julilili42/papers huggingface dataset:
Large-field-of-view optical elastography using digital image correlation for biological soft tissue investigation
2017-03-16

In minimally invasive surgery the haptic feedback, which represents an important tool for the localization of abnormalities, is no longer available. Elastography is an imaging technique that results in quantitative elastic parameters. It can hence be used to replace the lost sense of touch, as to enable tissue localization and discrimination. Digital image correlation is the chosen elastographic imaging technique. The implementation discussed here is clinically sound, based on a spectrally engineered illumination source that enables imaging of biological surface markers (blood vessels) with high contrast. Mechanical loading and deformation of the sample is performed using a rolling indenter, which enables the investigation of large organs (size of kidney) with reduced measurement time compared to a scanning approach. Furthermore, the rolling indentation results in strain contrast improvement and an increase in detection accuracy. The successful application of digital image correlation is first demonstrated on a silicone phantom and later on biological samples. Elasticity parameters and their corresponding four-dimensional distribution are generated via solving the inverse problem (only two-dimensional displacement field and strain map experimentally available) using a well-matched hyperelastic finite element model.
Kuntillet ʿAjrud Inscription 4.3: A Note on the Alleged Exodus Tradition
2017-03-16

It has been proposed recently to read the heavily fragmented plaster inscription 4.3 from Kuntillet ʿAjrud as an attestation of the Exodus tradition. Based on the marked differences from the comparative biblical material, far-reaching conclusions regarding the evolution of the Exodus tradition have been drawn. But the reading suffers from serious problems.
The Volatility of the Discourse on Refugees in Germany
2017-03-16

The anti-immigration continuum of public attitude-media-politics has undergone changes in the course of the "refugee crisis" in Germany. By examining migrant representations and discursive events taking place in 2015 and early 2016, we will show the volatility of the recent discourse on refugees. A historical/critical discourse analysis will show how new topoi arose and old topoi of the security/power paradigm have lastly reconquered the discourse. Using newspaper coverage, we discuss discursive events in three main sections: borders, arrival, and presence. Discursive shifts have taken place that have had an impact on the configuration of migration categories such as migrants or refugees.
VIII. New Zr IV-VII, Xe IV-V, and Xe VII Oscillator Strengths and the Al, Zr, and Xe Abundances in the Hot White Dwarfs G191-B2B and RE0503-289
2017-03-16

Context: For the spectral analysis of high-resolution and high-signal-to-noise spectra of hot stars, state-of-the-art non-local thermodynamic equilibrium (NLTE) model atmospheres are mandatory. These are strongly dependent on the reliability of the atomic data that is used for their calculation. Aims: To search for zirconium and xenon lines in the ultraviolet (UV) spectra of G191−B2B and RE 0503−289, new Zr iv-vii, Xe iv-v, and Xe vii oscillator strengths were calculated. This allows, for the first time, determination of the Zr abundance in white dwarf (WD) stars and improvement of the Xe abundance determinations.Methods: We calculated Zr iv-vii, Xe iv-v, and Xe vii oscillator strengths to consider radiative and collisional bound-bound transitions of Zr and Xe in our NLTE stellar-atmosphere models for the analysis of their lines exhibited in UV observations of the hot WDs G191−B2B and RE 0503−289. Results: We identified one new Zr iv, 14 new Zr v, and ten new Zr vi lines in the spectrum of RE 0503−289. Zr was detected for the first time in a WD. We measured a Zr abundance of −3.5 +/- 0.2 (logarithmic mass fraction, approx. 11 500 times solar). We identified five new Xe vi lines and determined a Xe abundance of −3.9 +/- 0.2 (approx. 7500 times solar). We determined a preliminary photospheric Al abundance of −4.3 +/- 0.2 (solar) in RE 0503−289. In the spectra of G191−B2B, no Zr line was identified. The strongest Zr iv line (1598.948 A) in our model gave an upper limit of −5.6 +/- 0.3 (approx. 100 times solar). No Xe line was identified in the UV spectrum of G191−B2B and we confirmed the previously determined upper limit of −6.8 +/- 0.3 (ten times solar). Conclusions: Precise measurements and calculations of atomic data are a prerequisite for advanced NLTE stellar-atmosphere modeling. Observed Zr iv-vi and Xe vi-vii line profiles in the UV spectrum of RE 0503−289 were simultaneously well reproduced with our newly calculated oscillator strengths.
Prediction of Postoperative Risks in Laparoscopic Partial Nephrectomy Using RENAL, Mayo Adhesive Probability and Renal Pelvic Score
2017-03-17

