julilili42/papers huggingface dataset:
Dynamical Formation of Scalarized Black Holes and Neutron Stars through Stellar Core Collapse
2021-10-15

In a certain class of scalar-Gauss-Bonnet gravity, the black holes and the neutron stars can undergo spontaneous scalarization-a strong gravity phase transition triggered by a tachyonic instability due to the nonminimal coupling between the scalar field and the spacetime curvature. Studies of this phenomenon have, so far, been restricted mainly to the study of the tachyonic instability and stationary scalarized black holes and neutron stars. To date, no realistic physical mechanism for the formation of isolated scalarized black holes and neutron stars has been proposed. We study, for the first time, the spherically symmetric fully nonlinear stellar core collapse to a black hole and a neutron star in scalar-Gauss-Bonnet theories allowing for a spontaneous scalarization. We show that the core collapse can produce scalarized black holes and scalarized neutron stars starting with a nonscalarized progenitor star. The possible paths to reach the end (non)scalarized state are quite rich leading to interesting possibilities for observational manifestations.
Gastrointestinal bleeding and endoscopic findings in critically and non‐critically ill patients with corona virus disease 2019 (COVID‐19): Results from Lean European Open Survey on SARS‐CoV‐2 (LEOSS) and COKA registries
2021-10-15

Abstract Background Corona virus disease 2019 (COVID‐19) patients are at increased risk for thromboembolic events. It is unclear whether the risk for gastrointestinal (GI) bleeding is also increased. Methods We considered 4128 COVID‐19 patients enrolled in the Lean European Open Survey on SARS‐CoV‐2 (LEOSS) registry. The association between occurrence of GI bleeding and comorbidities as well as medication were examined. In addition, 1216 patients from COKA registry were analyzed focusing on endoscopy diagnostic findings. Results A cumulative number of 97 patients (1.8%) with GI bleeding were identified in the LEOSS registry and COKA registry. Of 4128 patients from the LEOSS registry, 66 patients (1.6%) had a GI bleeding. The rate of GI bleeding in patients with intensive care unit (ICU) admission was 4.5%. The use of therapeutic dose of anticoagulants showed a significant association with the increased incidence of bleeding in the critical phase of disease. The Charlson comorbidity index and the COVID‐19 severity index were significantly higher in the group of patients with GI bleeding than in the group of patients without GI bleeding (5.83 (SD = 2.93) vs. 3.66 (SD = 3.06), p &lt; 0.01 and 3.26 (SD = 1.69) vs. 2.33 (SD = 1.53), p &lt; 0.01, respectively). In the COKA registry 31 patients (2.5%) developed a GI bleeding. Of these, the source of bleeding was identified in upper GI tract in 21 patients (67.7%) with ulcer as the most frequent bleeding source (25.8%, n = 8) followed by gastroesophageal reflux (16.1%, n = 5). In three patients (9.7%) GI bleeding source was located in lower GI tract caused mainly by diverticular bleeding (6.5%, n = 2). In seven patients (22.6%) the bleeding localization remained unknown. Conclusion Consistent with previous research, comorbidities and disease severity correlate with the incidence of GI bleeding. Also, therapeutic anticoagulation seems to be associated with a higher risk of GI bleeding. Overall, the risk of GI bleeding seems not to be increased in COVID‐19 patients.
Spectral inference reveals principal cone-integration rules of the zebrafish inner retina
2021-10-15

Retinal bipolar cells integrate cone signals at dendritic and axonal sites. The axonal route, involving amacrine cells, remains largely uncharted. However, because cone types differ in their spectral sensitivities, insights into bipolar cells' cone integration might be gained based on their spectral tunings. We therefore recorded in vivo responses of bipolar cell presynaptic terminals in larval zebrafish to widefield but spectrally resolved flashes of light and mapped the results onto spectral responses of the four cones. This "spectral circuit mapping" allowed explaining ∼95% of the spectral and temporal variance of bipolar cell responses in a simple linear model, thereby revealing several notable integration rules of the inner retina. Bipolar cells were dominated by red-cone inputs, often alongside equal sign inputs from blue and green cones. In contrast, UV-cone inputs were uncorrelated with those of the remaining cones. This led to a new axis of spectral opponency where red-, green-, and blue-cone "Off" circuits connect to "natively-On" UV-cone circuits in the outermost fraction of the inner plexiform layer-much as how key color opponent circuits are established in mammals. Beyond this, and despite substantial temporal diversity that was not present in the cones, bipolar cell spectral tunings were surprisingly simple. They either approximately resembled both opponent and non-opponent spectral motifs already present in the cones or exhibited a stereotyped non-opponent broadband response. In this way, bipolar cells not only preserved the efficient spectral representations in the cones but also diversified them to set up a total of six dominant spectral motifs, which included three axes of spectral opponency.
Topographical Vacuum Sealing of 3D-Printed Multiplanar Microfluidic Structures
2021-10-15

