julilili42/papers huggingface dataset:
Formulation of topical acidic products and acidification of the skin – Contribution of glycolic acid
2021-04-17

Abstract Objective The acidic skin pH is one of the regulating factors of skin barrier homeostasis. Topical products as extrinsic factors which influence skin pH could be used for acidification of the skin and consequent beneficial effect. To formulate stabile and safe topical emulsion product with low pH is on‐going challenge and areas interesting to explore are related to the effect of acidic products on the skin pH together with development of protocols for these studies. Aim of our work was to investigate formulations of acidic topical products with glycolic acid (GA) stabilized with long chain alkyl polyglucoside emulsifier, in regard to the specific colloidal structure of the vehicle, together with effect of products with different concentration of acidic active on skin pH. Methods Investigated formulations were basic vehicle and two creams with glycolic acid (concentration 2 and 10 wt%). Microstructure was investigated by polarization microscopy, Raman spectral imaging, thermal analysis and rheological measurements. Effects on the skin were assessed by measurement of biophysical skin parameters in vivo studies (5‐hour, 24‐hour and 7‐days). In vitro screening of antimicrobial activity was performed against bacteria Staphylococcus epidermidis . Results Polarization micrographs and Raman images have shown that GA does not disturb the specific colloidal structure. Together with rheological and thermal analysis obtained results have shown that GA in higher concentrations contributes to vehicles’ lamellar structure. In 5‐hour study the mean values of skin pH ranged from 3.98‐4.25 and 3.89‐4.10 after application of products with smaller and higher GA concentration. GA samples lowered skin surface pH to 5 and less in 24‐hour and 7‐day study, with stronger effect of sample with more GA. Sample with 10% of GA had significant inhibitory effect on growth of S. epidermidis in 1:1 concentration. Conclusions Investigated APG emulsifier could be used as a stabilizer for acidic topical products with GA which are characterized by satisfactory safety profile. Topical products induce acidification of the skin after short‐ and long‐term application without barrier impairment or sign of irritation. Acidification of the skin depends on presence of ingredients which are proton donors and their concentrations.
Variation of salinity and nitrogen concentration affects the pentacyclic triterpenoid inventory of the haloalkaliphilic aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum
2021-04-18

Abstract The occurrence and activity of aerobic methanotrophs are influenced by environmental conditions, including pH, temperature, salinity, methane and oxygen concentrations, and nutrient availability. Aerobic methanotrophs synthesize a variety of lipids important for cell functions. However, culture-based experiments studying the influence of environmental parameters on lipid production by aerobic methanotrophs are scarce. Such information is crucial to interpret lipid patterns of methanotrophic bacteria in the environment. In this study, the alkaliphilic strain Methylotuvimicrobium alcaliphilum was cultivated under different salinities and different nitrate concentrations to assess the effect of changing conditions on the inventory of pentacyclic triterpenoids. The results indicate that hopanoid abundance is enhanced at lower salinity and higher nitrate concentration. The production of most pentacyclic triterpenoids was favored at low salinity, especially for aminotriol. Interestingly, 3-methyl-aminotetrol and tetrahymanol were favored at higher salinity. Bacteriohopanepolyols (BHPs), particularly aminotriol and 3-methyl-aminotriol, increased considerably at higher nitrate concentrations. Four novel N -containing BHPs—aminodiol, 3-methyl-aminodiol, and isomers of aminotriol and 3-methyl-aminotriol—were identified. This study highlights the significance of environmental factors for bacterial lipid production and documents the need for cultivation studies under variable conditions to utilize the full potential of the biomarker concept.
Sustainable data analysis with Snakemake
2021-04-19

