julilili42/papers huggingface dataset:
Mural Cell SRF Controls Pericyte Migration, Vessel Patterning and Blood Flow
2022-07-14

Background: Pericytes and vascular smooth muscle cells, collectively known as mural cells, are recruited through PDGFB (platelet-derived growth factor B)-PDGFRB (platelet-derived growth factor receptor beta) signaling. MCs are essential for vascular integrity, and their loss has been associated with numerous diseases. Most of this knowledge is based on studies in which MCs are insufficiently recruited or fully absent upon inducible ablation. In contrast, little is known about the physiological consequences that result from impairment of specific MC functions. Here, we characterize the role of the transcription factor SRF (serum response factor) in MCs and study its function in developmental and pathological contexts. Methods: We generated a mouse model of MC-specific inducible Srf gene deletion and studied its consequences during retinal angiogenesis using RNA-sequencing, immunohistology, in vivo live imaging, and in vitro techniques. Results: By postnatal day 6, pericytes lacking SRF were morphologically abnormal and failed to properly comigrate with angiogenic sprouts. As a consequence, pericyte-deficient vessels at the retinal sprouting front became dilated and leaky. By postnatal day 12, also the vascular smooth muscle cells had lost SRF, which coincided with the formation of pathological arteriovenous shunts. Mechanistically, we show that PDGFB-dependent SRF activation is mediated via MRTF (myocardin-related transcription factor) cofactors. We further show that MRTF-SRF signaling promotes pathological pericyte activation during ischemic retinopathy. RNA-sequencing, immunohistology, in vivo live imaging, and in vitro experiments demonstrated that SRF regulates expression of contractile SMC proteins essential to maintain the vascular tone. Conclusions: SRF is crucial for distinct functions in pericytes and vascular smooth muscle cells. SRF directs pericyte migration downstream of PDGFRB signaling and mediates pathological pericyte activation during ischemic retinopathy. In vascular smooth muscle cells, SRF is essential for expression of the contractile machinery, and its deletion triggers formation of arteriovenous shunts. These essential roles in physiological and pathological contexts provide a rationale for novel therapeutic approaches through targeting SRF activity in MCs.
Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter
2022-07-14

Ultrahigh-resolution Fourier transform mass spectrometry (FTMS) has revealed unprecedented details of natural complex mixtures such as dissolved organic matter (DOM) on a molecular formula level, but we lack approaches to access the underlying structural complexity. We here explore the hypothesis that every DOM precursor ion is potentially linked with all emerging product ions in FTMS<sup>2</sup> experiments. The resulting mass difference (Δ<i>m</i>) matrix is deconvoluted to isolate individual precursor ion Δ<i>m</i> profiles and matched with structural information, which was derived from 42 Δ<i>m</i> features from 14 in-house reference compounds and a global set of 11 477 Δ<i>m</i> features with assigned structure specificities, using a dataset of ∼18 000 unique structures. We show that Δ<i>m</i> matching is highly sensitive in predicting potential precursor ion identities in terms of molecular and structural composition. Additionally, the approach identified unresolved precursor ions and missing elements in molecular formula annotation (P, Cl, F). Our study provides first results on how Δ<i>m</i> matching refines structural annotations in van Krevelen space but simultaneously demonstrates the wide overlap between potential structural classes. We show that this effect is likely driven by chemodiversity and offers an explanation for the observed ubiquitous presence of molecules in the center of the van Krevelen space. Our promising first results suggest that Δ<i>m</i> matching can both unfold the structural information encrypted in DOM and assess the quality of FTMS-derived molecular formulas of complex mixtures in general.
Analyzing multi-level governance dynamics from a discourse network perspective: the debate over air pollution regulation in Germany
2022-07-14

