julilili42/papers huggingface dataset:
A Stiff Extracellular Matrix Favors the Mechanical Cell Competition that Leads to Extrusion of Bacterially-Infected Epithelial Cells
2022-06-22

Cell competition refers to the mechanism whereby less fit cells (“losers”) are sensed and eliminated by more fit neighboring cells (“winners”) and arises during many processes including intracellular bacterial infection. Extracellular matrix (ECM) stiffness can regulate important cellular functions, such as motility, by modulating the physical forces that cells transduce and could thus modulate the output of cellular competitions. Herein, we employ a computational model to investigate the previously overlooked role of ECM stiffness in modulating the forceful extrusion of infected “loser” cells by uninfected “winner” cells. We find that increasing ECM stiffness promotes the collective squeezing and subsequent extrusion of infected cells due to differential cell displacements and cellular force generation. Moreover, we discover that an increase in the ratio of uninfected to infected cell stiffness as well as a smaller infection focus size, independently promote squeezing of infected cells, and this phenomenon is more prominent on stiffer compared to softer matrices. Our experimental findings validate the computational predictions by demonstrating increased collective cell extrusion on stiff matrices and glass as opposed to softer matrices, which is associated with decreased bacterial spread in the basal cell monolayer in vitro . Collectively, our results suggest that ECM stiffness plays a major role in modulating the competition between infected and uninfected cells, with stiffer matrices promoting this battle through differential modulation of cell mechanics between the two cell populations.
Flexible minds make more moderate views: Subtractive counterfactuals mitigate strong views about immigrants’ trustworthiness
2022-06-22

Public discourse on immigration has seemed to polarize over recent years—with some people strongly trusting, but others strongly distrusting immigrants. We examined whether a cognitive strategy could mitigate these biased outgroup judgments. Given that subtractive counterfactual thoughts (“If only I had not done X. . .”) facilitate cognitive flexibility and especially a relational processing style, we hypothesized that these thoughts (vs. additive counterfactuals “If only I had done X. . .” and no counterfactuals) would weaken the relationship between people’s political orientation and the perceived trustworthiness of immigrants. In five experiments (two preregistered; total N = 1,189), we found that inducing subtractive (but not additive) counterfactuals—either via rhetorical questions in a political speech or via mindset priming—had the predicted debiasing effect. Taken together, subtle means such as using subtractive counterfactual questions in political communication seem to be a promising way to reduce biased outgroup judgments in heated public debates.
What happens in the course of positive mirror exposure? Effects on eating pathology, body satisfaction, affect, and subjective physiological arousal in patients with anorexia and bulimia nervosa
2022-06-22

Abstract Objective Mirror exposure (ME) is a therapeutic technique to improve body image disturbance. However, evidence on the effectiveness of different forms of ME in clinical populations is lacking. The present study therefore analysed effects of ME on trait‐like and state measures of body image in patients with anorexia nervosa (AN) and bulimia nervosa (BN). Method The present study therefore analysed effects of ME on trait‐like and state measures of body image in patients with anorexia nervosa (AN) and bulimia nervosa (BN). In total, 47 inpatients underwent 3 ME sessions guided by a therapist, with instructions to exclusively verbalise positively about their whole body. Participants completed questionnaires on trait‐like eating pathology and body image at the start and end of the study, and instruments on state affect and body satisfaction were administered directly before and after each ME session. Subjective physiological arousal and emotional valence relating to each body part were assessed within each session. Results The results indicate significant improvements in eating pathology and body image regarding trait‐like measures in patients with AN and BN. Concerning state measures, negative affect significantly decreased and body satisfaction increased during ME. Physiological arousal decreased and positively valenced emotions relating to the various body parts increased. Conclusions These findings suggest that positively verbalising about one's body during ME improves eating pathology, body image, affect, and subjective physiological arousal, and thus seems to be an effective form of ME.
Adaptively coping with concept drifts in energy time series forecasting using profiles
2022-06-22