<ns4:p>Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that data analyses should ideally be conducted in a reproducible way. Reproducibility enables technical validation and regeneration of results on the original or even new data. However, reproducibility alone is by no means sufficient to deliver an analysis that is of lasting impact (i.e., sustainable) for the field, or even just one research group. We postulate that it is equally important to ensure adaptability and transparency. The former describes the ability to modify the analysis to answer extended or slightly different research questions. The latter describes the ability to understand the analysis in order to judge whether it is not only technically, but methodologically valid.</ns4:p><ns4:p>Here, we analyze the properties needed for a data analysis to become reproducible, adaptable, and transparent. We show how the popular workflow management system Snakemake can be used to guarantee this, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.</ns4:p>
Dimethyl fumarate induces ferroptosis and impairs NF-κB/STAT3 signaling in DLBCL
2021-04-19

Abstract Despite the development of novel targeted drugs, the molecular heterogeneity of diffuse large B-cell lymphoma (DLBCL) still poses a substantial therapeutic challenge. DLBCL can be classified into at least 2 major subtypes (germinal center B cell [GCB]-like and activated B cell [ABC]-like DLBCL), each characterized by specific gene expression profiles and mutation patterns. Here we demonstrate a broad antitumor effect of dimethyl fumarate (DMF) on both DLBCL subtypes, which is mediated by the induction of ferroptosis, a form of cell death driven by the peroxidation of phospholipids. As a result of the high expression of arachidonate 5-lipoxygenase in concert with low glutathione and glutathione peroxidase 4 levels, DMF induces lipid peroxidation and thus ferroptosis, particularly in GCB DLBCL. In ABC DLBCL cells, which are addicted to NF-κB and STAT3 survival signaling, DMF treatment efficiently inhibits the activity of the IKK complex and Janus kinases. Interestingly, the BCL-2–specific BH3 mimetic ABT-199 and an inhibitor of ferroptosis suppressor protein 1 synergize with DMF in inducing cell death in DLBCL. Collectively, our findings identify the clinically approved drug DMF as a promising novel therapeutic option in the treatment of both GCB and ABC DLBCLs.
Behavioral and Neuronal Representation of Numerosity Zero in the Crow
2021-04-19

Different species of animals can discriminate numerosity, the countable number of objects in a set. The representations of countable numerosities have been deciphered down to the level of single neurons. However, despite its importance for human number theory, a special numerical quantity, the empty set (numerosity zero), has remained largely unexplored. We explored the behavioral and neuronal representation of the empty set in carrion crows. Crows were trained to discriminate small numerosities including the empty set. Performance data showed a numerical distance effect for the empty set in one crow, suggesting that the empty set and countable numerosities are represented along the crows' “mental number line.” Single-cell recordings in the endbrain region nidopallium caudolaterale (NCL) showed a considerable proportion of NCL neurons tuned to the preferred numerosity zero. As evidenced by neuronal distance and size effects, NCL neurons integrated the empty set in the neural number line. A subsequent neuronal population analysis using a statistical classifier approach showed that the neuronal numerical representations were predictive of the crows' success in the task. These behavioral and neuronal data suggests that the conception of the empty set as a cognitive precursor of a zero-like number concept is not an exclusive property of the cerebral cortex of primates. Zero as a quantitative category cannot only be implemented in the layered neocortex of primates, but also in the anatomically distinct endbrain circuitries of birds that evolved based on convergent evolution. SIGNIFICANCE STATEMENT The conception of “nothing” as number “zero” is celebrated as one of the greatest achievements in mathematics. To explore whether precursors of zero-like concepts can be found in vertebrates with a cerebrum that anatomically differs starkly from our primate brain, we investigated this in carrion crows. We show that crows can grasp the empty set as a null numerical quantity that is mentally represented next to number one. Moreover, we show that single neurons in an associative avian cerebral region specifically respond to the empty set and show the same physiological characteristics as for countable quantities. This suggests that zero as a quantitative category can also be implemented in the anatomically distinct endbrain circuitries of birds that evolved based on convergent evolution.
NirA Is an Alternative Nitrite Reductase from Pseudomonas aeruginosa with Potential as an Antivirulence Target
2021-04-19