Abstract Background Designed to set limits to air pollutant emissions, EU Directive 2008/50/EG has pushed city administrations to strengthen their commitment to environmental protection with mixed results. However, the effectiveness of these policies remains suboptimal. Within this context, this paper provides original empirical evidence on the nature and evolution of the debate over air pollution in the EU that helps readers understand how the interplay among discourse coalitions across levels of governance relates to the implementation of air pollution directives in Europe. To provide this evidence, we apply the discourse-coalition framework to a multi-level governance context by comparing debates over air pollution and examining their evolution in different contexts through the use of discourse network analysis. Results Our results show that the debate in the EU institutions is largely dominated by pro-environmental coalitions, whereas discussions in Stuttgart and Berlin show different degrees of permeability to such arguments. Hence, the relative prominence of certain actors and levels of governance in the local discourse helps explain the extent to which debates at the local level align with the arguments put forward by the EU institutions. For their part, governmental organizations have a tendency to act as bridges between discourse coalitions. Conclusions This novel empirical evidence provides clues that help make sense of the varying levels of implementation of EU air pollution directives at the local level. In this regard, the ability of supranational and national bodies to align their discourse with those of local organizations might facilitate a common understanding and the successful implementation of EU policies. Policymakers aiming to improve air quality at the local level may want to consider engaging actively with this debate by reinforcing the arguments of pro-environmental coalitions. They may also want to make a special effort to ensure that the messages conveyed to supranational and national bodies are also effectively conveyed to lower levels of governance.
Optimized Whole-Body PET MRI Sequence Workflow in Pediatric Hodgkin Lymphoma Patients
2022-07-14

<sup>18</sup>F-FDG PET/MRI might be the diagnostic method of choice for Hodgkin lymphoma patients, as it combines significant metabolic information from PET with excellent soft-tissue contrast from MRI and avoids radiation exposure from CT. However, a major issue is longer examination times than for PET/CT, especially for younger children needing anesthesia. Thus, a targeted selection of suitable whole-body MRI sequences is important to optimize the PET/MRI workflow. <b>Methods:</b> The initial PET/MRI scans of 84 EuroNet-PHL-C2 study patients from 13 international PET centers were evaluated. In each available MRI sequence, 5 PET-positive lymph nodes were assessed. If extranodal involvement occurred, 2 splenic lesions, 2 skeletal lesions, and 2 lung lesions were also assessed. A detection rate was calculated dividing the number of visible, anatomically assignable, and measurable lesions in the respective MRI sequence by the total number of lesions. <b>Results:</b> Relaxation time-weighted (T2w) transverse sequences with fat saturation (fs) yielded the best result, with detection rates of 95% for nodal lesions, 62% for splenic lesions, 94% for skeletal lesions, and 83% for lung lesions, followed by T2w transverse sequences without fs (86%, 49%, 16%, and 59%, respectively) and longitudinal relaxation time-weighted contrast-enhanced transverse sequences with fs (74%, 35%, 57%, and 55%, respectively). <b>Conclusion:</b> T2w transverse sequences with fs yielded the highest detection rates and are well suited for accurate whole-body PET/MRI in lymphoma patients. There is no evidence to recommend the use of contrast agents.
Pharmacokinetic Optimization of Small Molecule Janus Kinase 3 Inhibitors to Target Immune Cells
2022-07-14

Modulation of Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling is a promising method of treating autoimmune diseases, and the profound potency of clinical compounds makes this mode of action particularly attractive. Other questions that remain unanswered also include: What is the ideal selectivity between JAK1 and JAK3? Which cells are most relevant to JAK blockade? And what is the ideal tissue distribution pattern for addressing specific autoimmune conditions? We hypothesized that JAK3 selectivity is most relevant to low-dose clinical effects and interleukin-10 (IL-10) stimulation in particular, that immune cells are the most important compartment, and that distribution to inflamed tissue is the most important pharmacokinetic characteristic for <i>in vivo</i> disease modification. To test these hypotheses, we prepared modified derivatives of JAK3 specific inhibitors that target C909 near the ATP binding site based on FM-381, first reported in 2016; a compound class that was hitherto limited in uptake and exposure <i>in vivo</i>. These limits appear to be due to metabolic instability of side groups binding in the selectivity pocket. We identified derivatives with improved stability and tissue exposure. Conjugation to macrolide scaffolds with medium chain linkers was sufficient to stabilize the compounds and improve transport to organs while maintaining JAK3 affinity. These conjugates are inflammation targeted JAK3 inhibitors with long tissue half-lives and high exposure to activated immune cells.
Dual-Energy Computed Tomography-Based Quantitative Bone Marrow Imaging in Non-Hematooncological Subjects: Associations with Age, Gender and Other Variables
2022-07-14