Accurate electrical load forecasts are necessary to stabilize the electricity grid, e.g., by optimally operating energy storage systems or using demand-side management. However, an implicit assumption of most load forecasting methods is that future data looks similar to past data. Unfortunately, this assumption often does not hold; for example, recruiting new staff or a pandemic can lead to demand changes resulting in so-called concept drifts in the underlying data. Most methods for coping with such concept drifts rely on computationally expensive retraining. We propose a new method for coping with concept drifts based on profiles and a linear regression model that avoids expensive retraining. Compared to a simple baseline and five state-of-the-art benchmark models on two different data sets, our method has lower computational costs and higher forecast accuracy, making it especially interesting for smart grid applications.
Renormalizability of a Yang-Mills center-vortex ensemble
2022-06-22

Recently, a new procedure to quantize the Yang-Mills theory in the nonperturbative regime was proposed. The idea is to divide the configuration space into sectors labeled by different topological degrees of freedom and fix the gauge separately on each one of them. As Singer's theorem on gauge copies only refers to gauge fixing conditions that are global in , this construction might avoid the Gribov problem. In this work, we present a proof of the renormalizability in the center-vortex sectors, thus establishing the calculability of the Yang-Mills center-vortex ensemble.
Truly invasive or simply non‐native? Insights from an artificial crested newt hybrid zone
2022-06-22

Abstract Introductions of non‐native species can pose serious threats to native populations and ecosystems. However, the impact of introduced species depends on intrinsic characteristics, local habitat conditions, and the interaction with native species. Case‐specific management strategies may therefore be required. Using phenotypic characters and molecular markers for species identification, we provide insights into an artificial hybrid zone between two closely related newt species, the native Triturus cristatus and the introduced T. carnifex , near Tübingen, south‐west Germany. Our analyses revealed a central Italian origin of the non‐native T. carnifex and suggested their sustained presence in the study area for at least six years, probably much longer. In some ponds, extensive hybridization with native T. cristatus was detected. However, we found no evidence for a displacement of the native species by its non‐native congener. The gradient from pure T. carnifex to pure T. cristatus currently extends over 7 km. A future expansion of the hybrid zone and swamping of a neighboring T. cristatus meta‐population appears unlikely under the local configuration of breeding ponds. We propose to monitor the hybrid zone using genetic markers for evaluating the direction and speed of gene flow, complemented by capture‐recapture studies to reveal trends in species‐specific population sizes. To protect the native T. cristatus , we recommend practitioners to maintain their habitats, for example, by preventing illegal release of gold fish, by counteracting early drying of the breeding ponds, and by regularly cutting back trees and shrubs along the shoreline.
The prognostic role of the immunohistochemical expression of S100 in meningiomas
2022-06-22

Abstract Background:Despite best clinical management meningioma patients experience tumor recurrence. Efforts have been made to improve the prognostic stratification of meningiomas. Recently a multi-faceted molecular classification suggested that the marker S100 is associated with a favorable outcome, making a further analysis is a larger cohort interesting. Material and Methods:The immunohistochemical staining for S100 was analyzed in 1669 paraffin-embedded meningioma samples. The distribution and association with clinical data and progression-free survival via radiographic tumor recurrence were assessed. Results:Of 1669 cases 218 tumors showed strong S100 expression (13.1%). A significantly higher frequency of S100 positive meningiomas was observed in meningiomas of female patients, tumors with spinal and convexity/falx location, primary tumor surgery, NF2, higher extent of resection, lower WHO CNS grade, adjuvant radiotherapy and recurrence-free tumors during follow-up. Univariate analysis revealed a favorable progression-free survival for meningiomas with S100 expression (p=0.0059) but not in the multivariate analysis. Higher S100 frequency was independently associated with female gender (p=0.0003), NF2 (p&lt;0.0001), tumor location (p&lt;0.0001) and lower WHO CNS grade (p=0.0133).Conclusions:The positive prognostic impact of S100 is mostly attributed to the confounding clinical factors gender, tumor location, NF2 status and WHO CNS grade.
A GIS-based Simulation and Visualization Tool for the Assessment of Gully Erosion Processes
2022-06-22