We demonstrate a novel way of creating three-dimensional microfluidic channels capable of following complex topographies. To this end, substrates with open channels and different geometries were 3D-printed, and the open channels were consecutively closed with a thermoplastic using a low-resolution vacuum-forming approach. This process allows the sealing of channels that are located on the surface of complex multiplanar topographies, as the thermoplastic aligns with the surface-shape (the macrostructure) of the substrate, while the microchannels remain mostly free of thermoplastic as their small channel size resists thermoplastic inflow. This new process was analyzed for its capability to consistently close different substrate geometries, which showed reliable sealing of angles &gt;90°. Furthermore, the thermoplastic intrusion into channels of different widths was quantified, showing a linear effect of channel width and percentage of thermoplastic intrusion; ranging from 43.76% for large channels with 2 mm width to only 5.33% for channels with 500 μm channel width. The challenging sealing of substrate ‘valleys’, which are created when two large protrusions are adjacent to each other, was investigated and the correlation between protrusion distance and height is shown. Lastly, we present three application examples: a serpentine mixer with channels spun around a cuboid, increasing the usable surface area; a cuvette-inspired flow cell for a 2-MXP biosensor based on molecular imprinted polymers, fitting inside a standard UV/Vis-Spectrophotometer; and an adapter system that can be manufactured by one-sided injection molding and is self-sealed before usage. These examples demonstrate how this novel technology can be used to easily adapt microfluidic circuits for application in biosensor platforms.
Non‐invasive brain stimulation in modulation of mental rotation ability: A systematic review and meta‐analysis
2021-10-15

Abstract Mental rotation, the ability to manipulate mental images, is an important function in human cognition. This systematic review and meta‐analysis investigates the potential of non‐invasive brain stimulation in modulation of this component of visuo‐spatial perception. The PubMed database was reviewed prior to 31 September 2020 on randomized controlled trials investigating the effects of repetitive transcranial magnetic stimulation (rTMS), transcranial direct current stimulation (tDCS), and transcranial alternating current stimulation (tACS) on the mental rotation ability in healthy persons. A total of 17 studies (including 485 subjects) matched our inclusion criteria. Within their scope, overall, 46 sham‐controlled experiments were performed. Methodology and results of each experiment are presented in a meta‐analysis. The data show a large variety of methods and effects. The influence of (1) stimulation‐technique (tDCS, tACS, and rTMS), (2) stimulation protocol (anodal, cathodal, bilateral tDCS, tACS, high‐frequency rTMS, low‐frequency rTMS, paired pulse rTMS, and theta burst stimulation), (3) stimulation timing (preconditioning and simultaneous), (4) stimulation location (left, right hemisphere, frontal, and parietal area), and (5) stimulus type (bodily and non‐bodily) is discussed. The data indicate a beneficial effect of anodal tDCS and of tACS and no effect of cathodal tDCS on the mental rotation ability. Bilateral tDCS protocols both improved and worsened the parameters assessed. The small effect sizes obtained in mostly rTMS experiments require cautious interpretation.
A Simulation Study on Latent Transition Analysis for Examining Profiles and Trajectories in Education: Recommendations for Fit Statistics
2021-10-15

Latent transition analysis is an informative statistical tool for depicting heterogeneity in learning as latent profiles. We present a Monte Carlo simulation study to guide researchers in selecting fit indices for identifying the correct number of profiles. We simulated data representing profiles of learners within a typical pre- post- follow up-design with continuous indicators, varying sample size (N from 50 to 1000), attrition rate (none/10% per wave), and profile separation (entropy; from .73 to .87). Results indicate that the most commonly used fit index, the Bayesian information criterion (BIC), and the consistent Akaike information criterion (CAIC) consistently underestimate the real number of profiles. A combination of the AIC or the AIC3 with the adjusted Bayesian Information Criterion (aBIC) provides the most precise choice for selecting the number of profiles and is accurate with sample sizes of at least N = 200. The AIC3 excels starting from N = 500. Results were mostly robust towards differing numbers of time points, profiles, indicator variables, and alternative profiles. We provide an online tool for computing these fit indices and discuss implications for research.
Arthroscopic Minimal Invasive Treatment of Posterolateral Tibial Plateau Impression Fractures
2021-10-15