Background: Our aim is to assess the utility and associations of quantitative bone marrow attenuation (BMA) values measured on clinical dual-energy computed tomography (DECT) exams in non-hematooncologic subjects with skeletal regions, patient age, gender, and other clinical variables. Methods: Our local ethics committee approved this retrospective image data analysis. Between July 2019 and July 2021, 332 eligible patients (mean age, 64 ± 18 years; female, 135) were identified. Inclusion criteria were the availability of a standardized abdominopelvic DECT data set acquired on the same scanner with identical protocol. Eleven regions-of-interest were placed in the T11-L5 vertebral bodies, dorsal iliac crests, and femur necks. Patient age, gender, weight, clinical, habitual variables, inflammation markers, and anemia were documented in all cases. Results: Multi-regression analyses (all, p &lt; 0.05) identified age as the strongest predictor of lumbar BMA (standardized coefficient: β = −0.74), followed by CRP (β = 0.11), LDH (β = 0.11), and gender (β = −0.10). In the lower thoracic spine, age was the strongest predictor (β = −0.58) of BMA, followed by gender (β = −0.09) and LDH (β = 0.12). In femoral bones, age was negatively predictive of BMA (β = −0.12), whereas LDH and anemia were positively predictive (β = 0.16 both). Heart insufficiency significantly decreased (β = 0.12, p = 0.034) a BMA value gradient from higher to lower HU values along the vertebrae T11 and L5, whereas age significantly increased this gradient (β = −0.2, p ≤ 0.001). Conclusions: DECT-based BMA measurements can be obtained from clinical CT exams. BMA values are negatively associated with patient age and influenced by gender, anemia, and inflammatory markers.
Interrelated effects of age and parenthood on whole-brain controllability: protective effects of parenthood in mothers
2022-07-14

Abstract Background Controllability is a measure of the brain’s ability to orchestrate neural activity which can be quantified in terms of properties of the brain’s network connectivity. Evidence from the literature suggests that aging can exert a general effect on whole-brain controllability. Mounting evidence, on the other hand, suggests that parenthood and motherhood in particular lead to long-lasting changes in brain architecture that effectively slow down brain aging. We hypothesize that parenthood might preserve brain controllability properties from aging. Methods In a sample of 814 healthy individuals (aged 33.9±12.7 years, 522 females), we estimate whole-brain controllability and compare the aging effects in subjects with vs. those without children. We use diffusion tensor imaging (DTI) to estimate the brain structural connectome. The level of brain control is then calculated from the connectomic properties of the brain structure. Specifically, we measure the network control over many low-energy state transitions (average controllability) and the network control over difficult-to-reach states (modal controllability). Results and conclusion In nulliparous females, whole-brain average controllability increases, and modal controllability decreases with age, a trend that we do not observe in parous females. Statistical comparison of the controllability metrics shows that modal controllability is higher and average controllability is lower in parous females compared to nulliparous females. In men, we observed the same trend, but the difference between nulliparous and parous males do not reach statistical significance. Our results provide strong evidence that parenthood contradicts aging effects on brain controllability and the effect is stronger in mothers.
Diagnostic Performance of Sex-Specific Modified Metabolite Patterns in Urine for Screening of Prediabetes
2022-07-14