Abstract Gully erosion is known to affect soil productivity, limit land use, and to pose threats on infrastructure in many parts of the world. Gully erosion has been largely neglected because it is difficult to model and visualize its effects. Many gullies grow rapidly to large sizes, making effective control technically difficult and often too expensive. To assess the susceptibility of soils and substrates to gully erosion, the triggering factors must be identified and analyzed. For this study, a simulation of gully development over time was implemented in Python based on the topographic characteristics of the test watershed, soil properties, and measured runoff. The full simulation GIS was tested on a gully in the KwaThunzi region, South Africa. The results are very promising and allow a 2D/3D visualization of the time series of gully evolution.
Analytical uncertainty propagation and storage usage in a high RES Turkish transmission grid scenario
2022-06-22

The rapid integration of renewable energy into power systems calls for thorough system analysis, for which optimal power flow methods are used. However, these optimal power flow methods are mostly evaluated on test grids instead of real-world power grids. In this paper, we provide a model of the real-world Turkish transmission grid to allow more realistic modelling and test a newly proposed optimal power flow method, a second-order cone problem formulation, on this Turkish network. Furthermore, we combine the network with real-world wind power data to investigate the influence of storage placement on power flows. Our results show that the proposed optimal power flow method can be used to investigate the optimal placement of storage. On the Turkish transmission grid, storage (as expected) leads to a more stable and predictable generation and is best placed close to demand. Thus storage can play an essential role as a flexibility provider in Turkey.
Embedding obtained in the paper "Two-dimensional visualization of large document libraries using t-SNE"
2022-06-22

Embedding obtained in the paper "Two-dimensional visualization of large document libraries using t-SNE" (https://openreview.net/forum?id=Hebl3EZ16lq, https://github.com/berenslab/pubmed-tsne-iclr). The paper used the PubMed 2020 baseline originally obtained from https://www.nlm.nih.gov/databases/download/pubmed_medline.html, courtesy of the U.S. National Library of Medicine. That exact dataset is not available anymore. Now (June 2022) one can access the 2021 baseline, which includes our data and new works published in 2021, plus some revised and deleted citations. The dataset provided here includes: - from the PubMed database: article title, journal, PMID, and publication year. - produced by us: t-SNE embedding X and Y coordinates, label, and color.
Dynamical behavior of the C-metric: Charged scalar fields, quasinormal modes, and superradiance
2022-06-23

The -metric is a boost-symmetric spacetime solution to the vacuum Einstein\\nfield equations which describes black holes that are uniformly accelerated\\nunder the tension of a cosmic string. Only recently the thermodynamics of\\naccelerating black holes and their modal stability against neutral scalar\\nperturbations were concisely established. The generalization of accelerating\\nblack holes to incorporate an electric charge, namely the charged -metric,\\npossess three distinct families of quasinormal mode frequencies; the complex\\nphoton surface quasinormal modes associated with unstable null particles at the\\nequatorial plane of the photon surface, the purely imaginary acceleration modes\\nwhose existence solely depends on the acceleration of spacetime and the purely\\nimaginary near-extremal modes which dominate the dynamics of the ringdown at\\nlate times when the event and Cauchy horizon approach each other. We extend the\\nquasinormal mode analysis to charged scalar fluctuations and find that the\\nphoton surface modes are continuously deformed with respect to their neutral\\ncounterpart as the scalar charge is increased. We further find that the\\nacceleration and near-extremal families acquire an oscillation frequency when\\nthe scalar charge is introduced. Finally, we study the superradiant\\namplification of charged scalar monochromatic waves impinging charged\\naccelerating black holes. We find that even though the frequency range of\\nsuperradiant amplification is lessened due to the acceleration, the\\namplification factors are considerably elevated with respect to those\\ntranspiring in Reissner-Nordstr\\\\"om black holes and are maximized when the\\nscalar charge is significantly large.\\n
Data-Driven Identification of Biomarkers for In Situ Monitoring of Drug Treatment in Bladder Cancer Organoids
2022-06-23

