julilili42/papers huggingface dataset:
Molecular archaeoparasitology identifies cultural changes in the Medieval Hanseatic trading centre of Lübeck
2018-10-03

Throughout history, humans have been afflicted by parasitic worms, and eggs are readily detected in archaeological deposits. This study integrated parasitological and ancient DNA methods with a large sample set dating between Neolithic and Early Modern periods to explore the utility of molecular archaeoparasitology as a new approach to study the past. Molecular analyses provided unequivocal species-level parasite identification and revealed location-specific epidemiological signatures. Faecal–oral transmitted nematodes ( Ascaris lumbricoides and Trichuris trichiura ) were ubiquitous across time and space. By contrast, high numbers of food-associated cestodes ( Diphyllobothrium latum and Taenia saginata ) were restricted to medieval Lübeck. The presence of these cestodes and changes in their prevalence at approximately 1300 CE indicate substantial alterations in diet or parasite availability. Trichuris trichiura ITS-1 sequences grouped into two clades; one ubiquitous and one restricted to medieval Lübeck and Bristol. The high sequence diversity of T.t .ITS-1 detected in Lübeck is consistent with its importance as a Hanseatic trading centre. Collectively, these results introduce molecular archaeoparasitology as an artefact-independent source of historical evidence.
VHE γ-ray discovery and multi-wavelength study of the blazar 1ES 2322-409
2018-10-03

A hotspot at a position compatible with the BL Lac object 1ES 2322−409 was serendipitously detected with H.E.S.S. during observations performed in 2004 and 2006 on the blazar PKS 2316−423. Additional data on 1ES 2322−409 were taken in 2011 and 2012, leading to a total live-time of 22.3 h. Point-like very-high-energy (VHE; ⁠) γ-ray emission is detected from a source centred on the 1ES 2322−409 position, with an excess of 116.7 events at a significance of 6.0σ. The average VHE γ-ray spectrum is well described with a power law with a photon index Γ = 3.40 ± 0.66stat ± 0.20sys and an integral flux = ⁠, which corresponds to 1.1 of the Crab nebula flux above ⁠. Multiwavelength data obtained with Fermi LAT, Swift XRT and UVOT, RXTE PCA, ATOM, and additional data from WISE, GROND, and Catalina are also used to characterize the broad-band non-thermal emission of 1ES 2322−409. The multiwavelength behaviour indicates day-scale variability. Swift UVOT and XRT data show strong variability at longer scales. A spectral energy distribution (SED) is built from contemporaneous observations obtained around a high state identified in Swift data. A modelling of the SED is performed with a stationary homogeneous one-zone synchrotron-self-Compton leptonic model. The redshift of the source being unknown, two plausible values were tested for the modelling. A systematic scan of the model parameters space is performed, resulting in a well-constrained combination of values providing a good description of the broad-band behaviour of 1ES 2322−409.
Impacts of species richness on productivity in a large-scale subtropical forest experiment
2018-10-04

Tree diversity improves forest productivity Experimental studies in grasslands have shown that the loss of species has negative consequences for ecosystem functioning. Is the same true for forests? Huang et al. report the first results from a large biodiversity experiment in a subtropical forest in China. The study combines many replicates, realistic tree densities, and large plot sizes with a wide range of species richness levels. After 8 years of the experiment, the findings suggest strong positive effects of tree diversity on forest productivity and carbon accumulation. Thus, changing from monocultures to more mixed forests could benefit both restoration of biodiversity and mitigation of climate change. Science , this issue p. 80
[PtZn2Ge18(Hyp)8] (Hyp = Si(SiMe3)3): A Neutral Polynuclear Chain Compound with Ge9(Hyp)3 Units
2018-10-04