Aims/Hypothesis Large-scale prediabetes screening is still a challenge since fasting blood glucose and HbA 1c as the long-standing, recommended analytes have only moderate diagnostic sensitivity, and the practicability of the oral glucose tolerance test for population-based strategies is limited. To tackle this issue and to identify reliable diagnostic patterns, we developed an innovative metabolomics-based strategy deviating from common concepts by employing urine instead of blood samples, searching for sex-specific biomarkers, and focusing on modified metabolites. Methods Non-targeted, modification group-assisted metabolomics by liquid chromatography–mass spectrometry (LC-MS) was applied to second morning urine samples of 340 individuals from a prediabetes cohort. Normal ( n = 208) and impaired glucose-tolerant (IGT; n = 132) individuals, matched for age and BMI, were randomly divided in discovery and validation cohorts. ReliefF, a feature selection algorithm, was used to extract sex-specific diagnostic patterns of modified metabolites for the detection of IGT. The diagnostic performance was compared with conventional screening parameters fasting plasma glucose (FPG), HbA 1c , and fasting insulin. Results Female- and male-specific diagnostic patterns were identified in urine. Only three biomarkers were identical in both. The patterns showed better AUC and diagnostic sensitivity for prediabetes screening of IGT than FPG, HbA 1c , insulin, or a combination of FPG and HbA 1c . The AUC of the male-specific pattern in the validation cohort was 0.889 with a diagnostic sensitivity of 92.6% and increased to an AUC of 0.977 in combination with HbA 1c . In comparison, the AUCs of FPG, HbA 1c , and insulin alone reached 0.573, 0.668, and 0.571, respectively. Validation of the diagnostic pattern of female subjects showed an AUC of 0.722, which still exceeded the AUCs of FPG, HbA 1c , and insulin (0.595, 0.604, and 0.634, respectively). Modified metabolites in the urinary patterns include advanced glycation end products (pentosidine-glucuronide and glutamyl-lysine-sulfate) and microbiota-associated compounds (indoxyl sulfate and dihydroxyphenyl-gamma-valerolactone-glucuronide). Conclusions/Interpretation Our results demonstrate that the sex-specific search for diagnostic metabolite biomarkers can be superior to common metabolomics strategies. The diagnostic performance for IGT detection was significantly better than routinely applied blood parameters. Together with recently developed fully automatic LC-MS systems, this opens up future perspectives for the application of sex-specific diagnostic patterns for prediabetes screening in urine.
Phosphorylation and ubiquitination independent endocytosis of BRI1
2022-07-14

Abstract The brassinosteroid (BR) hormone and its plasma membrane receptor BR INSENSITIVE1 (BRI1) is one of the best-studied receptor-ligand pairs for understanding the interplay between receptor endocytosis and signaling in plants. BR signaling is mainly determined by the plasma membrane pool of BRI1, whereas BRI1 endocytosis ensures signal attenuation. Since BRs are ubiquitously distributed in the plant, the tools available to study BRI1 function without interference from endogenous BRs are limited. Here, we designed a BR-binding-deficient mutant based on protein sequence-structure analysis and homology modeling of BRI1 and its close homologues. This new tool allowed us to re-examine the BRI1 endocytosis and signal attenuation model. We show that despite decreased phosphorylation and ubiquitination, the BR-binding-deficient BRI1 was internalized similar to the wild type form. These results reinforce the hypothesis that BRI1 is internalized via parallel endocytic routes and machineries. In addition, BR-binding-deficient mutant provides opportunities to study non-canonical ligand-independent BRI1 functions.
VIPurPCA: Visualizing and Propagating Uncertainty in Principal Component Analysis
2022-07-14

&lt;p&gt;This work offers a generic example for the visualization of uncertainty propagated through nonlinear algorithms by automatic differentiation. Scientists use increasingly elaborate algorithms to assess and analyze empirical data. Uncertainty estimates — error bars — are crucial for scientific analysis, but many modern computational analysis methods do not propagate uncertainty from their inputs to their outputs. Our example treatment of PCA combines the classic notion of linearization for error propagation with the power of modern automatic differentiation, and can be applied to other methods, too. We provide a visualization technique to go alongside this approach: Animations along orbits of the probability distribution provide an additional visual channel to represent uncertainty even in plots that are already visually dense as point estimates.&lt;/p&gt;
Review on Higgs Tools
2022-07-14

A plethora of tools for the investigation of properties of Higgs bosons in the Standard Model and beyond is available nowadays. The aim of this proceedings contribution is to give an overview about the existing tools starting with high-precision tools for Standard Model Higgs-boson analyses. Tools addressing specific extensions of the Standard Model are as well mentioned as tools that can be applied to develop missing components for one's own Higgs study.
Structural and functional analysis of natural capsid variants reveals sialic-acid independent entry of BK polyomavirus
2022-07-14