The MAP score and RENAL nephrometry score seem to be able to predict a complex or complicated intra- and postoperative course, while the renal pelvis score is not suitable for predicting postoperative complications, especially urine leakage.
Bacillus subtilis single-stranded DNA-binding protein SsbA is phosphorylated at threonine 38 by the serine/threonine kinase YabT
2017-03-17

Background and purpose: Single-stranded DNA-binding proteins participate in all stages of DNA metabolism that involve single-stranded DNA, from replication, recombination, repair of DNA damage, to natural competence in species such as Bacillus subtilis. B. subtilis single-stranded DNA-binding proteins have previously been found to be phosphorylated on tyrosine and arginine residues. While tyrosine phosphorylation was shown to enhance the DNA-binding properties of SsbA, arginine phosphorylation was not functionally characterized.Materials and methods: We used mass spectrometry analysis to detect phosphorylation of SsbA purified from B. subtilis cells. The detected phosphorylation site was assessed for its influence on DNA-binding in vitro, using electrophoretic mobility shift assays. The ability of B. subtilis serine/threonine kinases to phosphorylate SsbA was assessed using in vitro phosphorylation assays.Results: In addition to the known tyrosine phosphorylation of SsbA on tyrosine 82, we identified a new phosphorylation site: threonine 38. The in vitro assays demonstrated that SsbA is preferentially phosphorylated by the B. subtilis Hanks-type kinase YabT, and phosphorylation of threonine 38 leads to enhanced cooperative binding to DNA.Conclusions: Our findings contribute to the emerging picture that bacterial proteins, exemplified here by SsbA, undergo phosphorylation at multiple residues. This results in a complex regulation of cellular functions, and suggests that the complexity of the bacterial cellular regulation may be underestimated.
Trust 3D Dust Rt Slab Benchmark Data
2017-03-17

Output global SEDs and images at selected wavelengths for the Slab benchmark of the TRUST collaboration. TRUST is a suite of benchmarks for 3D dust radiative transfer codes in astronomy. Paper describing the TRUST Slab benchmark is Gordon et al. (2017, A&amp;A, 603, 114; http://adsabs.harvard.edu/abs/2017A&amp;A...603A.114G) More details on TRUST at http://ipag.osug.fr/RT13/RTTRUST/. Code to make plots using this data at: https://github.com/karllark/trust_slab
The impact of sedimentary anisotropy on solute mixing in stacked scour‐pool structures
2017-03-19

Abstract The spatial variability of hydraulic conductivity is known to have a strong impact on solute spreading and mixing. In most investigations, its local anisotropy has been neglected. Recent studies have shown that spatially varying orientation in sedimentary anisotropy can lead to twisting flow enhancing transverse mixing, but most of these studies used geologically implausible geometries. We use an object‐based approach to generate stacked scour‐pool structures with either isotropic or anisotropic filling which are typically reported in glacial outwash deposits. We analyze how spatially variable isotropic conductivity and variation of internal anisotropy in these features impacts transverse plume deformation and both longitudinal and transverse spreading and mixing. In five test cases, either the scalar values of conductivity or the spatial orientation of its anisotropy is varied between the scour‐pool structures. Based on 100 random configurations, we compare the variability of velocity components, stretching and folding metrics, advective travel‐time distributions, one and two‐particle statistics in advective‐dispersive transport, and the flux‐related dilution indices for steady state advective‐dispersive transport among the five test cases. Variation in the orientation of internal anisotropy causes strong variability in the lateral velocity components, which leads to deformation in transverse directions and enhances transverse mixing, whereas it hardly affects the variability of the longitudinal velocity component and thus longitudinal spreading and mixing. The latter is controlled by the spatial variability in the scalar values of hydraulic conductivity. Our results demonstrate that sedimentary anisotropy is important for transverse mixing, whereas it may be neglected when considering longitudinal spreading and mixing.
A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina
2017-03-19

