26 Works

Topological structure and dynamics of three-dimensional active nematics

Guillaume Duclos, Thomas Powers, Aparna Baskaran, Zvonimir Dogic, Vincenzo Vitelli, Federico Toschi, Raymond Adkins, Debarghya Banerjee, Matthew Peterson, Minu Varghese, Itamar Kolvin, Robert Pelcovits, Sebastian Streichan, Daniel Beller, Arvind Baskaran, Michael Hagan, Matthew S. E. Peterson, Robert A. Pelcovits, Thomas R. Powers, Michael F. Hagan & Sebastian J. Streichan
Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination...

X-Ray CT scans of barley panicles and their individual seeds from the Composite Cross II experiment

Erik Amézquita, Michelle Quigley, Tim Ophelders, Jacob Landis, Daniel Koenig, Elizabeth Munch & Daniel Chitwood
Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare, and analyze this information embedded in a robust and concise way, we turn to Topological Data Analysis (TDA), specifically the Euler Characteristic Transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to...

Depression, anxiety, and post-traumatic stress disorder symptoms after hyperemesis gravidarum: a prospective cohort study

Kelly Nijsten, Loïs M. van der Minnen, Caitlin Dean, Joke M. J. Bais, Carrie Ris-Stalpers, Rik van Eekelen, Henk A. Bremer, David P. van der Ham, Wieteke M. Heidema, Anjoke Huisjes, Gunilla Kleiverda, Simone M. Kuppens, Judith O. E. H. van Laar, Josje Langenveld, Flip van der Made, Dimitri Papatsonis, Marie-José Pelinck, Paula J. Pernet, Leonie van Rheenen-Flach, Robbert J. Rijnders, Hubertina C. J. Scheepers, Tatjana Vogelvang, Ben W. Mol, Miranda Olff, Tessa J. Roseboom … & Rebecca C. Painter
To determine the prevalence of depression, anxiety, and posttraumatic stress disorder (PTSD) years after hyperemesis gravidarum (HG) and its association with HG severity. This prospective cohort study consisted of a follow-up of 215 women admitted for HG, who were eligible to participate in a randomized controlled trial and either declined or agreed to be randomized between 2013 and 2016 in 19 hospitals in the Netherlands. Participants completed the Hospital Anxiety and Depression Scale (HADS) six...

Additional file 5 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 5. Simulation results (Power) for linear interaction effects with $$M=48$$ M = 48 of GLMM and GEE at aggregated level with AR1 correlation structure $$\sigma_{c}^{2}=0.8,\ r=0.8$$ σ c 2 = 0.8 , r = 0.8 under USDo2 with different hypothesis testing methods and with different estimators for the standard error of the parameter estimates.

Additional file 2 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 2. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for linear interaction effects with $$M=192$$ M = 192 .

Additional file 3 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 3. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for symmetric interaction effects with $$M=48$$ M = 48 .

Additional file 4 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 4. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for symmetric interaction effects with $$M=192$$ M = 192 .

Additional file 4 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 4. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for symmetric interaction effects with $$M=192$$ M = 192 .

Data from: A method for time-resolved measurements of the mechanics of phagocytic cups

Matthias Irmscher, Arthur M. De Jong, Holger Kress & Menno W. J. Prins
The internalization of matter by phagocytosis is of key importance in the defense against bacterial pathogens and in the control of cancerous tumor growth. Despite the fact that phagocytosis is an inherently mechanical process, little is known about the forces and energies that a cell requires for internalization. Here we use functionalized magnetic particles as phagocytic targets and track their motion while actuating them in an oscillating magnetic field, in order to measure the translational...

Electronic structure and interface energetics of CuBi2O4 photoelectrodes - data

Freddy E Oropeza, Nelson Y Dzade, Amalia Pons-Marti, Zhenni Yang, Kelvin H L Zhang, Nora H De Leeuw, Emiel J M Hensen & Jan P Hofmann
In this study, the electronic structure of CuBi2O4 has been studied by a combination of hard X-ray photoemission, resonant photoemission and X-ray absorption spectroscopies, and compared with density functional theory (DFT) calculations. The photoemission study indicates that there is a strong Bi 6s-O 2p hybrid electronic state at 2.3 eV below the Fermi level, whereas the valence band maximum (VBM) has a predominant Cu 3d – O 2p hybrid character. XAS at the O K-edge...

Additional file 1 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 1. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for linear interaction effects with $$M=48$$ M = 48 .

Additional file 2 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 2. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for linear interaction effects with $$M=192$$ M = 192 .

