julilili42/papers huggingface dataset:
Proteasomal degradation of NOD2 by NLRP12 in monocytes promotes bacterial tolerance and colonization by enteropathogens
2018-12-11

Abstract Mutations in the nucleotide-binding oligomerization domain protein 12 (NLRP12) cause recurrent episodes of serosal inflammation. Here we show that NLRP12 efficiently sequesters HSP90 and promotes K48-linked ubiquitination and degradation of NOD2 in response to bacterial muramyl dipeptide (MDP). This interaction is mediated by the linker-region proximal to the nucleotide-binding domain of NLRP12. Consequently, the disease-causing NLRP12 R284X mutation fails to repress MDP-induced NF-κB and subsequent activity of the JAK/STAT signaling pathway. While NLRP12 deficiency renders septic mice highly susceptible towards MDP, a sustained sensing of MDP through NOD2 is observed among monocytes lacking NLRP12. This loss of tolerance in monocytes results in greater colonization resistance towards Citrobacter rodentium . Our data show that this is a consequence of NOD2-dependent accumulation of inflammatory mononuclear cells that correlates with induction of interferon-stimulated genes. Our study unveils a relevant process of tolerance towards the gut microbiota that is exploited by an attaching/effacing enteric pathogen.
Bulk structural information from density functionals for patchy particles
2018-12-11

We investigate bulk structural properties of tetravalent associating particles within the framework of classical density functional theory, building upon Wertheim’s thermodynamic perturbation theory. To this end, we calculate density profiles within an effective test-particle geometry and compare to radial distribution functions obtained from computer simulations. We demonstrate that a modified version of the functional proposed by Yu and Wu [J. Chem. Phys. 116, 7094 (2002)] based on fundamental measure theory for hard spheres produces accurate results, although the functional does not satisfy the exactly known low-density limit. In addition, at low temperatures where particles start to form an amorphous tetrahedral network, quantitative differences between simulations and theory emerge due to the absence of geometrical information regarding the patch arrangement in the latter. Indeed, here we find that the theory fits better to simulations of the floating-bond model [E. Zaccarelli et al., J. Chem. Phys. 127, 174501 (2007)], which exhibits a weaker tetrahedral order due to more flexible bonds between particles. We also demonstrate that another common density functional approach by Segura et al. [Mol. Phys. 90, 759 (1997)] fails to capture fundamental structural properties.
A Comparison of Stress Perception in International and Local First Semester Medical Students Using Psychometric, Psychophysiological, and Humoral Methods
2018-12-11

(1) Medical doctors and medical students show increased psychological stress levels. International medical students seem to be particularly vulnerable. (2) We compared different methods of assessing stress levels in international and local first year medical students. First, study participants completed questionnaires related to stress, depression, empathy, and self-efficacy (MBI, PSQ, PHQ-9, JSPE-S, and GSE) at three separate points in time (T1 to T3). Second, their heart rate variabilities (HRVs) were recorded in an oral examination, a seminar, and in a relaxing situation. Third, hair samples were collected at the beginning and at the end of the semester to assess the cortisol concentration. (3) Included were 20 international and 20 local first semester medical students. At T1, we found considerable differences between international and local students in the JSPE-S; at T2 in the MBI factor “professional efficacy”, the PHQ-9, and in the JSPE-S; and at T3 in the MBI factors “cynicism” and “professional efficacy”, the PHQ-9, and in the JSPE-S. International and local students also differed concerning their HRVs during relaxation. Over the course of the semester, international students showed changes in the MBI factors “emotional exhaustion” and “professional efficacy”, the PHQ-9, and the GSE. Local students showed changes in the GSE. No effects were found for students’ hair cortisol concentrations. (4) All participants showed low levels of stress. However, while international students experienced their stress levels to decrease over the course of the semester, local students found their stress levels to increase.
Above-ground biomass estimates based on active and passive microwave sensor imagery in low-biomass savanna ecosystems
2018-12-11