The emergence of widespread antimicrobial resistance has led to the need for development of novel therapeutic interventions. Antivirulence strategies are an attractive alternative to classic antimicrobial therapy; however, they require identification of new specific targets which can be exploited in drug discovery programs.
CFHloss in human RPE cells leads to inflammation and complement system dysregulationviathe NF-κB pathway
2021-04-19

Abstract Age-related macular degeneration (AMD), the leading cause of vision loss in the elderly, is a degenerative disease of the macula, where retinal pigment epithelium (RPE) cells are damaged in the early stages of the disease and chronic inflammatory processes may be involved. Besides ageing and lifestyle factors as drivers of AMD, a strong genetic association to AMD is found in genes of the complement system, with a single polymorphism in the complement factor H gene ( CFH) , accounting for the majority of AMD risk. However, the exact mechanism by which CFH dysregulation confers such a great risk for AMD and its role in RPE cells homeostasis is unclear. To explore the role of endogenous CFH locally in RPE cells, we silenced CFH in human hTERT-RPE1 cells. We demonstrate that endogenously expressed CFH in RPE cells modulates inflammatory cytokine production and complement regulation, independent of external complement sources or stressors. We show that loss of the factor H protein (FH) results in increased levels of inflammatory mediators ( e . g . IL-6, IL-8, GM-CSF) and altered levels of complement proteins ( e . g. C3, CFB upregulation and C5 downregulation) that are known to play a role in AMD. Moreover, we identified the NF-κB pathway as the major pathway involved in the regulation of these inflammatory and complement factors. Our findings suggest that in RPE cells, FH and the NF-κB pathway work in synergy to maintain inflammatory and complement balance and in case either one of them is dysregulated, the RPE microenvironment changes towards a pro-inflammatory AMD-like phenotype.
Ultra-rare constrained missense variants in the epilepsies: Shared and specific enrichment patterns in neuronal gene-sets
2021-04-19

Abstract Background Burden analysis in epilepsy has shown an excess of deleterious ultra-rare variants (URVs) in few gene-sets, such as known epilepsy genes, constrained genes, ion channel or GABA A receptor genes. We set out to investigate the burden of URVs in a comprehensive range of gene-sets presumed to be implicated in epileptogenesis. Methods We investigated several constraint and conservation-based strategies to study whole exome sequencing data from European individuals with developmental and epileptic encephalopathies (DEE, n = 1,003), genetic generalized epilepsy (GGE, n = 3,064), and non-acquired focal epilepsy (NAFE, n = 3,522), collected by the Epi25 Collaborative, compared to 3,962 ancestry-matched controls. The burden of 12 non-synonymous URVs types in 92 gene-sets was compared between epilepsy cases (DDE, GGE, NAFE) and controls using logistic regression analysis. Results Burden analysis of brain-expressed genes revealed an excess of different URVs types in all three epilepsy categories which was largest for missense variants in highly constrained sites (constrained missense variants). The URVs burden was prominent in neuron-specific, synaptic and developmental genes as well as genes encoding ion channels and receptors, and it was generally higher for DEE and GGE compared to NAFE. The patterns of URVs burden in gene-sets expressed in inhibitory vs. excitatory neurons or receptors suggested a high burden in both groups in DEE but a differential involvement of inhibitory genes in GGE, while excitatory genes were predominantly affected in NAFE. Top ranking susceptibility genes from a recent genome-wide association study (GWAS) of generalized and focal epilepsies displayed a higher URVs burden in constrained coding regions in GGE and NAFE, respectively. Conclusions Using exome-based gene-set burden analysis, we demonstrate that missense URVs affecting mainly constrained sites are enriched in neuronal genes in both common and rare severe epilepsy syndromes. Our results indicate a differential impact of these URVs in genes expressed in inhibitory vs. excitatory neurons and receptors in generalized vs. focal epilepsies. The excess of URVs in top-ranking GWAS risk-genes suggests a convergence of rare deleterious and common risk-variants in the pathogenesis of generalized and focal epilepsies.
Ultra-rare constrained missense variants in the epilepsies: Shared and specific enrichment patterns in neuronal gene-sets 2021.04.18.440264
2021-04-19