Three-dimensional (3D) organoid culture recapitulating patient-specific histopathological and molecular diversity offers great promise for precision medicine in cancer. In this study, we established label-free imaging procedures, including Raman microspectroscopy (RMS) and fluorescence lifetime imaging microscopy (FLIM), for in situ cellular analysis and metabolic monitoring of drug treatment efficacy. Primary tumor and urine specimens were utilized to generate bladder cancer organoids, which were further treated with various concentrations of pharmaceutical agents relevant for the treatment of bladder cancer (i.e., cisplatin, venetoclax). Direct cellular response upon drug treatment was monitored by RMS. Raman spectra of treated and untreated bladder cancer organoids were compared using multivariate data analysis to monitor the impact of drugs on subcellular structures such as nuclei and mitochondria based on shifts and intensity changes of specific molecular vibrations. The effects of different drugs on cell metabolism were assessed by the local autofluorophore environment of NADH and FAD, determined by multiexponential fitting of lifetime decays. Data-driven neural network and data validation analyses (k-means clustering) were performed to retrieve additional and non-biased biomarkers for the classification of drug-specific responsiveness. Together, FLIM and RMS allowed for non-invasive and molecular-sensitive monitoring of tumor-drug interactions, providing the potential to determine and optimize patient-specific treatment efficacy.
Cortico-Hippocampal Oscillations Are Associated With the Developmental Onset of Hippocampal-Dependent Memory
2022-06-23

Hippocampal-dependent memories emerge late during postnatal development, aligning with hippocampal maturation. During sleep, the two-stage memory formation model states that through hippocampal-neocortical interactions, cortical slow-oscillations (SO), thalamocortical Spindles, and hippocampal sharp-wave ripples (SWR) are synchronized, allowing for the consolidation of hippocampal-dependent memories. However, evidence supporting this hypothesis during development is still lacking. Therefore, we performed successive object-in-place tests during a window of memory emergence and recorded in vivo the occurrence of SO, Spindles, and SWR during sleep, immediately after the memory encoding stage of the task. We found that hippocampal-dependent memory emerges at the end of the 4th postnatal week independently of task overtraining. Furthermore, we observed that those animals with better performance in the memory task had increased Spindle density and duration and lower density of SWR. Moreover, we observed changes in the SO-Spindle and Spindle-SWR temporal-coupling during this developmental period. Our results provide new evidence for the onset of hippocampal-dependent memory and its relationship to the oscillatory phenomenon occurring during sleep that helps us understand how memory consolidation models fit into the early stages of postnatal development.
Mapping magnetism: Geophysical modelling of stratigraphic features by using in situ magnetic susceptibility measurements at Pinnacle Point 5‐6 North, South Africa
2022-06-23

Abstract This study utilizes geostatistical modelling of magnetic susceptibility (MS) for geophysical prospection of archaeological stratigraphy at the Middle Stone Age rock shelter site of Pinnacle Point 5‐6 North. These models are overlaid onto high‐resolution photography of the stratigraphic sequence to study the lateral and vertical changes within the magnetic signature of the archaeological sequence and correlate these changes to micromorphological interpretations previously made at the site. In situ analysis is reinforced by laboratory magnetic mineralogical analysis utilizing MS; frequency‐dependent susceptibility ( χ FD ); isothermal remanent magnetization; and anhysteric remanent magnetization to understand the composition of the magnetic minerals creating the in situ signature. This study shows that there is consistent variation in the magnetic signatures of the sequence that can be mapped with in situ MS; there is a correlation with laboratory analysis of magnetic mineralogy, which provides insight into changes in human behaviour; and our models correlate well with micromorphological interpretations of the site.
Source Data files for: Primary cilia and SHH signaling impairments in human and mouse models of Parkinson's disease
2022-06-23