Abstract BK Polyomavirus (BKPyV) is an opportunistic pathogen that causes nephropathy in kidney transplant recipients. The BKPyV major capsid protein, VP1, engages gangliosides, lipid-linked sialylated glycans at the cell surface, to gain entry into cells. Here, we characterise the influence of VP1 mutations observed in patients with persistent post-transplant BKPyV replication on ganglioside binding, VP1 protein structure, and the tropism of the virus in two renal cell lines: 293TT and immortalised renal tubular epithelial (RS) cells. Infectious entry of single mutants E73Q, E73A and the triple mutant A72V-E73Q-E82Q (VQQ) remained sialic acid-dependent. These three variants acquired binding to a-series gangliosides, including GD1a, although only E73Q was able to infect GD1a-supplemented LNCaP or GM95 cells. Crystal structures of the three mutants showed a clear shift of the BC2 loop in mutants E73A and VQQ that correlated with the inability of these VP1 variants to infect ganglioside complemented cells. On the other hand, the double mutant K69N-E82Q lost the ability to bind sialic acid, with the K69N mutation leading to a steric clash which precludes sialic acid binding. Nevertheless, this mutant retained significant infectivity in 293TT cells that was not dependent on heparan sulphate proteoglycans, implying that an unknown sialic acid-independent entry receptor for BKPyV exists.
Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation
2022-07-14

ABSTRACT BACKGROUND Eukaryotes employ epigenetic marks such as DNA methylation at cytosines both for gene regulation and genome defense. In Arabidopsis thaliana , a central role is played by methylation in the CG context, with profound effects on gene expression and transposable element (TE) silencing. Nevertheless, despite its conserved role, genome-wide CG methylation differs substantially between wild A. thaliana accessions. RESULTS We hypothesized that global reduction of CG methylation would reduce epigenomic, transcriptomic and phenotypic diversity in A. thaliana accessions. To test our hypothesis, we knocked out MET1 , which is required for CG methylation, in 18 early-flowering A. thaliana accessions. Homozygous met1 mutants in all accessions suffered from a range of common developmental defects such as dwarfism and delayed flowering, in addition to accession-specific abnormalities in rosette leaf architecture, silique morphology and fertility. Integrated analysis of genome-wide methylation, chromatin accessibility and transcriptomes confirmed that inactivation of MET1 greatly reduces CG methylation and alters chromatin accessibility at thousands of loci. While the effects on TE activation were similarly drastic in all accessions, the quantitative effects on non-TE genes varied greatly. The expression profiles of accessions became considerably more divergent from each other after genome-wide removal of CG methylation, although the expression of genes with diverse expression profiles across wild-type accessions tended to become more similar in mutants. CONCLUSIONS Our systematic analysis of MET1 requirement for genome function in different A. thaliana accessions revealed a dual role for CG methylation: for many genes, CG methylation appears to canalize expression levels, with methylation masking regulatory divergence. However, for a smaller subset of genes, CG methylation increases expression diversity beyond genetically encoded differences.
Novel aspects of Raman spectroscopy in skin research
2022-07-15

Abstract The analytical technology of Raman spectroscopy has an almost 100‐year history. During this period, many modifications and developments happened in the method like discovery of laser, improvements in optical elements and sensitivity of spectrometer and also more advanced light detection systems. Many types of the innovative techniques appeared (e.g. Transmittance Raman spectroscopy, Coherent Raman Scattering microscopy, Surface‐Enhanced Raman scattering and Confocal Raman spectroscopy/microscopy). This review article gives a short description about these different Raman techniques and their possible applications. Then, a short statistical part is coming about the appearance of Raman spectroscopy in the scientific literature from the beginnings to these days. The third part of the paper shows the main application options of the technique (especially confocal Raman spectroscopy) in skin research, including skin composition analysis, drug penetration monitoring and analysis, diagnostic utilizations in dermatology and cosmeto‐scientific applications. At the end, the possible role of artificial intelligence in Raman data analysis and the regulatory aspect of these techniques in dermatology are briefly summarized. For the future of Raman Spectroscopy, increasing clinical relevance and in vivo applications can be predicted with spreading of non‐destructive methods and appearance with the most advanced instruments with rapid analysis time.