julilili42/papers huggingface dataset:
Structure, stability and ecological significance of natural epigenetic variation: a large‐scale survey in Plantago lanceolata
2018-09-17

Summary Within‐species diversity is an important driver of ecological and evolutionary processes. Recent research has found that plants can harbour significant epigenetic diversity, but its extent, stability and ecological significance in natural populations is largely unexplored. We analysed genetic, epigenetic and phenotypic variation in a large number of natural grassland populations of Plantago lanceolata , covering a broad geographical and environmental range. Within‐population diversity and among‐population differentiation were calculated from genetic and epigenetic marker data and from measurements of phenotypic traits, both for plants in the field and for the F 1 generation grown in a common environment. We found weak but significant epigenetic population structure. A large part of the epigenetic population differences observed in the field was maintained in a common environment. Epigenetic differences were consistently related to genetic and environmental variation, and to a lesser degree to phenotypic variation and land use, with more grazed populations harbouring greater epigenetic diversity. Our study demonstrates that epigenetic diversity exists in natural populations of a common grassland species, and that at least part of this epigenetic diversity is stable, nonrandom and related to environmental variation. Experimental and more detailed molecular studies are needed to elucidate the mechanistic basis of these observed patterns.
Aerobic exercise inhibits acute lung injury: from mouse to human evidence Exercise reduced lung injury markers in mouse and in cells.
2018-09-17

Acute respiratory distress syndrome (ARDS) is defined as hypoxemic respiratory failure with intense pulmonary inflammation, involving hyperactivation of endothelial cells and neutrophils. Given the anti-inflammatory effects of aerobic exercise (AE), this study investigated whether AE performed daily for 5 weeks would inhibit extra-pulmonary LPS-induced ARDS. C57Bl/6 mice were distributed into Control, Exercise, LPS and Exercise+LPS groups. AE was performed on a treadmill for 5x/week for four weeks before LPS administration. 24hours after the final AE physical test, animals received 100ug of LPS intra-peritoneally. In addition, whole blood cell culture, neutrophils and human endothelial cells were preincubated with IL-10, an anti-inflammatory cytokine induced by exercise. AE reduced total protein levels (p<0.01) and neutrophil accumulation in bronchoalveolar lavage (BAL) (p<0.01) and lung parenchyma (p<0.01). AE reduced BAL inflammatory cytokines IL-1β, IL-6 and GM-CSF (p<0.001), CXCL1/KC, IL-17, TNF-alpha and IGF-1 (p<0.01). Systemically, AE reduced IL-1β, IL-6 and IFN-gamma (p<0.001), CXCL1/KC (p<0.01) and TNF-alpha (p<0.05). AE increased IL-10 levels in serum (p<0.001) and BAL (p<0.001). Furthermore, AE increased superoxide dismutase SOD (p<0.01) and decreased superoxide anion accumulation in the lungs (p<0.01). Lastly, pre-incubation with IL-10 significantly reduced LPS-induced activation of whole blood cells, neutrophils and HUVECs, as observed by reduced production of IL-1β, IL-6, IL-8 and TNF-alpha. Our data suggest that AE inhibited LPS-induced lung inflammation by attenuating inflammatory cytokines and oxidative stress markers in mice and human cell culture via enhanced IL-10 production.
Dissociation of Fatty Liver and Insulin Resistance in I148M PNPLA3 Carriers: Differences in Diacylglycerol (DAG) FA18:1 Lipid Species as a Possible Explanation
2018-09-17

