&amp;gt;This data entry contains &amp;lt;strong&amp;gt;annotated mouse data from the &amp;lt;a href="https://www.nature.com/articles/s41593-018-0209-y"&amp;gt;DeepLabCut Nature Neuroscience paper&amp;lt;/a&amp;gt;&amp;lt;/strong&amp;gt;.&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;This data entry contains a public release of annotated mouse data from the DeepLabCut paper. The trail-tracking behavior is part of an investigation into odor guided navigation, where one or multiple wildtype (C57BL/6J) mice are running on a paper spool and following&amp;nbsp; odor&amp;nbsp; trails. These experiments were carried out by Alexander Mathis &amp;amp; Mackenzie Mathis in&amp;nbsp; the Murthy lab at Harvard University. &amp;nbsp;&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;Data&amp;nbsp; was&amp;nbsp; recorded by&amp;nbsp; two&amp;nbsp; different&amp;nbsp; cameras&amp;nbsp; (640&amp;times;480&amp;nbsp; pixels with Point Grey Firefly (FMVU-03MTM-CS),&amp;nbsp; and&amp;nbsp; at&amp;nbsp; approximately 1,700&amp;times;1,200 pixels with Grasshopper 3 4.1MP Mono USB3 Vision (CMOSIS CMV4000-3E12)) at 30 Hz.&amp;nbsp; The latter images were&amp;nbsp; cropped around mice to generate images that are approximately 800&amp;times;800. &amp;nbsp;&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;Here we share 1066, frames from multiple experimental sessions observing 7 different mice.&amp;nbsp;&amp;nbsp; Pranav Mamidanna labeled the snout, the tip of the left and right ear as well as the base of the tail in the example images. The data is organized in &amp;lt;a href="https://www.nature.com/articles/s41596-019-0176-0"&amp;gt;DeepLabCut 2.0 project structure&amp;lt;/a&amp;gt; with images and annotations in the labeled-data folder.&amp;nbsp; The names are pseudocodes indicating mouse id and session id, e.g. m4s1 = mouse 4 session 1.&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;Code for loading, visualizing &amp;amp; training deep neural networks available at &amp;lt;a href="http://https://github.com/DeepLabCut/DeepLabCut"&amp;gt; https://github.com/DeepLabCut/DeepLabCut&amp;lt;/a&amp;gt;.&amp;lt;/p&amp;gt;
Data And Generating Files For The Manuscript "A Multi-Model Analysis Of Solute Plume Behavior In A Synthetic Braided-River Deposit", Submitted To Water Resources Research, August 2018.
2018-08-20

Data and generating files for the manuscript "A Multi-Model Analysis of Solute Plume Behavior in a Synthetic Braided-River Deposit", submitted to Water Resources Research, August 2018. This zipped folder contains the codes and data generated for the manuscript. The main routine for generating the ensembles is fidelity/run_fidelity.py. The folders 'dtgeostats', 'flowtrans', and 'hyvr' contain utilities for generating parameter fields and running flow-and-transport simulations. Note that the codes and data are provided as-is and relative pathways, etc. in the code may not function correctly. The data can be found in the fidelity/runfiles/braid005 directory and includes the outputs for the synthetic virtual reality (fidelity/runfiles/braid005/braid_vr) and the following model ensembles: object-based with no conditioning (fidelity/runfiles/braid005/braid_1a), object-based with soft conditioning (fidelity/runfiles/braid005/braid_1b), MPS (fidelity/runfiles/braid005/braid_2a/), isotropic multi-Gaussian (fidelity/runfiles/braid005/braid_3/isn/), and anisotropic multi-Gaussian (fidelity/runfiles/braid005/braid_3/ann/) .
The effects of getting a new teacher on the consistency of personality
2018-08-21

Abstract Objective In the present research, we examined the effect of getting a new teacher on consistency in students’ personality measures, including trait and social cognitive constructs. Method To test the effect of this kind of situational transition, we analyzed two large longitudinal samples ( N = 5,628; N = 2,458) with quasi‐experimental study designs. We used two consistency measures (i.e., rank‐order clations and changes in variance over time) to compare students who got a new teacher with students who kept the same teacher. Results Multiple‐group latent variable analyses showed no differences in the rank‐order correlations for the math‐related social cognitive constructs of interest, effort, self‐concept, self‐regulation, anxiety, and the Big Five personality traits. Significantly lower rank‐order correlations were found for some of the German‐ and English‐related social cognitive constructs (i.e., effort measures) for the group of students who got a new teacher. Regarding the changes in variance (over time), we found no systematic differences between groups in both studies. Conclusions We found partial support for the idea that social cognitive variables are more susceptible to environmental changes (i.e., getting a new teacher) than the Big Five personality traits are.
Putting all students in one basket does not produce equality: gender-specific effects of curricular intensification in upper secondary school
2018-08-21

In recent decades, several countries have made an effort to increase the enrollment rates and performance of students in science and mathematics by means of mandatory, rigorous course work, which is often referred to as curricular intensification (CI). However, there is a lack of research on intended and unintended effects of CI reforms on achievement and motivation. Using representative data from the National Educational Panel Study, we examined effects of a prototypical CI reform in 1 German state. We compared data from the last student cohort before and the first student cohort after the reform at the end of upper secondary school. There was no statistically significant effect on average achievement. However, we found first evidence for differential effects on English reading and a higher English self-concept of young men after the reform, whereas the reform had a negative effect on young women's math self-concept.