Although many studies exist on the estimation and monitoring of above-ground biomass (AGB) of forest ecosystems by methods of remote sensing, very little research has been carried out for ecosystems of low primary production, such as grasslands, steppes, or savannas. Our study intends to approach this gap and investigates the correlation between space-borne radar information and AGB at the scale of 10 tons per hectare and below. Additionally, we introduce the integration of passive brightness temperature as an additional covariate for biomass estimation, based on the hypothesis that it contains information complementary to microwave backscatter of the active sensors. Our findings show that large-scale estimates of AGB can be conducted for grasslands and savannas at high accuracy (R2 up to 0.52). Additionally, we found that the integration of passive radar can increase the quality of AGB estimates in terms of explained variance for selected cases. We hope that these indications are a starting point for more integrated approaches toward biomass estimations based on Earth observation methods.
Lying and the Arts
2018-12-11

Abstract This chapter investigates the significance of the topic of lying in the arts with an emphasis on the potential connection of lying with specific literary genres, such as the tall tale, the travelogue, the detective story, and the dystopian novel, and the related question whether fiction can be understood as a specific form of lying. Other sections deal with the depiction of lying characters and the representation of standard situations of lying. The major examples are drawn from literary texts, ranging from picturebooks and young adult novels to literature for adults, and films. Finally, this chapter gives a brief outlook on painting and photography by addressing the often-disputed issue of whether pictures are able to lie.
Building and hacking open source hardware
2018-12-11

The first edition of the Aspects of Neuroscience Brainhack took place at the Department of Physics at University of Warsaw, Poland between November 17th and 19th 2017. This hackathon was one of the satellite events of the Aspects of Neuroscience conference, it was organized by the Brainhack organization to promote interaction between researchers, encouraging open (neuro)science and collaborations on projects related to the study of the nervous system. The event had a total of nine projects on many different topics including functional connectivity research, white matter tractography, classification of brain-ageing biomarkers through machine learning, presentation of a portable one channel EEG registration device and a do it yourself 3D-printed neurobiology lab. The latter is highlighted in this paper.
Global Water Transfer Megaprojects: A Potential Solution for the Water-Food-Energy Nexus?
2018-12-12

Globally, freshwater is unevenly distributed, both in space and time. Climate change, land use alteration, and increasing human exploitation will further increase the pressure on water as a resource for human welfare and on inland water ecosystems. Water transfer megaprojects (WTMP) are defined here as large-scale engineering interventions to divert water within and between river basins that meet one of the following criteria: construction costs &amp;gt;US . Among future projects, 42 are for agricultural development, 13 for hydropower development and 10 combine both purposes. Future megaprojects are also planned to support mining, ecosystem restoration and navigation. Our results underscore the extent to which humans have and are planning to re-engineer the global hydrological network and flows through WTMP, creating a network of “artificial rivers.” They emphasize the need to ensure the inclusion of these projects in global and basin hydrological models, and to develop internationally agreed criteria to assess the ecological, social and economic impacts of WTMP.
An integrated method for understanding the function of macro-lithic tools. Use wear, 3D and spatial analyses of an Early Upper Palaeolithic assemblage from North Eastern Italy
2018-12-12

The article presents an original analysis which combines use-wear, 3D modelling and spatial analyses to experimental archaeology in order to investigate Early Upper Palaeolithic flintknapping gestures and techniques involving the use of macro-lithic tools. In particular, the methodological framework proposed in this paper was applied to the study of Protoaurignacian and Aurignacian macro-tools from Fumane Cave (Verona, Italy). Combining spatial analysis and use wear investigation, both at low and high magnifications, permitted the identification and detailed description of the use-related traces affecting both the hammerstones and retouchers which, at Fumane Cave, were used at different stages during flint tool production. Several experimental activities were performed including core reduction, maintenance, and blank production together with different types of edge retouching. From a methodological perspective, the protocol of analysis permitted to codify specific traces and to produce quantitative data related to their geometry and distribution over the tool’s surface, according to the activities and gestures performed. The results obtained allowed a careful investigation of the function and the gestures associated to the use of the macro-lithic tools coming from the Protoaurignacian and Aurignacian levels of Fumane Cave while providing a methodological tool for interpreting different archaeological samples
Increases in sampling support the southern Gondwanan hypothesis for the origin of dinosaurs
2018-12-12