Data from: Continuum of vasodilator stress from rest to contrast medium to adenosine hyperemia for fractional flow reserve assessment

Nils P. Johnson, Allen Jeremias, Frederik M. Zimmermann, Julien Adjedj, Nils Witt, Barry Hennigan, Bon-Kwon Koo, Akiko Maehara, Mitsuaki Matsumura, Emanuele Barbato, Giovanni Esposito, Bruno Trimarco, Gilles Rioufol, Seung-Jung Park, Hyoung-Mo Yang, Sérgio B. Baptista, George S. Chrysant, Antonio M. Leone, Colin Berry, Bernard De Bruyne, K. Lance Gould, Richard L. Kirkeeide, Keith G. Oldroyd, Nico H. J. Pijls, William F. Fearon … & Nico H.J. Pijls
OBJECTIVES: We compared the diagnostic performance with adenosine-derived fractional flow reserve (FFR) #0.8 of contrast-based FFR (cFFR), resting distal pressure (Pd)/aortic pressure (Pa), and the instantaneous wave-free ratio (iFR). BACKGROUND: FFR objectively identifies lesions that benefit from medical therapy versus revascularization. However, FFR requires maximal vasodilation, usually achieved with adenosine. Radiographic contrast injection causes submaximal coronary hyperemia. Therefore, intracoronary contrast could provide an easy and inexpensive tool for predicting FFR. METHODS: We recruited patients undergoing...

Data from: A 45-second self-test for cardiorespiratory fitness: heart rate-based estimation in healthy individuals

Francesco Sartor, Matteo Bonato, Gabriele Papini, Andrea Bosio, Rahil A. Mohammed, Alberto G. Bonomi, Jonathan P. Moore, Giampiero Merati, Antonio La Torre & Hans-Peter Kubis
Cardio-respiratory fitness (CRF) is a widespread essential indicator in Sports Science as well as in Sports Medicine. This study aimed to develop and validate a prediction model for CRF based on a 45 second self-test, which can be conducted anywhere. Criterion validity, test re-test study was set up to accomplish our objectives. Data from 81 healthy volunteers (age: 29 ± 8 years, BMI: 24.0 ± 2.9), 18 of whom females, were used to validate this...

Redefining Near-Unity Luminescence in Quantum Dots with Photothermal Threshold Quantum Yield

David Hanifi, Noah Bronstein, Brent Koscher, Zach Nett, Joseph Swabeck, Kaori Takano, Adam Schwartzberg, Lorenzo Maserati, Koen Vandewal, Yoeri Van De Burgt, Alberto Salleo & Paul Alivisatos
Herin is the code and example data sets for the publication titled: "Redefining Near-Unity Luminescence in Quantum Dots with Photothermal Threshold Quantum Yield." The abstract of this paper is as follows. A variety of optical applications rely on the absorption and reemission of light. The quantum yield of this process often plays an essential role. When the quantum yield deviates from unity by significantly less than 1%, applications such as luminescent concentrators and optical refrigerators...

Data from: Quantification and optimization of ADF-STEM image contrast for beam sensitive materials

Karthikeyan Gnanasekaran, Gijsbertus De With & Heiner Friedrich
Many functional materials are difficult to analyze by Scanning Transmission Electron Microscopy (STEM) on account of their beam sensitivity and low contrast between different phases. The problem becomes even more severe when thick specimens need to be investigated, a situation that is common for materials that are ordered from the nanometer to micrometer length scales or when performing dynamic experiments in a TEM liquid cell. Here we report a method to optimize annular dark-field (ADF)...

Data from: How oscillating aerodynamic forces explain the timbre of the hummingbird's hum and other animals in flapping flight

Ben Hightower, Patrick Wijnings, Rick Scholte, Rivers Ingersoll, Diana Chin, Jade Nguyen, Daniel Shorr & David Lentink
The source of the hummingbird's distinctive hum is not fully understood, but there are clues to its origin in the acoustic nearfield. Hence we studied six freely hovering Anna’s hummingbirds, performing acoustic nearfield holography using a 2176 microphone array in vivo, while also directly measuring the 3D aerodynamic forces using a new aerodynamic force platform. We corroborate the acoustic measurements by developing a first-principles acoustic model that integrates the aerodynamic forces with wing kinematics, which...

Additional file 5 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 5. Simulation results (Power) for linear interaction effects with $$M=48$$ M = 48 of GLMM and GEE at aggregated level with AR1 correlation structure $$\sigma_{c}^{2}=0.8,\ r=0.8$$ σ c 2 = 0.8 , r = 0.8 under USDo2 with different hypothesis testing methods and with different estimators for the standard error of the parameter estimates.

Data from: Charting the complete elastic properties of inorganic crystalline compounds

Maarten De Jong, Wei Chen, Thomas Angsten, Anubhav Jain, Randy Notestine, Anthony Gamst, Marcel Sluiter, Chaitanya Krishna Ande, Sybrand Van Der Zwaag, Jose J. Plata, Cormac Toher, Stefano Curtarolo, Gerbrand Ceder, Kristin A. Persson & Mark Asta
The elastic constant tensor of an inorganic compound provides a complete description of the response of the material to external stresses in the elastic limit. It thus provides fundamental insight into the nature of the bonding in the material, and it is known to correlate with many mechanical properties. Despite the importance of the elastic constant tensor, it has been measured for a very small fraction of all known inorganic compounds, a situation that limits...