Fatty liver is tightly associated with insulin resistance and the development of type 2 diabetes. I148M variant in patatin-like phospholipase domain-containing protein 3 (PNPLA3) gene is associated with high liver fat but normal insulin sensitivity. The underlying mechanism of the disassociation between high liver fat but normal insulin sensitivity remains obscure. We investigated the effect of I148M variant on hepatic lipidome of subjects with or without fatty liver, using the Lipidyzer method. Liver samples of four groups of subjects consisting of normal liver fat with wild-type PNPLA3 allele (group 1); normal liver fat with variant PNPLA3 allele (group 2); high liver fat with wild-type PNPLA3 allele (group 3); high liver fat with variant PNPLA3 allele (group 4); were analyzed. When high liver fat to normal liver fat groups were compared, wild-type carriers (group 3 vs. group 1) showed similar lipid changes compared to I148M PNPLA3 carriers (group 4 vs. group 2). On the other hand, in wild-type carriers, increased liver fat significantly elevated the proportion of specific DAGs (diacylglycerols), mostly DAG (FA18:1) which, however, remained unchanged in I148M PNPLA3 carriers. Since DAG (FA18:1) has been implicated in hepatic insulin resistance, the unaltered proportion of DAG (FA18:1) in I148M PNPLA3 carriers with fatty liver may explain the normal insulin sensitivity in these subjects.
Feasibility, efficacy, and safety of percutaneous MR‐guided ablation of small (≤12 mm) hepatic malignancies
2018-09-17

Background Percutaneous tumor ablation is commonly performed using computed tomography (CT) or ultrasound (US) guidance, although reliable visualization of the target tumor may be challenging. MRI guidance provides more reliable visualization of target tumors and allows for real‐time imaging and multiplanar capabilities, making it the modality of choice, in particular if lesions are small. Purpose To investigate the feasibility, technical success, and safety of percutaneous MR‐guided ablation (RFA n = 27 / MWA n = 16) of small (≤12 mm) hepatic malignancies. Study Type Retrospective case study. Population In all, 45 patients (age: 61.1 ± 11.8) with hepatic malignancies and a lesion diameter of ≤12 mm scheduled for percutaneous MR‐guided tumor ablation based on a tumor board decision were included. Field Strength A 1.5T MR system was used for planning, targeting, and monitoring. Assessment Feasibility assessment included the detection of the target tumor, tumor delineation during MR‐fluoroscopy guided targeting, and the number of attempts needed for precise applicator placement. Technical success was defined as successful performance of the procedure including a safety margin of 5 mm. Safety evaluation was based on procedure‐related complications. Statistical Test Frequency. Results Tumor ablation (mean diameter 9.0 ± 2.1 mm) was successfully completed in 43/45 patients. Planning imaging was conducted without a contrast agent in 79% ( n = 37). In 64% ( n = 30), the target tumors were visible with MR‐fluoroscopy. In six patients (13%), planning imaging revealed new, unexpected small lesions, which were either treated in the same session ( n = 4) or changed therapy management ( n = 2) due to diffuse tumor progress. Postprocedural imaging revealed a technical success of 100% (43/43), with no major complications. During follow‐up, no local tumor progression was observed (mean follow‐up 24.7 ± 14.0 months) although 28% (12) patients developed new hepatic lesions distant to the ablation zone. No major complications were observed. Data Conclusion MR‐guided ablation is a feasible approach for an effective and safe treatment of small hepatic malignancies. Level of Evidence : 4 Technical Efficacy : Stage 4 J. Magn. Reson. Imaging 2019;49:374–381.
Windrose Planarity
2018-09-17

Given a planar graph G and a partition of the neighbors of each vertex v in four sets v ↗ , v ↖ , v ↙ , and v ↘ , the problem W indrose P lanarity asks to decide whether G admits a windrose-planar drawing , that is, a planar drawing in which (i) each neighbor u ∈ v ↗ v is above and to the right of v , (ii) each neighbor u ∈ v ↖ is above and to the left of v , (iii) each neighbor u ∈ v ↙ is below and to the left of v , (iv) each neighbor u ∈ v ↘ is below and to the right of v , and (v) edges are represented by curves that are monotone with respect to each axis. By exploiting both the horizontal and the vertical relationship among vertices, windrose-planar drawings allow us to simultaneously visualize two partial orders defined by means of the edges of the graph. Although the problem is NP -hard in the general case, we give a polynomial-time algorithm for testing whether there exists a windrose-planar drawing that respects a given combinatorial embedding. This algorithm is based on a characterization of the plane triangulations admitting a windrose-planar drawing. Furthermore, for any embedded graph with n vertices that has a windrose-planar drawing, we can construct one with at most one bend per edge and with at most 2 n −5 bends in total, which lies on the 3 n × 3 n grid. The latter result contrasts with the fact that straight-line windrose-planar drawings may require exponential area.
At What Sample Size Do Latent Variable Correlations Stabilize?
2018-09-17