Abstract Dinosaurs were ubiquitous in terrestrial ecosystems through most of the Mesozoic and are still diversely represented in the modern fauna in the form of birds. Recent efforts to better understand the origins of the group have resulted in the discovery of many new species of early dinosaur and their closest relatives (dinosauromorphs). In addition, recent re‐examinations of early dinosaur phylogeny have highlighted uncertainties regarding the interrelationships of the main dinosaur lineages (Sauropodomorpha, Theropoda and Ornithischia), and questioned the traditional hypothesis that the group originated in South Gondwana and gradually dispersed over Pangaea. Here, we use an historical approach to examine the impact of new fossil discoveries and changing phylogenetic hypotheses on biogeographical scenarios for dinosaur origins over 20 years of research time, and analyse the results in the light of different fossil record sampling regimes. Our results consistently optimize South Gondwana as the ancestral area for Dinosauria, as well as for more inclusive clades including Dinosauromorpha, and show that this hypothesis is robust to increased taxonomic and geographic sampling and divergent phylogenetic results. Our results do not find any support for the recently proposed Laurasian origin of dinosaurs and suggest that a southern Gondwanan origin is by far the most plausible given our current knowledge of the diversity of early dinosaurs and non‐dinosaurian dinosauromorphs.
The Gly385(388)Arg Polymorphism of the FGFR4 Receptor Regulates Hepatic Lipogenesis Under Healthy Diet
2018-12-12

Context: The effect of a lifestyle intervention to reduce liver fat content in nonalcoholic fatty liver disease in humans is influenced by genetics. We hypothesized that the amino acid exchange in human Gly388Arg (mouse homolog: Gly385Arg) in fibroblast growth factor receptor 4 (FGFR4), which regulates bile acid, lipid, and glucose metabolism, could determine hepatic lipid accumulation and insulin sensitivity. Mechanisms of this substitution were studied in mice under normal chow and high-fat diets.Design: In humans, the Gly388Arg polymorphism was studied for its relationship with changes in liver fat content and insulin sensitivity during 9 months of a lifestyle intervention. We also studied a knock-in mouse strain with an Arg385 allele introduced into the murine FGFR4 gene under normal chow and high-fat diets.Results: In humans, the FGFR4 Arg388 allele was not associated with liver fat content or insulin sensitivity in subjects who were overweight and obese before lifestyle intervention. However, it was associated with less decrease in liver fat content and less increase in insulin sensitivity during the intervention. In mice receiving normal chow, the FGFR4 Arg385 allele was associated with elevated hepatic triglyceride content, altered hepatic lipid composition, and increased hepatic expression of genes inducing de novo lipogenesis and glycolysis. Body fat mass and distribution, glucose tolerance, and insulin sensitivity were unaltered. The FGFR4 Arg385 allele had no effect on glucose or lipid metabolism under the high-fat diet.Conclusion: Our data indicate that the FGFR4 Arg388(385) allele affects hepatic lipid and glucose metabolism specifically during healthy caloric intake.
Effects of antiepileptic drugs on cortical excitability in humans: A TMS‐EMG and TMS‐EEG study
2018-12-13

Abstract Brain responses to transcranial magnetic stimulation (TMS) recorded by electroencephalography (EEG) are emergent noninvasive markers of neuronal excitability and effective connectivity in humans. However, the underlying physiology of these TMS‐evoked EEG potentials (TEPs) is still heavily underexplored, impeding a broad application of TEPs to study pathology in neuropsychiatric disorders. Here we tested the effects of a single oral dose of three antiepileptic drugs with specific modes of action (carbamazepine, a voltage‐gated sodium channel (VGSC) blocker; brivaracetam, a ligand to the presynaptic vesicle protein VSA2; tiagabine, a gamma‐aminobutyric acid (GABA) reuptake inhibitor) on TEP amplitudes in 15 healthy adults in a double‐blinded randomized placebo‐controlled crossover design. We found that carbamazepine decreased the P25 and P180 TEP components, and brivaracetam the N100 amplitude in the nonstimulated hemisphere, while tiagabine had no effect. Findings corroborate the view that the P25 represents axonal excitability of the corticospinal system, the N100 in the nonstimulated hemisphere propagated activity suppressed by inhibition of presynaptic neurotransmitter release, and the P180 late activity particularly sensitive to VGSC blockade. Pharmaco‐physiological characterization of TEPs will facilitate utilization of TMS‐EEG in neuropsychiatric disorders with altered excitability and/or network connectivity.
An empirical evaluation of multivariate lesion behaviour mapping using support vector regression
2018-12-13

