Works Published in 2021
Displaying works 101 - 120 of 207 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2021 journal article
The landscape of cell–cell communication through single-cell transcriptomics
Current Opinion in Systems Biology.
author keywords: Cell-cell interactions; Cell signaling; Inference; Intercellular communi- cation; Ligand-receptor interactions; Signaling networks; Single-cell RNA-Seq; Spatial transcriptomics
TL;DR:
This review discusses the recent explosion of methods that have been developed to infer cell-cell communication from non-spatial and spatial single-cell transcriptomics, two promising technologies which have complementary strengths and limitations.
(via Semantic Scholar)
doi.org (publisher)
Source: ORCID
Added: August 22, 2021
2021 journal article
Charge substitutions at the voltage-sensing module of domain III enhance actions of site-3 and site-4 toxins on an insect sodium channel
Insect Biochemistry and Molecular Biology, 137, 103625.
author keywords: Insect sodium channel; Scorpion alpha-toxin; Scorpion beta-toxin; Homology modeling; Mutagenesis; Electrophysiology
MeSH headings : Animals; Cnidarian Venoms / pharmacology; Drosophila melanogaster / drug effects; Drosophila melanogaster / genetics; Drosophila melanogaster / metabolism; Insect Proteins / genetics; Insect Proteins / metabolism; Oocytes / drug effects; Oocytes / metabolism; Scorpion Venoms / pharmacology; Sodium Channels / genetics; Sodium Channels / metabolism
TL;DR:
These results highlight the involvement of III-VSM in the actions of both site 3 and site 4 toxins, suggesting that charge reversing substitutions in III- VSM allosterically facilitate IIS4 or IVS4 voltage sensor trapping by these toxins.
(via Semantic Scholar)
Source: ORCID
Added: August 22, 2021
2021 journal article
A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development
PLOS Computational Biology, 17(3), e1008571.
Ed(s): D. Umulis
MeSH headings : Animals; Embryo, Mammalian / cytology; Embryo, Mammalian / metabolism; Embryo, Mammalian / physiology; Embryonic Development / genetics; Germ Layers / cytology; Germ Layers / metabolism; Germ Layers / physiology; Mice; Models, Biological; Single-Cell Analysis; Transcriptome / genetics
TL;DR:
This study provides a multiscale framework that incorporates single-cell gene expression datasets to analyze gene regulations, cell-cell communications, and physical interactions among cells in complex geometries at single- cell resolution, with direct application to late-stage development of embryogenesis.
(via Semantic Scholar)
Source: ORCID
Added: August 22, 2021
2021 journal article
Fixed Point Strategies in Data Science
IEEE Transactions on Signal Processing, 69, 3878–3905.
author keywords: Data science; Tools; Signal processing algorithms; Inverse problems; Convex functions; Standards; Neural networks; Convex optimization; fixed point; game theory; image recovery; inverse problems; machine learning; monotone inclusion; neural networks; nonexpansive operator; signal processing
TL;DR:
Fixed point strategies are seen to constitute a natural environment to explain the behavior of advanced convex optimization methods as well as of recent nonlinear methods in data science which are formulated in terms of paradigms that go beyond minimization concepts and involve constructs such as Nash equilibria or monotone inclusions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 16, 2021
2021 article
Classical and variational Poisson cohomology
Bakalov, B., De Sole, A., Heluani, R., Kac, V. G., & Vignoli, V. (2021, August 9). JAPANESE JOURNAL OF MATHEMATICS.
author keywords: Poisson vertex algebra (PVA); classical operad; classical PVA cohomology; variational PVA cohomology; sesquilinear Hochschild and Harrison cohomology
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science)
Source: Web Of Science
Added: August 16, 2021
2021 journal article
EFFICIENT ALGORITHMS FOR EIGENSYSTEM REALIZATION USING RANDOMIZED SVD
SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS, 42(2), 1045–1072.
author keywords: eigensystem realization algorithm; system identification; singular value decomposition; randomized algorithms
TL;DR:
Computationally efficient algorithms for reducing the computational cost of the SVD step by using randomized subspace iteration and exploiting the block Hankel structure of the matrix are developed.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 16, 2021
2021 journal article
Efficient Approximation of Potential Energy Surfaces with Mixed-Basis Interpolation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 17(9), 5673–5683.