Parkinson’s disease (PD) as a progressive neurodegenerative disorder arises from multiple genetic and environmental factors. However, underlying pathological mechanisms remain poorly understood. Using multiplexed single-cell transcriptomics, we analyze human neural precursor cells (hNPCs) from sporadic PD (sPD) patients. Alterations in gene expression appear in pathways related to primary cilia (PC). Accordingly, in these hiPSC-derived hNPCs and neurons, we observe a shortening of PC. Additionally, we detect a shortening of PC in <em>PINK1</em>-deficient human cellular and mouse models of familial PD. Furthermore, in sPD models, the shortening of PC is accompanied by an increased SHH signal transduction. Inhibition of this pathway rescues the alterations in PC morphology and mitochondrial dysfunction. Thus, increased SHH activity due to ciliary dysfunction is needed for the development of pathoetiological phenotypes observed in sPD, like mitochondrial dysfunction. In sum, altered PC function is part of early PD pathoetiology and inhibiting the overactive SHH signaling is a potential neuroprotective therapy.
A taste for numbers:Caenorhabditis elegansforaging follows a low-dimensional rule of thumb
2022-06-23

Abstract Rules of thumb are behavioral algorithms that approximate optimal behavior while lowering cognitive and sensory costs. One way to reduce these costs is by reducing dimensionality: While the theoretically optimal behavior may depend on many environmental variables, a rule of thumb may use a low-dimensional combination of variables that performs reasonably well. Experimental proof of a dimensionality reduction requires an exhaustive mapping of all relevant combinations of several environmental parameters, which we performed for Caenorhabditis elegans foraging by covering all combinations of food density (across 4 orders of magnitude) and food type (across 12 bacterial strains). We found a one-dimensional rule: Worms respond to food density measured as number of bacteria per unit surface, disregarding other factors such as biomass content or bacterial strain. We also measured fitness experimentally, determining that the rule is near-optimal and therefore constitutes a rule of thumb that leverages the most informative environmental variable.
Source Data files for: Primary cilia and SHH signaling impairments in human and mouse models of Parkinson's disease
2022-06-23

Parkinson’s disease (PD) as a progressive neurodegenerative disorder arises from multiple genetic and environmental factors. However, underlying pathological mechanisms remain poorly understood. Using multiplexed single-cell transcriptomics, we analyze human neural precursor cells (hNPCs) from sporadic PD (sPD) patients. Alterations in gene expression appear in pathways related to primary cilia (PC). Accordingly, in these hiPSC-derived hNPCs and neurons, we observe a shortening of PC. Additionally, we detect a shortening of PC in <em>PINK1</em>-deficient human cellular and mouse models of familial PD. Furthermore, in sPD models, the shortening of PC is accompanied by an increased SHH signal transduction. Inhibition of this pathway rescues the alterations in PC morphology and mitochondrial dysfunction. Thus, increased SHH activity due to ciliary dysfunction is important for the development of pathoetiological phenotypes observed in sPD, like mitochondrial dysfunction. In sum, altered PC function emerges as an important part of early PD pathoetiology. Inhibiting the overactive SHH signaling might emerge as a potential neuroprotective therapy.
The Interplay between cGMP and Calcium Signaling in Alzheimer’s Disease
2022-06-24

Cyclic guanosine monophosphate (cGMP) is a ubiquitous second messenger and a key molecule in many important signaling cascades in the body and brain, including phototransduction, olfaction, vasodilation, and functional hyperemia. Additionally, cGMP is involved in long-term potentiation (LTP), a cellular correlate of learning and memory, and recent studies have identified the cGMP-increasing drug Sildenafil as a potential risk modifier in Alzheimer’s disease (AD). AD development is accompanied by a net increase in the expression of nitric oxide (NO) synthases but a decreased activity of soluble guanylate cyclases, so the exact sign and extent of AD-mediated imbalance remain unclear. Moreover, human patients and mouse models of the disease present with entangled deregulation of both cGMP and Ca2+ signaling, e.g., causing changes in cGMP-mediated Ca2+ release from the intracellular stores as well as Ca2+-mediated cGMP production. Still, the mechanisms governing such interplay are poorly understood. Here, we review the recent data on mechanisms underlying the brain cGMP signaling and its interconnection with Ca2+ signaling. We also discuss the recent evidence stressing the importance of such interplay for normal brain function as well as in Alzheimer’s disease.