Abstract Multivariate lesion behaviour mapping based on machine learning algorithms has recently been suggested to complement the methods of anatomo‐behavioural approaches in cognitive neuroscience. Several studies applied and validated support vector regression‐based lesion symptom mapping (SVR‐LSM) to map anatomo‐behavioural relations. However, this promising method, as well as the multivariate approach per se, still bears many open questions. By using large lesion samples in three simulation experiments, the present study empirically tested the validity of several methodological aspects. We found that (i) correction for multiple comparisons is required in the current implementation of SVR‐LSM, (ii) that sample sizes of at least 100–120 subjects are required to optimally model voxel‐wise lesion location in SVR‐LSM, and (iii) that SVR‐LSM is susceptible to misplacement of statistical topographies along the brain's vasculature to a similar extent as mass‐univariate analyses.
Prospective Views for Whey Protein and/or Resistance Training Against Age-related Sarcopenia
2018-12-13

Skeletal muscle aging is characterized by decline in skeletal muscle mass and function along with growing age, which consequently leads to age-related sarcopenia, if without any preventive timely treatment. Moreover, age-related sarcopenia in elder people would contribute to falls and fractures, disability, poor quality of life, increased use of hospital services and even mortality. Whey protein (WP) and/or resistance training (RT) has shown promise in preventing and treating age-related sarcopenia. It seems that sex hormones could be potential contributors for gender differences in skeletal muscle and age-related sarcopenia. In addition, skeletal muscle and the development of sarcopenia are influenced by gut microbiota, which in turn is affected by WP or RT. Gut microbiota may be a key factor for WP and/or RT against age-related sarcopenia. Therefore, focusing on sex hormones and gut microbiota may do great help for preventing, treating and better understanding age-related sarcopenia.
μ-Rhythm Extracted With Personalized EEG Filters Correlates With Corticospinal Excitability in Real-Time Phase-Triggered EEG-TMS
2018-12-13

Ongoing brain activity has been implicated in the modulation of cortical excitability. The combination of electroencephalography (EEG) and transcranial magnetic stimulation (TMS) in a real-time triggered setup is a novel method for testing hypotheses about the relationship between spontaneous neuronal oscillations, cortical excitability, and synaptic plasticity. For this method, a reliable real-time extraction of the neuronal signal of interest from scalp EEG with high signal-to-noise ratio (SNR) is of crucial importance. Here we compare individually tailored spatial filters as computed by spatial-spectral decomposition (SSD), which maximizes SNR in a frequency band of interest, against established local C3-centered Laplacian filters for the extraction of the sensorimotor μ-rhythm. Single-pulse TMS over the left primary motor cortex was synchronized with the surface positive or negative peak of the respective extracted signal, and motor evoked potentials (MEP) were recorded with electromyography (EMG) of a contralateral hand muscle. Both extraction methods led to a comparable degree of MEP amplitude modulation by phase of the sensorimotor μ-rhythm at the time of stimulation. This could be relevant for targeting other brain regions with no working benchmark such as the local C3-centered Laplacian filter, as sufficient SNR is an important prerequisite for reliable real-time single-trial detection of EEG features.
The European network for care of children with paediatric rheumatic diseases: care across borders
2018-12-13

This study provides a comprehensive description of current specialist PR service provision across Europe and did not reveal any major differences between EU member states. Rarity, chronicity and complexity of diseases are major challenges to PR care. Future work should facilitate the development, dissemination and implementation of standards of care, treatment and service recommendations to further improve patient-centred health care across Europe.
SNCA overexpression disturbs hippocampal gene expression trajectories in midlife
2018-12-13