We conducted a Monte-Carlo simulation within a latent variable framework by varying the following characteristics: population correlation (ρ = .10, .20, .30, .40, .50, .60, .70, .80, .90, and 1.00) and composite score reliability (coefficient omega: ω = .40, .50, .60, .70, .80, and .90). The sample sizes required to estimate stable measurement-error-free correlations were found to approach N = 490 for typical research scenarios (population correlation ρ = .20; composite score reliability ω = .70) and as high as N = 1,000+ for data associated with lower, but still sometimes observed, reliabilities (ω = .40 to .50). We encourage researchers to take into consideration reliability, when evaluating the sample sizes required to produce stable measurement-error-free correlations.
Collective nonlinear optical effects in plasmonic oligomers using cylindrical vector beams (Conference Presentation)
2018-09-17

Plasmonic oligomers allow new ways to manipulate nonlinear optical effects such as second-harmonic generation (SHG) through collective resonances. However, earlier techniques to probe such effects have relied mostly on the use of plane waves or focused beam excitations with homogenous states-of-polarization (e.g., linear) that obviously do not match the spatial symmetries of the oligomer. Here, we investigate collective effects in the SHG from individual plasmonic oligomers using microscopy with cylindrical vector beams such as radial or azimuthal polarizations. The oligomers were prepared by electron-beam lithography. The oligomers consisted of gold nanorods that have a longitudinal plasmon resonance close to the fundamental wavelength that is used for SHG excitation and whose long axes are arranged locally such that they follow the distribution of the transverse component of the electric field of radial or azimuthal polarizations. We found that SHG from such oligomers is strongly modified by the interplay between the properties of the incident cylindrical vector beam and interparticle coupling. We find that the oligomers with radially-oriented nanorods exhibit small coupling effects. In contrast, we observed that the oligomers with azimuthally-oriented nanorods exhibit large coupling effects that lead to silencing of SHG from the whole structure. We found good qualitative agreement between our experimental findings and calculations using the method of moments. The work describes a new route to investigate coupling effects in arrangements of nanostructures and thereby to control the efficiency of nonlinear effects in these structures.
Coaching, Counseling, Case-Working: Do They Help the Older Unemployed Out of Benefit Receipt and Back Into the Labor Market?
2018-09-17

Abstract Intensified counseling, job search assistance and related policies have been found to be effective for labor market integration of the unemployed by a large number of studies, but the evidence for older and hard-to-place unemployed is more mixed. In this paper, we present key results for a large-scale active labor market program directed at the older unemployed in Germany. To identify the treatment effects, we exploit regional variation in program participation. We use a combination of different evaluation estimators to check the sensitivity of the results to selection, substitution and local labor market effects. We find positive effects of the program in the range of 5-10 percentage points on integration into unsubsidized employment. However, there are also substantial lock-in effects, such that program participants have a higher probability of remaining on public welfare benefit receipt for up to 1 year after commencing the program.
Sterilization impacts on marine sediment---Are we able to inactivate microorganisms in environmental samples?
2018-09-18