Data from: Quantitative multi-parametric magnetic resonance imaging of tumor response to photodynamic therapy

Tom J.L. Schreurs, Stefanie J. Hectors, Igor Jacobs, Holger Grüll, Klaas Nicolay, Gustav J. Strijkers & Tom J. L. Schreurs
Objective: The aim of this study was to characterize response to photodynamic therapy (PDT) in a mouse cancer model using a multi-parametric quantitative MRI protocol and to identify MR parameters as potential biomarkers for early assessment of treatment outcome. Methods: CT26.WT colon carcinoma tumors were grown subcutaneously in the hind limb of BALB/c mice. Therapy consisted of intravenous injection of the photosensitizer Bremachlorin, followed by 10 min laser illumination (200 mW/cm2) of the tumor 6...

Dataset for: Mid-infrared silicon-on-insulator wavegudes with single-mode propagation over an octave of frequency

Callum John Stirling, Wei Cao, Jamie Reynolds, Zhibo Qu, Thomas Bradley, Lorenzo Mastronardi, Frederic Gardes, Goran Mashanovich & Milos Nedeljkovic
Experimental and simulation data for the paper: Callum J. Stirling, Wei Cao, Jamie D. Reynolds, Zhibo Qu, Thomas D. Bradley, Lorenzo Mastronardi, Frederic Y. Gardes, Goran Z. Mashanovich, Milos Nedeljkovic. (2021). Mid-infrared silicon-on-insulator wavegudes with single-mode propagation over an octave of frequency, Optics Express

Anomaly Detection for a Large Number of Streams: A Permutation-Based Higher Criticism Approach

Ivo V. Stoepker, Rui M. Castro, Ery Arias-Castro & Edwin van den Heuvel
Anomaly detection when observing a large number of data streams is essential in a variety of applications, ranging from epidemiological studies to monitoring of complex systems. High-dimensional scenarios are usually tackled with scan-statistics and related methods, requiring stringent modeling assumptions for proper calibration. In this work we take a non-parametric stance, and propose a permutation-based variant of the higher criticism statistic not requiring knowledge of the null distribution. This results in an exact test in...

Additional file 1 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 1. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for linear interaction effects with $$M=48$$ M = 48 .

Additional file 3 of Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study

Zhuozhao Zhan, Geertruida H. de Bock & Edwin R. van den Heuvel
Additional file 3. Simulation results (Point estimates, Coverage probabilities, Type I error, and Power) for symmetric interaction effects with $$M=48$$ M = 48 .

Depression, anxiety, and post-traumatic stress disorder symptoms after hyperemesis gravidarum: a prospective cohort study

Kelly Nijsten, Loïs M. van der Minnen, Caitlin Dean, Joke M. J. Bais, Carrie Ris-Stalpers, Rik van Eekelen, Henk A. Bremer, David P. van der Ham, Wieteke M. Heidema, Anjoke Huisjes, Gunilla Kleiverda, Simone M. Kuppens, Judith O. E. H. van Laar, Josje Langenveld, Flip van der Made, Dimitri Papatsonis, Marie-José Pelinck, Paula J. Pernet, Leonie van Rheenen-Flach, Robbert J. Rijnders, Hubertina C. J. Scheepers, Tatjana Vogelvang, Ben W. Mol, Miranda Olff, Tessa J. Roseboom … & Rebecca C. Painter
To determine the prevalence of depression, anxiety, and posttraumatic stress disorder (PTSD) years after hyperemesis gravidarum (HG) and its association with HG severity. This prospective cohort study consisted of a follow-up of 215 women admitted for HG, who were eligible to participate in a randomized controlled trial and either declined or agreed to be randomized between 2013 and 2016 in 19 hospitals in the Netherlands. Participants completed the Hospital Anxiety and Depression Scale (HADS) six...

Registration Year

  • 2022
    13
  • 2021
    3
  • 2020
    3
  • 2019
    1
  • 2018
    1
  • 2016
    3
  • 2015
    1
  • 2013
    1

Resource Types

  • Dataset
    26

Affiliations

  • Eindhoven University of Technology
    26
  • University of Groningen
    10
  • Stanford University
    3
  • Arq Psychotrauma Expert Group
    2
  • University of Aberdeen
    2
  • Martini Ziekenhuis
    2
  • University of California, Berkeley
    2
  • Monash University
    2
  • Lawrence Berkeley National Laboratory
    2
  • Flevoziekenhuis
    2