Abstract The growing collection of sequenced or genotyped Arabidopsis thaliana accessions includes mostly individuals from the native Eurasian and N. African range and introduced North American populations. Here, we describe the genetic and phenotypic diversity, along with habitats and life history, of A. thaliana plants collected at the southernmost end of its worldwide distribution. Seed samples were harvested from plants growing in four sites within a ~3500‐km 2 ‐area in Patagonia, Argentina, and represent the first germplasm to be collected in South America for this species. Whole‐genome resequencing revealed that plants from the four sites and a Patagonia herbarium specimen collected in 1967 formed a single haplogroup (Pat), indicating that the phenotypic variation observed in the field reflected plastic responses to the environment. admixture and principal components analyses suggest that the ancestor of the Pat haplogroup either came from Italy or the Balkan/Caucasus regions of Eurasia. In the laboratory, plants from the Pat haplogroup were hyposensitive to continuous red (Rc) and shade light, with corresponding changes in the expression of phytochrome signalling genes. Pat had higher PIF 3 and PIF 5 and lower HY 5 expression under Rc light; and lower expression of PIL 1, ATHB 2 and HFR 1 under shade compared to Col‐0. In addition, Pat plants had a strong vernalization requirement associated with high levels of FLC expression. We conclude that including Pat in studies of natural variation and in comparison with other introduced populations will provide additional information for association studies and allow for a more detailed assessment of the demographic events following colonization.
Effects of extracts and compounds from Tricholoma populinum Lange on degranulation and IL-2/IL-8 secretion of immune cells
2017-03-19

Abstract: Tricholoma populinum Lange is an edible basidiomycete from the family Tricholomataceae. Extracts, fractions, and different metabolites isolated from the fruiting bodies of this mushroom were tested for degranulation-inhibiting activities on RBL-2H3 cells (rat basophils). Dichloromethane extracts decreased degranulation significantly, as did a fraction after column chromatography. In addition, the extract decreased the IL-2 release from Jurkat T cells and the release of IL-8 from HMC-1 human mast cells. The results show the significant effects of extracts of T. populinum on cells of the innate (basophils and mast cells) and adaptive (T cells) immune system and indicate the influence of the mushroom on different immunological processes. As one fraction showed activity, it seems to be possible that it includes an active principle. The compounds responsible for this effect, however, could not be identified as the contents oleic acid ( 1 ), ergosterol peroxide ( 2 ), and 9,11-dehydroergosterol peroxide ( 3 ) showed no effects. Nevertheless, the mushroom could be used for supporting allergy treatment in future studies.
Task Effects on Linguistic Complexity and Accuracy: A Large‐Scale Learner Corpus Analysis Employing Natural Language Processing Techniques
2017-03-20

Large‐scale learner corpora collected from online language learning platforms, such as the EF‐Cambridge Open Language Database (EFCAMDAT), provide opportunities to analyze learner data at an unprecedented scale. However, interpreting the learner language in such corpora requires a precise understanding of tasks: How does the prompt and input of a task and its functional requirements influence task‐based linguistic performance? This question is vital for making large‐scale task‐based corpora fruitful for second language acquisition research. We explore the issue through an analysis of selected tasks in EFCAMDAT and the complexity and accuracy of the language they elicit.
Heptacene: Characterization in Solution, in the Solid State, and in Films
2017-03-20

Acenes comprise an important class of organic semiconducting materials. As graphene nanoribbons of ultimate width, they are valuable atom-precise model systems for studying the properties of this form of nanoscale carbon materials. Heptacene is the smallest member of the acene series that could only be studied under matrix isolation conditions. Its existence in bulk had never been positively confirmed, despite efforts dating back more than 70 years. We report that the reduction of 7,16-heptacenequinone produces a mixture of two diheptacene molecules. The diheptacenes undergo thermal cleavage to heptacene at high temperatures in the solid state. Monitoring this cycloreversion by solid state <sup>13</sup>C cross-polarized magic angle spinning NMR reveals that solid heptacene has a half-life time of several weeks at room temperature. The diheptacenes are valuable precursors for generating films of heptacene by vapor phase deposition that can be studied below or at room temperature.
Regulation of oxidized platelet lipidome: implications for coronary artery disease
2017-03-20