The reaction of [ZnGe<sub>18</sub>(Hyp)<sub>6</sub>] (Hyp = Si(SiMe<sub>3</sub>)<sub>3</sub>) with Pt(PPh<sub>3</sub>)<sub>4</sub> gives the neutral polynuclear complex of Ge<sub>9</sub>(Hyp)<sub>3</sub> units [HypZn-Ge<sub>9</sub>(Hyp)<sub>3</sub>-Pt-Ge<sub>9</sub>(Hyp)<sub>3</sub>-ZnHyp], 1. Within 1, the central Pt atom is bound η<sup>3</sup> to both Ge<sub>9</sub>(Hyp)<sub>3</sub> units to which further ZnHyp units are bound again, symmetric η<sup>3</sup>, to the other side of the Ge<sub>9</sub>(Hyp)<sub>3</sub> units, leading to the longest chain compound exhibiting Ge<sub>9</sub>(Hyp)<sub>3</sub> units that is known to date. Dissolved crystals of 1 give a violet solution, showing an absorption maximum around 543 nm. Further UV-vis investigations on different M <sub>x</sub>Ge<sub>9</sub>(Hyp)<sub>3</sub> compounds show that the absorption maximum depends on the number of transition metal atoms bound to the Ge<sub>9</sub>(Hyp)<sub>3</sub> unit, which is supported by TD-DFT calculations.
Decay of internal reference information in duration discrimination: Intertrial interval modulates the Type B effect
2018-10-04

Psychophysical evidence suggests that human perception of a stimulus is assimilated towards previous stimuli. The internal reference model (IRM) explains such assimilation through an internal reference (IR), which integrates past and present stimulus representations and thus might be conceived as a form of perceptual memory. In this study, we investigated whether the IR decays with time, as previously shown for perceptual memory representations in general. One specific prediction of IRM is higher discrimination sensitivity when a constant standard precedes rather than follows a variable comparison in a two-alternative forced-choice (2AFC) discrimination task. Furthermore, the magnitude of this so-called negative Type B effect should decrease with decreasing weighting of past stimulus information in the integration process. Therefore, decay of the IR should result in a reduced Type B effect. To examine this prediction, we carried out a 2AFC duration discrimination experiment with a short (1,600 ms) and a long (3,200 ms) intertrial interval (ITI). As expected, a reduced negative Type B effect was observed at the long compared with the short ITI, consistent with the idea that humans rely on the immediate past when evaluating current sensory input, however, less so when the IR incorporating the perceptual short-term memory representation of these past stimuli has already decayed.
Transfection of Peripheral Blood Monocytes withSOX2Enhances Multipotency, Proliferation, and Redifferentiation into Neohepatocytes and Insulin-Producing Cells
2018-10-04

Following a several-day incubation in medium containing IL-3 and M-CSF to generate a more plastic intermediate “reprogrammed multipotent cells of monocytic origin (RMCMO),” peripheral blood mononuclear cells (PBMCs) can be efficiently converted to hepatocyte-like cells (neohepatocytes) and insulin-producing cells. However, continuous efforts are devoted to enhancing the proliferative capacity of these multipotent cells while maintaining or further increasing their redifferentiation potential. In the present work, PBMCs were transfected with one pluripotency gene ( SOX2 ) and the resulting RMCMO compared to standard RMCMO with respect to cell viability, proliferative activity, and redifferentiation potential. Ectopic SOX2 expression increased the number of viable RMCMO, activated cell cycle genes, and enhanced proliferation as shown by quantitative RT-PCR and Ki67 immunofluorescent staining, respectively. Redifferentiation of RMCMO derived from SOX2 -transfected PBMCs to neohepatocytes was more complete in comparison to control cells as revealed by higher urea and glucose secretion, increased activity of cytochrome P450 isoforms, and a phase II enzyme, while the same was true for insulin-producing cells as assessed by the expression of INS , PDX1 , and GLUT2 and glucose-stimulated insulin secretion. Our results indicate that SOX2 transfection increases both multipotency and proliferation of RMCMO, eventually allowing production of neohepatocytes and insulin-producing cells of higher quality and quantity for transplantation purposes.
Übernahmerechtliche Kontrolle
2018-10-04

In Germanys law on takeovers, the mandatory bid rule can come into force when a significant share of a company is acquired. Precisely when this should happen is defined by the concept of control. But is the right balance between outstanding shareholders and investors being struck, or does the demographic of the German shareholder base mean reform is needed?
The CTLA-4 rs231775 GG genotype is associated with favorable 90-day survival in Caucasian patients with sepsis
2018-10-05