Synucleinopathies like Parkinson's disease and dementia with Lewy bodies originate from a complex and still largely enigmatic interplay of genetic predisposition, age, and environmental factors. While progressively declining motor functions hallmark late-life symptoms, first signs of the disease often surface already decades earlier during midlife. To better understand early disease stages with respect to the genetic, temporal, and environmental dimension, we interrogated hippocampal transcriptome data obtained during midlife for a mouse model overexpressing human <i>SNCA</i>, a pivotal gene in synucleinopathies, under different environments. To relate differentially expressed genes to human, we integrated expression signatures for aging and Parkinson's disease. We identified two distinctive modes of age-dependent disturbances: First, cellular processes seemingly activated too early that reflected advanced stages of age and, second, typical longitudinal adaptations of the system that no longer occurred during midlife. Environmental enrichment prevented both disturbances modes despite persistent <i>SNCA</i> overload. Together, our results caution the view that expression changes characterising early stages of <i>SNCA</i>-related pathology reflect accelerated aging alone. Instead, we provide evidence that failure to undergo healthy adaptions during midlife represents a second origin of disturbances. This bimodal disturbance principle could inform therapeutic efforts to distinguish between preventive and restorative attempts to target the disease.
Eigenvector centrality mapping for ultrahigh resolution fMRI data of the human brain
2018-12-13

Eigenvector centrality mapping (ECM) is a popular technique for analyzing fMRI data of the human brain. It is used to obtain maps of functional hubs in networks of the brain in a manner similar to Google's PageRank algorithm. ECM attributes a score to the time course of each voxel that reflects its centrality within the network. Voxels that are strongly correlated with many other voxels that are themselves strongly correlated with other voxels receive high scores. Currently, there exist two different implementations ECM, one of which is very fast but limited to one particular type of correlation metric whose interpretation can be problematic. The second implementation supports many different metrics, but it is computationally costly and requires a very large main memory. Here we propose two new implementations of the ECM approach that resolve these issues. The first is based on a new correlation metric that we call "ReLU correlation (RLC)". The second method is based on matrix projections. We demonstrate the use of both techniques on standard fMRI data, as well as on high-resolution fMRI data acquired at 9.4 Tesla.
Modifiable Risk-factors for Keratinocyte Cancers in Australia: A Case-control Study
2018-12-13

Keratinocyte cancer is the most common malignancy in Caucasians. The aim of this study was to investigate risk-factors responsible for development of keratinocyte cancer in Australia. A case-control study was conducted, including 112 cases of squamous cell carcinoma (SCC), 95 cases of basal cell carcinoma (BCC) and 122 controls. Freckling during adolescence (SCC: odds ratio (OR) 1.04, p < 0.01; BCC: OR 1.05, p < 0.01), propensity to sunburn (SCC: OR 2.75, p = 0.01, BCC: OR 2.68 p = 0.01) and high cumulative sun-exposure (SCC: OR 2.43, p = 0.04; BCC: OR 2.36 p = 0.04) were independent risk-factors for both SCC and BCC. This study provides further evidence that a sun-sensitive phenotype and excessive sun-exposure during adulthood contribute to the risk of developing keratinocyte cancer. Wearing a hat, long-sleeved shirts, and sunscreen did not significantly reduce the risk of keratinocyte cancer in this study.
Policy relevant scholarship? the value of creating, framing and storytelling
2018-12-13

Once upon a time, academia and practice were joined at the hip, but as years went by, a yawning gap began dividing the two worlds.Today, while occasions of contact between academia and practice exist, they remain mainly ad hoc and superficial.To bridge the gap between academia and practice, many have called for policy relevant scholarship.But this misses the point: academics are and should continue to be academics, much like practitioners are and should continue to be practitioners.It is not up to the academic to come up with detailed policy proposals.They often lack the technical expertise, the bureaucratic experience or political instinct to know the specific what, when and how needed.Yet the academics' contribution to policy-making can be immense if they continue to be academics: using their unique skill set but with an eye for the concepts, the framing and the story-telling that are so essential to good policy-making.