TL;DR:
This method is the only known interpolative method that appropriately conserves total energy in systems with both periodic and nonperiodic reaction coordinates and is applied to MD simulations of possible isomerization pathways of azomethane between cis and trans conformers.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science
Added: August 6, 2021
2021 journal article
Randomized approaches to accelerate MCMC algorithms for Bayesian inverse problems
JOURNAL OF COMPUTATIONAL PHYSICS, 440.
author keywords: Inverse problems; Randomized algorithms; Bayesian methods; Markov chain Monte Carlo
UN Sustainable Development Goal Categories
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 2, 2021
2021 journal article
A High Order Compact FD Framework for Elliptic BVPs Involving Singular Sources, Interfaces, and Irregular Domains
JOURNAL OF SCIENTIFIC COMPUTING, 88(3).
author keywords: Elliptic BVP; Interface problem; Irregular domain; High order compact Cartesian mesh method; IIM & augmented IIM; Discontinuous coefficients; Gradient; Helmholtz equation
TL;DR:
An augmented third order compact finite difference method is further developed for elliptic interface problems with piecewise constant but discontinuous coefficients and the third order augmented method is applied to Poisson/Helmholtz equations on irregular domains with few changes along examples of Neumann, Robin, and Dirichlet boundary conditions.
(via Semantic Scholar)
Sources: ORCID, Web Of Science
Added: July 29, 2021
2021 journal article
A multiscale model of vascular function in chronic thromboembolic pulmonary hypertension
AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY, 321(2), H318–H338.
author keywords: hemodynamics; mathematical modeling; pulmonary circulation; pulmonary hypertension; wave propagation
MeSH headings : Angioplasty, Balloon; Chronic Disease; Hemodynamics; Humans; Hypertension, Pulmonary / diagnostic imaging; Hypertension, Pulmonary / etiology; Hypertension, Pulmonary / physiopathology; Hypertension, Pulmonary / therapy; Models, Cardiovascular; Models, Theoretical; Pulmonary Artery / diagnostic imaging; Pulmonary Artery / physiopathology; Pulmonary Embolism / complications; Pulmonary Embolism / diagnostic imaging; Pulmonary Embolism / physiopathology; Pulmonary Embolism / therapy
TL;DR:
A multiscale, image-to-hemodynamics pipeline for BPA therapy planning for inoperable CTEPH patients is provided, providing an integrative, holistic tool for identifying optimal target lesions for treatment.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: July 28, 2021
2021 journal article
Global sensitivity analysis informed model reduction and selection applied to a Valsalva maneuver model
JOURNAL OF THEORETICAL BIOLOGY, 526.
MeSH headings : Bayes Theorem; Blood Pressure; Heart Rate; Valsalva Maneuver
TL;DR:
This study compares four GSA methods based on Sobol' indices (SIs) quantifying the parameter influence on the difference between the model output and the heart rate data and shows that it is necessary to incorporate both the aortic and carotid regions to model the VM.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: July 26, 2021
2021 journal article
Normal-Bundle Bootstrap
SIAM JOURNAL ON MATHEMATICS OF DATA SCIENCE, 3(2), 573–592.
author keywords: probabilistic learning; data manifold; dynamical systems; resampling; data augmentation
TL;DR:
Normal-bundle bootstrap (NBB) is presented, a method that generates new data which preserve the geometric structure of a given data set and applies the method to the inference of density ridge and related statistics, and data augmentation to reduce overfitting.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 26, 2021
2021 journal article
Hypercontractivity of the semigroup of the fractional Laplacianon the n-sphere
JOURNAL OF FUNCTIONAL ANALYSIS, 281(8).
author keywords: Hypercontractivity; Poisson semigroup; n-Sphere
Source: Web Of Science
Added: July 26, 2021
2021 article
Predicting Inter-individual Variability During Lipid Resuscitation of Bupivacaine Cardiotoxicity in Rats: A Virtual Population Modeling Study
McDaniel, M., Flores, K. B., & Akpa, B. S. (2021, July 19). DRUGS IN R&D.