Abstract Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) is a surface protein on T cells, that has an inhibitory effect on the host immune reaction and prevents overreaction of the immune system. Because the functional single-nucleotide polymorphism (SNP) rs231775 of the CTLA-4 gene is associated with autoimmune diseases and because of the critical role of the immune reaction in sepsis, we intended to examine the effect of this polymorphism on survival in patients with sepsis. 644 septic adult Caucasian patients were prospectively enrolled in this study. Patients were followed up for 90 days. Mortality risk within this period was defined as primary outcome parameter. Kaplan-Meier survival analysis revealed a significantly lower 90-day mortality risk among GG homozygous patients (n = 101) than among A allele carriers (n = 543; 22% and 32%, respectively; p = 0.03565). Furthermore, the CTLA-4 rs231775 GG genotype remained a significant covariate for 90-day mortality risk after controlling for confounders in the multivariate Cox regression analysis (hazard ratio: 0.624; 95% CI: 0.399–0.975; p = 0.03858). In conclusion, our study provides the first evidence for CTLA-4 rs231775 as a prognostic variable for the survival of patients with sepsis and emphasizes the need for further research to reveal potential functional associations between CTLA-4 and the immune pathophysiology of sepsis.
In vivo Assessment of an Endolymphatic Hydrops Gradient Along the Cochlea in Patients With Menière's Disease by Magnetic Resonance Imaging—A Pilot Study
2018-10-05

Objective: To assess three strategies for evaluation and description of potential endolymphatic hydrops (EH) gradients along the cochlea in patients with Menière's disease. Study Design: Prospective observational study. Methods: Ten patients with definite Menière's disease revealed by magnetic resonance imaging were included in this prospectively conducted pilot study. The presence of cochlear endolymphatic hydrops as well as a potential hydrops gradient along the cochlea were subjectively evaluated by two readers. Furthermore, both readers performed planimetric measurements of the relative extent of endolymphatic hydrops in the cochlear turns for calculation of an apico-basal-index (ABI) and an average gradient slope of the endolymphatic hydrops. These models were correlated with the available pure tone audiometry (PTA). Results: Qualitatively, 13 of 16 inner ears presented an apical EH distribution. The median ABI was 1.69 for patients with low-tone hearing loss and 1.17 for patients with a flat PTA curve ( p = 0.03). The median EH slope was 7.44 and correlated with the steepness of the PTA ( ρ = 0.583; p = 0.018). The subjective analysis and the slope model were best fit for prediction of a low-tone hearing loss type with sensitivities of 100% (specificity, 42.86%) and 88.9% (specificity, 71.4%), respectively. The inter-reader agreement in all three approaches was considered substantial to perfect. Conclusion: The presented qualitative approach and the slope model represent reliable methods for the description of a potential EH gradient along the cochlea. Furthermore, the average EH steepness along the cochlea correlates with the type of hearing loss.
Vertebral Comparative Anatomy and Morphological Differences in Anguine Lizards With a Special Reference to Pseudopus apodus
2018-10-06

ABSTRACT The article reports on the first detailed vertebral and rib morphology of anguine taxon Pseudopus apodus using micro‐computed tomography. A comparison shows significant morphological differences of vertebrae of Pseudopus relative to those of Anguis and Ophisaurus. Usually, there are 55 presacral vertebrae, two sacral, and 95–97 caudal vertebrae. Pseudopus apodus can be defined by 23 diagnostic features concerning the vertebral column. Although zygapophyseal articulation between atlas and axis is well developed in limbed anguid gerrhonotine lizards like Abronia or Barisia , it is absent in the extant representatives of the clade Anguinae, which are limbless. Thus, our study brings further support to the hypothesis about the complete reduction of this articulation in forms with reduced or absent limbs. Comparison of adult and juvenile morphology of vertebrae of P. apodus was also analyzed. Heterochrony in the evolution of this taxon was previously confirmed by its skull morphology and it can be also documented on the basis of vertebrae. Our data suggest that a peramorphic heterochronic process played a role in the evolution of this largest extant anguine species. Geometric morphometric analyses revealed a pattern of high vertebral disparity among species. We found a clear separation of limbless forms in morphospace. Pseudopus apodus always clusters within Ophisaurus ‐species confirming molecular and some morphological phylogenies. Only the first tail vertebra shows a distinct difference to those of other anguids, which might be related to altered locomotion associated to the larger body size in this species. Anat Rec, 302:232–257, 2019. © 2018 Wiley Periodicals, Inc.
How do speculators in agricultural commodity markets impact production decisions and commodity prices? A theoretical analysis
2018-10-06