To distinguish between biotic and abiotic processes in laboratory experiments with environmental samples, an effective sterilization method is required that prevents biological activity but does not change physico-geochemical properties of samples. We compared standard sterilization methods with respect to their impact on microbial abundance and activity. We exposed marine sediment to (i) autoclaving, (ii) gamma-radiation or (iii) sodium azide (NaN3) and determined how nucleic acids, microbial productivity, colony forming units (CFUs) and community composition of microorganisms, fungi, unicellular protists and protozoa were affected. In autoclaved and gamma-sterilized sediments, only few colonies formed within 16 days. After addition of NaN3 to the sediment, numerous CFUs (>50) but lower 3H-leucine incorporation rates, i.e. lower protein biosynthesis rates, were found compared to the other two sterilization techniques. Extractable RNA was detected immediately after all sterilization treatments (0.2-17.9 ng/g dry sediment) but decreased substantially by 84%-98% after 16 days of incubation. The total organic carbon content increased from 18 mg L-1 to 220 mg L-1 (autoclaving) and 150 mg L-1 (gamma-radiation) after sterilization. We compare advantages and disadvantages for each tested sterilization method and provide a helpful decision-making resource for choosing the appropriate sterilization technique for environmental studies, particularly for marine sediments.
Titration and optimization trial for the initiation of insulin glargine 100 U/mL in patients with inadequately controlled type 2 diabetes on oral antidiabetic drugs
2018-09-18

For patients with type 2 diabetes mellitus (T2DM) and inadequate glycaemic control, addition of basal insulin is recommended, but titration and optimization of basal insulin therapy in primary care is not well understood. We conducted an observational trial in 2470 patients with T2DM who initiated insulin glargine 100 U/L (Gla‐100) on top of oral antidiabetic drugs. Physicians were free to choose either a “Davies,” “Fritsche” or “individual” titration algorithm. We found that fasting blood glucose (FBG) and glycated haemoglobin (HbA1c) levels were effectively reduced by Gla‐100; 65.9% of patients achieved the primary endpoint (FBG ≤6.1 mmol/L (110 mg/dL) or an individual HbA1c target). There were no significant differences in efficacy and safety between the algorithms used. The mean FBG decreased by 3.2 mmol/L (59 mg/dL) over 12 months, while the mean HbA1c decreased by 15.3 mmol/mol (1.4%)%. From a starting dose of 11.7 U/d, the Gla‐100 dosage was 22.8 U/d at 12 months, with similar values in each group. Rates of hypoglycaemia were low and did not differ by titration algorithm. We conclude that Gla‐100 was effective at reducing FBG and HbA1c, independent of the titration algorithm, but observed that algorithms were inconsistently applied in clinical practice.
The Language Resource Switchboard
2018-09-18

The CLARIN research infrastructure gives users access to an increasingly rich and diverse set of language-related resources and tools. Whereas there is ample support for searching resources using metadata-based search, or full-text search, or for aggregating resources into virtual collections, there is little support for users to help them process resources in one way or another. In spite of the large number of tools that process texts in many different languages, there is no single point of access where users can find tools to fit their needs and the resources they have. In this squib, we present the Language Resource Switchboard (LRS), which helps users to discover tools that can process their resources. For this, the LRS identifies all applicable tools for a given resource, lists the tasks the tools can achieve, and invokes the selected tool in such a way so that processing can start immediately with little or no prior tool parameterization.
The Use of Local and Global Ordering Strategies in Number Line Estimation in Early Childhood
2018-09-18

A lot of research has been devoted to number line estimation in primary school. However, less is known about the early onset of number line estimation before children enter formal education. We propose that ordering strategies are building blocks of number line estimation in early childhood. In a longitudinal study, children completed a non-symbolic number line estimation task at age 3.5 and 5 years. Two ordering strategies were identified based on the children's estimation patterns: local and global ordering. Local ordering refers to the correct ordering of successive quantities, whereas global ordering refers to the correct ordering of all quantities across the number line. Results indicated a developmental trend for both strategies. The percentage of children applying local and global ordering strategies increased steeply from 3.5 to 5 years of age. Moreover, children used more advanced local and global ordering strategies at 5 years of age. Importantly, level of strategy use was related to more traditional number line estimation outcome measures, such as estimation accuracy and regression fit scores. These results provide evidence that children use dynamic ordering strategies when solving the number line estimation task in early stages of numerical development.
Typing, representing, and abstracting control: functional pearl
2018-09-18