MeSH headings : Anesthetics, Local / toxicity; Animals; Bupivacaine / toxicity; Cardiotoxicity; Lipids; Rats; Rats, Sprague-Dawley
TL;DR:
A mechanistic model predicted a plausible range of treatment outcomes that accurately predicts changes in LD50 when extrapolated to putatively toxic doses of bupivacaine, and causal analysis of the predicted survival outcomes indicated a critical synergy between scavenging and direct cardiotonic mechanisms of ILE action.
(via Semantic Scholar)
Source: Web Of Science
Added: July 26, 2021
2021 journal article
Metric Entropy for Functions of Bounded Total Generalized Variation
SIAM Journal on Mathematical Analysis, 53(1), 1168–1190.
author keywords: metric entropy; doubling dimension; total generalized variation
TL;DR:
A sharp estimate is established for a minimal number of binary digits needed to represent all bounded total generalized variation functions taking values in a general totally bounded metric space up to an accuracy of $\varepsilon>0$ with respect to the ${\bf L}^1$-distance.
(via Semantic Scholar)
Source: ORCID
Added: July 22, 2021
2021 journal article
Nonlinear quasi-static poroelasticity & nbsp;
Nonlinear quasi-static poroelasticity & nbsp; JOURNAL OF DIFFERENTIAL EQUATIONS, 296, 242–278.
author keywords: Poroelasticity; Nonlinear coupling; Implicit evolution; Fixed point methods
Sources: Web Of Science, ORCID
Added: July 19, 2021
2021 article
Rapid evolution of knockdown resistance haplotypes in response to pyrethroid selection in Aedes aegypti
Baltzegar, J., Vella, M., Gunning, C., Vasquez, G., Astete, H., Stell, F., … Gould, F. (2021, July 9). EVOLUTIONARY APPLICATIONS, Vol. 7.
author keywords: Aedes aegypti; dominance; insecticide resistance; kdr; knockdown resistance; selection
TL;DR:
This study describes the evolution of knockdown resistance (kdr) haplotypes in Aedes aegypti in response to pyrethroid insecticide use over the course of 18 years in Iquitos, Peru, providing evidence for the direct connection between programmatic citywidepyrethroid spraying and the increase in frequency of specific kdr haplotypes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(OpenAlex)
Sources: Web Of Science, ORCID
Added: July 19, 2021
2021 journal article
Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis
PLOS COMPUTATIONAL BIOLOGY, 17(6).
MeSH headings : Algorithms; Animals; Blood Vessels / anatomy & histology; Blood Vessels / growth & development; Blood Vessels / physiology; Chemotaxis; Computational Biology; Computer Simulation; Humans; Models, Cardiovascular; Neoplasms / blood supply; Neovascularization, Pathologic; Neovascularization, Physiologic; Spatio-Temporal Analysis
TL;DR:
This work simulates the Anderson-Chaplain model of angiogenesis at different parameter values, and proposes a topological data analysis (TDA) pipeline for systematic analysis of the model and shows that TDA of model simulation data stratifies parameter space into regions with similar vessel morphology.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(OpenAlex)
Source: Web Of Science
Added: July 19, 2021
2021 journal article
Channels, Billiards, and Perfect Matching 2-Divisibility
ELECTRONIC JOURNAL OF COMBINATORICS, 28(2).
TL;DR:
A new combinatorial proof of Lovász's result that the existence of a nontrivial channel is equivalent to $m_G$ being even is given and it is strengthened by showing that the number of channels gives a lower bound on the power of 2 dividing m_G when $G$ is planar.
(via Semantic Scholar)
Source: Web Of Science
Added: July 19, 2021
2021 journal article
Reconstruction of functions from prescribed proximal points
Journal of Approximation Theory, 268, 105606.
author keywords: Best approximation algorithm; Constrained interpolation; Firmly nonexpansive operator; Nonlinear signal recovery; Proximal point
TL;DR:
This work shows that in many instances these prescriptions can be represented using firmly nonexpansive operators, even when the original observation process is discontinuous, and captures a large body of classical and contemporary best approximation problems arising in areas such as harmonic analysis, statistics, interpolation theory, and signal processing.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities
(Web of Science)
Sources: Web Of Science, ORCID
Added: July 12, 2021
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