Abstract Aims Hyperlipidaemia enhances susceptibility to thrombosis, while platelet oxidixed LDL (oxLDL) binding in acute coronary syndrome (ACS) correlates with activation status. This study explores the platelet lipidome in symptomatic coronary artery disease (CAD) patients and the functional consequences of the chemokine CXCL12 and its receptors CXCR-4/-7 on lipid uptake in platelets. Methods and results Platelet–oxLDL detected by flow cytometry was enhanced (P = 0.04) in CAD patients, moderately correlated with platelet CXCR7 surface expression (ρ = 0.39; P &amp;lt; 0.001), while inversely with CXCR4 (ρ = 0.35; P &amp;lt; 0.001). Platelet–oxLDL was elevated (P = 0.01) in ACS patients with angiographic evidence of intracoronary thrombi. Ex vivo analysis of intracoronary thrombi sections revealed oxLDL deposition in platelet-enriched areas verified by immunofluorescence confocal microscopy. LDL–oxLDL uptake enhanced reactive oxygen species, mitochondrial superoxide generation, intraplatelet LDL to oxLDL conversion, and lipid peroxidation, counteracted by SOD2–mimetic MnTMPyP. Lipidomic analysis revealed enhanced intraplatelet-oxidized phospholipids, cholesteryl esters, sphingomyelin, ceramides, di- and triacylglycerols, acylcarnitines in CAD patients compared with age-matched controls as ascertained by liquid chromatography hyphenated to high-resolution mass spectrometry. LDL–oxLDL induced degranulation, αIIbβ3-integrin activation, apoptosis, thrombin generation estimated by calibrated automated thrombinoscopy, and shape change verified by live imaging using scanning ion conductance microscopy. Further, LDL–oxLDL enhanced thrombus formation ex vivo and in vivo in mice (ferric chloride-induced carotid artery injury). LDL–oxLDL enhanced platelet CXCL12 release, differentially regulated CXCR4–CXCR7 surface exposure, while CXCL12 prompted LDL–oxLDL uptake and synergistically augmented the LDL–oxLDL-induced pro-oxidative, thrombogenic impact on platelet function. Conclusion An altered platelet lipidome might be associated with thrombotic disposition in CAD, a mechanism potentially regulated by CXCL12–CXCR4–CXCR7 axis.
Chromium(0), Molybdenum(0), and Tungsten(0) Isocyanide Complexes as Luminophores and Photosensitizers with Long‐Lived Excited States
2017-03-20

Abstract Arylisocyanide complexes based on earth‐abundant Group 6 d 6 metals are interesting alternatives to photoactive complexes made from precious metals such as Ru II , Re I , Os II , or Ir III . Some of these complexes have long‐lived 3 MLCT excited states that exhibit luminescence with good quantum yields as well as nano‐ to microsecond lifetimes, and they are very strongly reducing. Recent studies have demonstrated that Cr 0 , Mo 0 , and W 0 arylisocyanide complexes have great potential for applications in luminescent devices, photoredox catalysis, and dye‐sensitized solar cells.
Vagueness and Imprecise Imitation in Signalling Games
2017-03-20

Signalling games are popular models for studying the evolution of meaning, but typical approaches do not incorporate vagueness as a feature of successful signalling. Complementing recent like-minded models, we describe an aggregate population-level dynamic that describes a process of imitation of successful behaviour under imprecise perception and realization of similar stimuli. Applying this new dynamic to a generalization of Lewis's signalling games, we show that stochastic imprecision leads to vague, yet by-and-large efficient signal use, and, moreover, that it unifies evolutionary outcomes and helps avoid sub-optimal categorization. The upshot of this is that we see 'as-if'-generalization at an aggregate level, without agents actually generalizing. 1 Introduction2 Background 2.1 Sim-max games and conceptual spaces 2.2 Vagueness in sim-max games and conceptual spaces 2.3 Vagueness, functional pressure, and transmission biases3 Imprecise Imitation 3.1 Replicator dynamic in behavioural strategies 3.2 Noise-perturbed conditional imitation4 Exploring Imprecise Imitation 4.1 Setting the stage 4.2 Simulation set-up 4.3 Measures of interest 4.4 Results5 Discussion 5.1 Levels of vagueness 5.2 Evolutionary benefits of imprecision 5.3 Related work6 ConclusionAppendix
Modeling real shim fields for very high degree (and order) B0 shimming of the human brain at 9.4 T
2017-03-20