Abstract Background Burden analysis in epilepsy has shown an excess of deleterious ultra-rare variants (URVs) in few gene-sets, such as known epilepsy genes, constrained genes, ion channel or GABA A receptor genes. We set out to investigate the burden of URVs in a comprehensive range of gene-sets presumed to be implicated in epileptogenesis. Methods We investigated several constraint and conservation-based strategies to study whole exome sequencing data from European individuals with developmental and epileptic encephalopathies (DEE, n = 1,003), genetic generalized epilepsy (GGE, n = 3,064), and non-acquired focal epilepsy (NAFE, n = 3,522), collected by the Epi25 Collaborative, compared to 3,962 ancestry-matched controls. The burden of 12 non-synonymous URVs types in 92 gene-sets was compared between epilepsy cases (DDE, GGE, NAFE) and controls using logistic regression analysis. Results Burden analysis of brain-expressed genes revealed an excess of different URVs types in all three epilepsy categories which was largest for missense variants in highly constrained sites (constrained missense variants). The URVs burden was prominent in neuron-specific, synaptic and developmental genes as well as genes encoding ion channels and receptors, and it was generally higher for DEE and GGE compared to NAFE. The patterns of URVs burden in gene-sets expressed in inhibitory vs. excitatory neurons or receptors suggested a high burden in both groups in DEE but a differential involvement of inhibitory genes in GGE, while excitatory genes were predominantly affected in NAFE. Top ranking susceptibility genes from a recent genome-wide association study (GWAS) of generalized and focal epilepsies displayed a higher URVs burden in constrained coding regions in GGE and NAFE, respectively. Conclusions Using exome-based gene-set burden analysis, we demonstrate that missense URVs affecting mainly constrained sites are enriched in neuronal genes in both common and rare severe epilepsy syndromes. Our results indicate a differential impact of these URVs in genes expressed in inhibitory vs. excitatory neurons and receptors in generalized vs. focal epilepsies. The excess of URVs in top-ranking GWAS risk-genes suggests a convergence of rare deleterious and common risk-variants in the pathogenesis of generalized and focal epilepsies.
Ultra-fast, high throughput and inexpensive detection of SARS-CoV-2 seroconversion
2021-04-19

ABSTRACT A technique allowing high throughput, fast and low-cost quantitative analysis of human IgG antibodies reacting to SARS-CoV-2 antigens will be required to understand the levels of protecting antibodies in the population raised in response to infections and/or to immunization. We described previously a fast, simple, and inexpensive Ni 2+ magnetic bead immunoassay which allowed detection of human antibodies reacting against the SARS-CoV-2 nucleocapsid protein using a minimal amount of serum or blood. A major drawback of the previously described system was that it only processed 12 samples simultaneously. Here we describe a manually operating inexpensive 96 well plate magnetic extraction / homogenization process which allows high throughput analysis delivering results of 96 samples in chromogenic format in 12 minutes or in fluorescent ultrafast format which takes only 7 minutes. We also show that His tag antigen purification can be performed on the fly while loading antigens to the Ni 2+ magnetic beads in a process which takes only 12 min reducing the pre analytical time and cost. Finally, we show that the magnetic bead immunoassay is antigen flexible and can be performed using either Nucleocapsid, Spike or Spike RBD. The method performed with low inter and intra assay variability using different antigens and detection modes and was able to deliver &gt;99.5% specificity and &gt;95% sensitivity for a cohort of 203 pre pandemic and 63 COVID-19 positive samples.
H.E.S.S. and MAGIC observations of a sudden cessation of a very-high-energy γ-ray flare in PKS 1510−089 in May 2016
2021-04-20