Posterolateral fractures of the tibial plateau are difficult to address. Malunion can lead to early posttraumatic arthritis of the knee due to instability and elevated joint reaction forces. Arthroscopically assisted percutaneous reduction facilitates visualization and avoids open approaches either directly from posterolateral or from lateral with optional extension via a lateral epicondylus osteotomy. We describe and illustrate a minimal invasive technique using an arthroscopic posterolateral viewing portal. Using this technique, we demonstrated very good clinical outcome with excellent patient satisfaction. Key words: Schatzker, tibia head fracture, knee arthroscopy, multiligamentary injury.
SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
2021-10-15

In systems biology, biological phenomena are often modeled by Ordinary Differential Equations (ODEs) and distributed in the de facto standard file format SBML. The primary analyses performed with such models are dynamic simulation, steady-state analysis, and parameter estimation. These methodologies are mathematically formalized, and libraries for such analyses have been published. Several tools exist to create, simulate, or visualize models encoded in SBML. However, setting up and establishing analysis environments is a crucial hurdle for non-modelers. Therefore, easy access to perform fundamental analyses of ODE models is a significant challenge. We developed SBMLWebApp, a web-based service to execute SBML-based simulation, steady-state analysis, and parameter estimation directly in the browser without the need for any setup or prior knowledge to address this issue. SBMLWebApp visualizes the result and numerical table of each analysis and provides a download of the results. SBMLWebApp allows users to select and analyze SBML models directly from the BioModels Database. Taken together, SBMLWebApp provides barrier-free access to an SBML analysis environment for simulation, steady-state analysis, and parameter estimation for SBML models. SBMLWebApp is implemented in JavaTM based on an Apache Tomcat® web server using COPASI, the Systems Biology Simulation Core Library (SBSCL), and LibSBMLSim as simulation engines. SBMLWebApp is licensed under MIT with source code freely available. At the end of this article, the Data Availability Statement gives the internet links to the two websites to find the source code and run the program online.
Dataset (XI) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
2021-10-15

Well-tempered metadynamics simulation data of compounds <strong>1 </strong>and<strong> 2</strong> of the related to the publication Pantsar et al.: <em>Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors.</em> Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files). All datasets related to this publication: https://doi.org/10.5281/zenodo.4568113(compound <strong>1</strong>; dataset: I) https://doi.org/10.5281/zenodo.4572444 (compound <strong>1</strong>; dataset: II) https://doi.org/10.5281/zenodo.4561797(compound <strong>2</strong>; dataset: III) https://doi.org/10.5281/zenodo.4563896 (compound <strong>2</strong>; dataset: IV) https://doi.org/10.5281/zenodo.5563359 (<strong>SB203580</strong>; dataset: V) https://doi.org/10.5281/zenodo.5563655 (<strong>SB203580</strong>; dataset: VI) https://doi.org/10.5281/zenodo.5564118 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VII) https://doi.org/10.5281/zenodo.5564208 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VIII) https://doi.org/10.5281/zenodo.5564586 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: IX) https://doi.org/10.5281/zenodo.5570882 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: X) https://doi.org/10.5281/zenodo.5571352 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: XI) The datasets include original Desmond raw-trajectories (datasets I–VIII), PDB-coordinates for the energy minimized metastable state derived structures (datasets II, IV and VI) and raw-trajectories of the well-tempered metadynamics simulations (dataset IX–XI).
Dataset (VI) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
2021-10-15

MD simulation data of <strong>SB203580</strong> related to the publication Pantsar et al.: <em>Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors.</em> Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files). All datasets related to this publication: https://doi.org/10.5281/zenodo.4568113(compound <strong>1</strong>; dataset: I) https://doi.org/10.5281/zenodo.4572444 (compound <strong>1</strong>; dataset: II) https://doi.org/10.5281/zenodo.4561797(compound <strong>2</strong>; dataset: III) https://doi.org/10.5281/zenodo.4563896 (compound <strong>2</strong>; dataset: IV) https://doi.org/10.5281/zenodo.5563359 (<strong>SB203580</strong>; dataset: V) https://doi.org/10.5281/zenodo.5563655 (<strong>SB203580</strong>; dataset: VI) https://doi.org/10.5281/zenodo.5564118 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VII) https://doi.org/10.5281/zenodo.5564208 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VIII) https://doi.org/10.5281/zenodo.5564586 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: IX) https://doi.org/10.5281/zenodo.5570882 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: X) https://doi.org/10.5281/zenodo.5571352 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: XI) The datasets include original Desmond raw-trajectories (datasets I–VIII), PDB-coordinates for the energy minimized metastable state derived structures (datasets II, IV and VI) and raw-trajectories of the well-tempered metadynamics simulations (dataset IX–XI).
Dataset (VII) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
2021-10-15