A well known technique to implement programming languages with delimited control operators shift and reset is to translate programs into continuation passing style (CPS). We can iterate the CPS translation to obtain the CPS hierarchy and to implement a family of control operators shifti and reseti. This functional pearl retells the story of a family of delimited control operators and their translation to lambda calculus via the CPS hierarchy. Prior work on the CPS hierarchy fixes a level of n control operators for the entire program upfront, but we allow different parts of the program to live at different levels. It turns out that taking shift0 rather than shift as the basis for the family of control operators is essential for this. Our source language is a typed embedding in the dependently typed language Idris. Our target language is a HOAS embedding in Idris. The translation avoids administrative beta- and eta-redexes at all levels of the CPS hierarchy, by iterating well-known techniques for the non-iterated CPS translation.
Automatic place-value activation in magnitude-irrelevant parity judgement
2018-09-18

Research on multi-digit number processing suggests that, in Arabic numerals, their place-value magnitude is automatically activated, whenever a magnitude-relevant task was employed: However, so far, it is unknown, whether place-value is also activated when the target task is magnitude-irrelevant. The current study examines this question by using the parity congruency effect in two-digit numbers: It describes that responding to decade-digit parity congruent numbers (e.g., 35, 46; same parity of decades and units) is faster than to decade-digit parity incongruent numbers (e.g., 25; 36; different parities of decades and units). Here we investigate the (a-)symmetry of the parity congruency effect; i.e. whether it makes a difference whether participants are assessing the parity of the unit digit or the decade digit. We elaborate, how and why such an asymmetry is related to place-value processing, because the parity of the unit digit only interferes with the parity of the decade digit, while the parity of the decade digit interferes with both the parity of the unit digit and the integrated parity of the whole two-digit number. We observed a significantly larger parity congruency effect in the decade parity decision than in the unit parity decision. This suggests that automatic place-value processing also takes place in a typical parity judgment task, in which magnitude is irrelevant. Finally, because of the cross-lingual design of the study, we can show that these results and their implications were language-independent.
Premedication for Neonates Requiring Nonemergency Intubation
2018-09-18

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Biomarkers of Neurodegeneration in Autoimmune-Mediated Encephalitis
2018-09-19

Progranulin (PGRN), Total-Tau (t-tau), and Neurofilament light chain (NfL) are well known biomarkers of neurodegeneration. The objective of the present study was to investigate whether these parameters represent also biomarkers in autoimmune-mediated Encephalitis (AE) and may give us insights into the pathomechanisms of AE. We retrospectively examined the concentration of PGRN in the cerebrospinal fluid (CSF) and serum of 38 patients suffering from AE in acute phase and/or under treatment. This AE cohort comprises patients with autoantibodies against: NMDAR (<i>n</i> = 18 patients), Caspr2 (<i>n</i> = 8), Lgi-1 (<i>n</i> = 10), GABAB(R) (<i>n</i> = 1), and AMPAR (<i>n</i> = 1). Additionally, the concentrations of NfL (<i>n</i> = 25) and t-tau (<i>n</i> = 13) in CSF were measured when possible. Follow up data including MRI were available in 13 patients. Several age-matched cohorts with neurological diseases besides neuroinflammation or neurodegeneration served as control groups. We observed that PGRN was significantly elevated in the CSF of patients with NMDAR-AE in the acute phase, but normalized at follow up under treatment (<i>p</i> < 0.01). In the CSF of other patients with AE PGRN was in the range of the CSF levels of control groups. T-tau was highly elevated in the CSF of patients with temporal FLAIR-signal in the MRI and in patients developing a hippocampal sclerosis. NfL was exceptionally high initially in Patients with AE with a paraneoplastic or parainfectious cause and also normalized under treatment. The normalizations of all biomarkers were mirrored in an improvement on the modified Rankin scale. The data suggest that the concentration of PGRN in CSF might be a biomarker for acute NMDAR-AE. Pathological high t-tau levels may indicate a risk for hippocampal sclerosis. The biomarker properties of NfL remain unclear since the levels decrease under treatment, but it could not predict severity of disease in this small cohort. According to our results, we recommend to measure in clinical practice PGRN and t-tau in the CSF of patients with AE.