Abstract We analyze the impact of speculative trading in agricultural commodity markets on major economic quantities. We consider a theoretical model with production shocks, in which a farmer interacts with a retailer in both the spot and the forward market. The contribution of the paper is twofold. First, we show that the current forward price drives agricultural production decisions. Since the forward trading of speculators influences the forward price, they indirectly affect production decisions. Second, we identify crucial variables determining whether speculative trading is beneficial or dangerous, such as the correlation between the speculators’ portfolio and the commodity prices, the risk premium of the forward, and the producer's gains.
Compatibility of a Silicone Impression/Adhesive System to FDM-Printed Tray Materials—A Laboratory Peel-off Study
2018-10-07

Computer-aided design (CAD) and additive manufacturing (AM) have shown promise in facilitating the fabrication of custom trays. Due to the clinical requirements, custom tray materials should achieve good bonding to the impression/adhesive systems. This study evaluated the retention of three fused deposition modeling (FDM) custom tray materials to a silicone impression/adhesive system before and after gritblasting (GB) by peel-off test. CAD-designed experimental test blocks were printed by FDM using acrylonitrile butadiene styrene (ABS), polyethylene terephthalate glycol copolyester (PETG), and high impact polystyrene (HIPS), and the reference test blocks were made of a conventional light-curing resin (n = 11). Before and after GB, the surface topography of all tray materials was analysed, and the maximum strength of the test block peeled off from a silicone impression/adhesive system was measured. After GB, the arithmetic mean height (Sa) and the valley fluid retention index (Svi) of the four material groups declined (p &lt; 0.05). The peel-off strength of each of the four material groups significantly decreased by GB (p &lt; 0.05), but no statistical difference could be found among them before or after GB. In all peel-off tests, adhesive failure occurred at the adhesive-impression material interface. The results indicated ABS, HIPS, and PETG could provide sufficient adhesion to the adhesive as the conventional light-curing resin, and GB could reduce the roughness generated by FDM and weaken the bonding between the adhesive and the silicone impression.
The EVcouplings Python framework for coevolutionary sequence analysis
2018-10-08

Abstract Summary Coevolutionary sequence analysis has become a commonly used technique for de novo prediction of the structure and function of proteins, RNA, and protein complexes. We present the EVcouplings framework, a fully integrated open-source application and Python package for coevolutionary analysis. The framework enables generation of sequence alignments, calculation and evaluation of evolutionary couplings (ECs), and de novo prediction of structure and mutation effects. The combination of an easy to use, flexible command line interface and an underlying modular Python package makes the full power of coevolutionary analyses available to entry-level and advanced users. Availability and implementation https://github.com/debbiemarkslab/evcouplings
Investigating Multidimensional Interoceptive Awareness in a Japanese Population: Validation of the Japanese MAIA-J
2018-10-08

The Multidimensional Assessment of Interoceptive Awareness (MAIA) is a self-report instrument to assess relevant dimensions of bodily awareness. The aim of this study was to offer a Japanese version and adaptation of the MAIA (MAIA-J), as well as to analyse its psychometric properties in a Japanese population. The English MAIA was systematically forward and backward translated by bi-lingual Japanese experts; additionally, content validity aspects regarding language were discussed by a panel of experts. The MAIA-J was administered to 390 Japanese young adults (age: 20.3 ± 2.2), 67.7% women and 32.2% men. Exploratory factor analysis (EFA) reduced the questionnaire from 32 to 25 items and from 8 to 6 factors (Noticing, Not-Distracting, Attention Regulation, Emotional Awareness, Body Listening, and Trusting). The Japanese version showed appropriate indicators of construct validity and reliability, with Cronbach's α between 0.67 and 0.87 for the 6 MAIA-J dimensions. The findings demonstrate that MAIA-J has a slightly different factor structure compared to the original English MAIA. Results are discussed with respect to cultural differences. However, the study results support acceptable reliability of the MAIA-J in the Japanese sample, warranting its use for future studies with Japanese populations.
Effect of changing vegetation and precipitation on denudation – Part 2: Predicted landscape response to transient climate and vegetation cover over millennial to million-year timescales
2018-10-08