Purpose To describe the process of calibrating a B 0 shim system using high‐degree (or high order) spherical harmonic models of the measured shim fields, to provide a method that considers amplitude dependency of these models, and to show the advantage of very high‐degree B 0 shimming for whole‐brain and single‐slice applications at 9.4 Tesla (T). Methods An insert shim with up to fourth and partial fifth/sixth degree (order) spherical harmonics was used with a Siemens 9.4T scanner. Each shim field was measured and modeled as input for the shimming algorithm. Optimal shim currents can therefore be calculated in a single iteration. A range of shim currents was used in the modeling to account for possible amplitude nonlinearities. The modeled shim fields were used to compare different degrees of whole‐brain B 0 shimming on healthy subjects. Results The ideal shim fields did not correctly shim the subject brains. However, using the modeled shim fields improved the B 0 homogeneity from 55.1 (second degree) to 44.68 Hz (partial fifth/sixth degree) on the whole brains of 9 healthy volunteers, with a total applied current of 0.77 and 6.8 A, respectively. Conclusions The necessity of calibrating the shim system was shown. Better B 0 homogeneity drastically reduces signal dropout and distortions for echo‐planar imaging, and significantly improves the linewidths of MR spectroscopy imaging. Magn Reson Med 79:529–540, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Design and Synthesis of Novel Anti‐Plasmodial Histone Deacetylase Inhibitors Containing an Alkoxyamide Connecting Unit
2017-03-20

Despite recent declines in mortality, malaria remains an important global health problem. New therapies are needed, including new drugs with novel modes of action compared to existing agents. Among new potential therapeutic targets for malaria, inhibition of parasitic histone deacetylases (HDACs) is a promising approach. Homology modeling of Pf HDAC1, a known target of some anti‐plasmodial HDAC inhibitors, revealed a unique threonine residue at the rim of the active site in close proximity to the location of the cap group of vorinostat‐type HDAC inhibitors. Aiming to obtain HDAC inhibitors with potent and preferential anti‐plasmodial activity, we synthesized a mini‐library of alkoxyamide‐based HDAC inhibitors containing hydrogen bond acceptors in the cap group. Using a 5‐step synthetic route, 12 new inhibitors were synthesized and assayed against Plasmodium falciparum asexual blood stage parasites (clones 3D7 and Dd2) and human cells (HepG2). The most active compound 6h ( Pf 3D7 IC 50 : 0.07 μM; Pf Dd2 IC 50 : 0.07 μM) was 25‐fold more toxic against the parasite versus human HepG2 cells. Selected compounds were shown to cause hyperacetylation of P. falciparum histone H4, indicating inhibition of one or more Pf HDACs.
Ubiquitously expressed Human Beta Defensin 1 (hBD1) forms bacteria-entrapping nets in a redox dependent mode of action
2017-03-21

Ever since the discovery of endogenous host defense antimicrobial peptides it has been discussed how these evolutionary conserved molecules avoid to induce resistance and to remain effective. Human ß-defensin 1 (hBD1) is an ubiquitously expressed endogenous antimicrobial peptide that exhibits qualitatively distinct activities between its oxidized and reduced forms. Here, we explore these antimicrobial mechanisms. Surprisingly, using electron microscopy we detected a so far unknown net-like structure surrounding bacteria, which were treated with the reduced but not the oxidized form of hBD1. A transmigration assay demonstrated that hBD1-derived nets capture bacteria and inhibit bacterial transmigration independent of bacterial killing. The presence of nets could completely prevent migration of hBD1 resistant pathogens and are stable in the presence of human duodenal secretion with a high amount of proteases. In contrast to HD6, cysteins are necessary for net formation. This redox-dependent function serves as an additional mechanism of action for hBD1 and differs from net formation by other defensins such as Paneth cell-derived human α-defensin 6 (HD6). While hBD1red and hBD1ox have distinct antimicrobial profiles and functions, only the reduced form provides additional host protection by entrapping bacteria in extracellular net structures preventing bacterial invasion. Better understanding of the modes of action of endogenous host peptides will help to find new antimicrobial strategies.