MD simulation data of compound <strong>1</strong> in MSM <strong>2-<em>S</em><sub>3</sub></strong> conformations of the related to the publication Pantsar et al.: <em>Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors.</em> Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files). All datasets related to this publication: https://doi.org/10.5281/zenodo.4568113(compound <strong>1</strong>; dataset: I) https://doi.org/10.5281/zenodo.4572444 (compound <strong>1</strong>; dataset: II) https://doi.org/10.5281/zenodo.4561797(compound <strong>2</strong>; dataset: III) https://doi.org/10.5281/zenodo.4563896 (compound <strong>2</strong>; dataset: IV) https://doi.org/10.5281/zenodo.5563359 (<strong>SB203580</strong>; dataset: V) https://doi.org/10.5281/zenodo.5563655 (<strong>SB203580</strong>; dataset: VI) https://doi.org/10.5281/zenodo.5564118 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VII) https://doi.org/10.5281/zenodo.5564208 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VIII) https://doi.org/10.5281/zenodo.5564586 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: IX) https://doi.org/10.5281/zenodo.5570882 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: X) https://doi.org/10.5281/zenodo.5571352 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: XI) The datasets include original Desmond raw-trajectories (datasets I–VIII), PDB-coordinates for the energy minimized metastable state derived structures (datasets II, IV and VI) and raw-trajectories of the well-tempered metadynamics simulations (dataset IX–XI).
Dataset (V) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
2021-10-15

MD simulation data of <strong>SB203580</strong> related to the publication Pantsar et al.: <em>Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors.</em> Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files). All datasets related to this publication: https://doi.org/10.5281/zenodo.4568113(compound <strong>1</strong>; dataset: I) https://doi.org/10.5281/zenodo.4572444 (compound <strong>1</strong>; dataset: II) https://doi.org/10.5281/zenodo.4561797(compound <strong>2</strong>; dataset: III) https://doi.org/10.5281/zenodo.4563896 (compound <strong>2</strong>; dataset: IV) https://doi.org/10.5281/zenodo.5563359 (<strong>SB203580</strong>; dataset: V) https://doi.org/10.5281/zenodo.5563655 (<strong>SB203580</strong>; dataset: VI) https://doi.org/10.5281/zenodo.5564118 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VII) https://doi.org/10.5281/zenodo.5564208 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VIII) https://doi.org/10.5281/zenodo.5564586 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: IX) https://doi.org/10.5281/zenodo.5570882 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: X) https://doi.org/10.5281/zenodo.5571352 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: XI) The datasets include original Desmond raw-trajectories (datasets I–VIII), PDB-coordinates for the energy minimized metastable state derived structures (datasets II, IV and VI) and raw-trajectories of the well-tempered metadynamics simulations (dataset IX–XI).
Dataset (X) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
2021-10-15

Well-tempered metadynamics simulation data of compounds <strong>1 </strong>and<strong> 2</strong> of the related to the publication Pantsar et al.: <em>Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors.</em> Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files). All datasets related to this publication: https://doi.org/10.5281/zenodo.4568113(compound <strong>1</strong>; dataset: I) https://doi.org/10.5281/zenodo.4572444 (compound <strong>1</strong>; dataset: II) https://doi.org/10.5281/zenodo.4561797(compound <strong>2</strong>; dataset: III) https://doi.org/10.5281/zenodo.4563896 (compound <strong>2</strong>; dataset: IV) https://doi.org/10.5281/zenodo.5563359 (<strong>SB203580</strong>; dataset: V) https://doi.org/10.5281/zenodo.5563655 (<strong>SB203580</strong>; dataset: VI) https://doi.org/10.5281/zenodo.5564118 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VII) https://doi.org/10.5281/zenodo.5564208 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VIII) https://doi.org/10.5281/zenodo.5564586 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: IX) https://doi.org/10.5281/zenodo.5570882 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: X) https://doi.org/10.5281/zenodo.5571352 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: XI) The datasets include original Desmond raw-trajectories (datasets I–VIII), PDB-coordinates for the energy minimized metastable state derived structures (datasets II, IV and VI) and raw-trajectories of the well-tempered metadynamics simulations (dataset IX–XI).