The flat spectrum radio quasar (FSRQ) PKS 1510-089 is known for its complex multiwavelength behaviour and it is one of only a few FSRQs detected in very-high-energy (VHE, E&gt;100 GeV) gamma rays. The VHE gamma -ray observations with H.E.S.S. and MAGIC in late May and early June 2016 resulted in the detection of an unprecedented flare, which revealed, for the first time, VHE gamma -ray intranight variability for this source. While a common variability timescale of 1.5 h has been found, there is a significant deviation near the end of the flare, with a timescale of similar to 20 min marking the cessation of the event. The peak flux is nearly two orders of magnitude above the low-level emission. For the first time, a curvature was detected in the VHE gamma -ray spectrum of PKS 1510-089, which can be fully explained by the absorption on the part of the extragalactic background light. Optical R-band observations with ATOM revealed a counterpart of the gamma -ray flare, even though the detailed flux evolution differs from the VHE gamma -ray light curve. Interestingly, a steep flux decrease was observed at the same time as the cessation of the VHE gamma -ray flare. In the high-energy (HE, E&gt; 100 MeV) gamma -ray band, only a moderate flux increase was observed with Fermi-LAT, while the HE gamma -ray spectrum significantly hardens up to a photon index of 1.6. A search for broad-line region (BLR) absorption features in the gamma -ray spectrum indicates that the emission region is located outside of the BLR. Radio very-long-baseline interferometry observations reveal a fast-moving knot interacting with a standing jet feature around the time of the flare. As the standing feature is located similar to 50 pc from the black hole, the emission region of the flare may have been located at a significant distance from the black hole. If this is indeed a true correlation, the VHE gamma rays must have been produced far down in the jet, where turbulent plasma crosses a standing shock.
Association between cardiovascular risk factors and degenerative disc disease of the thoracolumbar spine in the general population: results from the KORA MRI Study
2021-04-20

Background Little is known about the associations between cardiovascular risk factors (CRF) and disc degeneration (DD). Purpose To evaluate the potential association between CRFs and intervertebral DD in a population-based sample. Methods A total of 400 participants from the community-based KORA-study were assessed in terms of CRFs, specifically obesity, hypertension, diabetes, elevated LDL-c, low HDL-c, elevated triglycerides, smoking status, and alcohol consumption. The patients additionally underwent whole-body magnetic resonance imaging (MRI) using T2-weighted single-shot fast-spin-echo and T1 dual-echo gradient-echo Dixon pulse sequences. Thoracic and lumbar DD were assessed using the Pfirrmann score and for the presence of disc bulging/protrusion. Cross-sectional associations between CRFs and MR-based Pfirrmann score were then analyzed. Results A total of 385 individuals (58.2% men; mean age 56.3 ± 9.2 years) were included. Prevalence of DD was 76.4%. Older age (β = 0.18; 95% CI 0.12–0.25; P &lt; 0.001) and higher body mass index (BMI) (β = 0.19; 95% CI 0.06–0.30; P = 0.003) were significantly associated with DD of the thoracolumbar spine. Diabetes was significantly associated with DD at T7/8 ( P = 0.029) and L3/4 ( P = 0.017). Hypertension correlated significantly with DD in univariate analysis, but the association did not persist using multivariate analysis (β = 0.53; 95% CI –0.74 to 1.81; P = 0.41). None of the other CRFs ( P ≥ 0.11) were associated with advanced DD. Disc bulging was independently associated with hypertension (β = 0.47; 95% CI 0.27–0.81; P = 0.01). Conclusion A significant independent association exists between age, BMI, and intervertebral DD. In contrast, there is no significant association between cardiovascular risk factors and DD. Providing strong evidence that the pathologic process undergirding DD is mechanical, rather than microvascular, in nature.