Abstract. We present a numerical modeling investigation into the interactions between transient climate and vegetation cover with hillslope and detachment limited fluvial processes. Model simulations were designed to investigate topographic patterns and behavior resulting from changing climate and the associated changes in surface vegetation cover. The Landlab surface process model was modified to evaluate the effects of temporal variations in vegetation cover on hillslope diffusion and fluvial erosion. A suite of simulations were conducted to represent present-day climatic conditions and satellite derived vegetation cover at four different research areas in the Chilean Coastal Cordillera. These simulations included steady-state simulations as well as transient simulations with forcings in either climate or vegetation cover over millennial to million-year timescales. Two different transient variations in climate and vegetation cover including a step change in climate or vegetation were used, as well as 100 kyr oscillations over 5 Myr. We conducted eight different step-change simulations for positive and negative perturbations in either vegetation cover or climate and six simulations with oscillating transient forcings for either vegetation cover, climate, or oscillations in both vegetation cover and climate. Results indicate that the coupled influence of surface vegetation cover and mean annual precipitation shifts basin landforms towards a new steady state, with the magnitude of the change being highly sensitive to the initial vegetation and climate conditions of the basin. Dry, non-vegetated basins show higher magnitudes of adjustment than basins that are situated in wetter conditions with higher vegetation cover. For coupled conditions when surface vegetation cover and mean annual precipitation change simultaneously, the landscape response tends to be weaker. When vegetation cover and mean annual precipitation change independently from one another, higher magnitude shifts in topographic metrics are predicted. Changes in vegetation cover show a higher impact on topography for low initial surface cover values; however, for areas with high initial surface cover, the effect of changes in precipitation dominate the formation of landscapes. This study demonstrates the sensitivity of catchment characteristics to different transient forcings in vegetation cover and mean annual precipitation, with initial vegetation and climate conditions playing a crucial role.
Effect of changing vegetation and precipitation on denudation – Part 1: Predicted vegetation composition and cover over the last 21 thousand years along the Coastal Cordillera of Chile
2018-10-08

Abstract. Vegetation is crucial for modulating rates of denudation and landscape evolution, as it stabilizes and protects hillslopes and intercepts rainfall. Climate conditions and the atmospheric CO2 concentration, hereafter [CO2], influence the establishment and performance of plants; thus, these factors have a direct influence on vegetation cover. In addition, vegetation dynamics (competition for space, light, nutrients, and water) and stochastic events (mortality and fires) determine the state of vegetation, response times to environmental perturbations and successional development. In spite of this, state-of-the-art reconstructions of past transient vegetation changes have not been accounted for in landscape evolution models. Here, a widely used dynamic vegetation model (LPJ-GUESS) was used to simulate vegetation composition/cover and surface runoff in Chile for the Last Glacial Maximum (LGM), the mid-Holocene (MH) and the present day (PD). In addition, transient vegetation simulations were carried out from the LGM to PD for four sites in the Coastal Cordillera of Chile at a spatial and temporal resolution adequate for coupling with landscape evolution models. A new landform mode was introduced to LPJ-GUESS to enable a better simulation of vegetation dynamics and state at a sub-pixel resolution and to allow for future coupling with landscape evolution models operating at different spatial scales. Using a regionally adapted parameterization, LPJ-GUESS was capable of reproducing PD potential natural vegetation along the strong climatic gradients of Chile, and simulated vegetation cover was also in line with satellite-based observations. Simulated vegetation during the LGM differed markedly from PD conditions. Coastal cold temperate rainforests were displaced northward by about 5∘ and the tree line and vegetation zones were at lower elevations than PD. Transient vegetation simulations indicate a marked shift in vegetation composition starting with the past glacial warming that coincides with a rise in [CO2]. Vegetation cover between the sites ranged from 13 % (LGM: 8 %) to 81 % (LGM: 73 %) for the northern Pan de Azúcar and southern Nahuelbuta sites, respectively, but did not vary by more than 10 % over the 21 000 year simulation. A sensitivity study suggests that [CO2] is an important driver of vegetation changes and, thereby, potentially landscape evolution. Comparisons with other paleoclimate model drivers highlight the importance of model input on simulated vegetation. In the near future, we will directly couple LPJ-GUESS to a landscape evolution model (see companion paper) to build a fully coupled dynamic-vegetation/landscape evolution model that is forced with paleoclimate data from atmospheric general circulation models.