Evaluating Neural Radiance Fields for 3D Plant Geometry Reconstruction in Field Conditions.

We evaluate different Neural Radiance Field (NeRF) techniques for the 3D reconstruction of plants in varied environments, from indoor settings to outdoor fields. Traditional methods usually fail to capture the complex geometric details of plants, which is crucial for phenotyping and breeding studies. We evaluate the reconstruction fidelity of NeRFs in 3 scenarios with increasing complexity and compare the results with the point cloud obtained using light detection and ranging as ground truth.

Successful Cardiac Resynchronization Therapy Reduces Negative Septal Work in Patient-Specific Models of Dyssynchronous Heart Failure.

In patients with dyssynchronous heart failure (DHF), cardiac conduction abnormalities cause the regional distribution of myocardial work to be non-homogeneous. Cardiac resynchronization therapy (CRT) using an implantable, programmed biventricular pacemaker/defibrillator, can improve the synchrony of contraction between the right and left ventricles in DHF, resulting in reduced morbidity and mortality and increased quality of life. Since regional work depends on wall stress, which cannot be measured in patients, we used computational methods to investigate regional work distributions and their changes after CRT.

Cyber-agricultural systems for crop breeding and sustainable production.

The cyber-agricultural system (CAS) represents an overarching framework of agriculture that leverages recent advances in ubiquitous sensing, artificial intelligence, smart actuators, and scalable cyberinfrastructure (CI) in both breeding and production agriculture. We discuss the recent progress and perspective of the three fundamental components of CAS - sensing, modeling, and actuation - and the emerging concept of agricultural digital twins (DTs). We also discuss how scalable CI is becoming a key enabler of smart agriculture.

A computational framework for transmission risk assessment of aerosolized particles in classrooms.

Unlabelled: Infectious airborne diseases like the recent COVID-19 pandemic render confined spaces high-risk areas. However, in-person activities like teaching in classroom settings and government services are often expected to continue or restart quickly. It becomes important to evaluate the risk of airborne disease transmission while accounting for the physical presence of humans, furniture, and electronic equipment, as well as ventilation.

Optimization framework for patient-specific modeling under uncertainty.

Estimating a patient-specific computational model's parameters relies on data that is often unreliable and ill-suited for a deterministic approach. We develop an optimization-based uncertainty quantification framework for probabilistic model tuning that discovers model inputs distributions that generate target output distributions. Probabilistic sampling is performed using a surrogate model for computational efficiency, and a general distribution parameterization is used to describe each input.

Deep Learning for Live Cell Shape Detection and Automated AFM Navigation.

Atomic force microscopy (AFM) provides a platform for high-resolution topographical imaging and the mechanical characterization of a wide range of samples, including live cells, proteins, and other biomolecules. AFM is also instrumental for measuring interaction forces and binding kinetics for protein-protein or receptor-ligand interactions on live cells at a single-molecule level. However, performing force measurements and high-resolution imaging with AFM and data analytics are time-consuming and require special skill sets and continuous human supervision.

GPU-Accelerated Collision Analysis of Vehicles in a Point Cloud Environment.

We present a GPU-accelerated collision detection method for the navigation of vehicles in enclosed spaces represented using large point clouds. Our approach takes a CAD model of a vehicle, converts it to a volumetric representation or voxels, and computes the collision of the voxels with a point cloud representing the environment to identify a suitable path for navigation. We perform adaptive and efficient collision of voxels with the point cloud without the need for mesh generation.

Polarized X-ray scattering measures molecular orientation in polymer-grafted nanoparticles.

Polymer chains are attached to nanoparticle surfaces for many purposes, including altering solubility, influencing aggregation, dispersion, and even tailoring immune responses in drug delivery. The most unique structural motif of polymer-grafted nanoparticles (PGNs) is the high-density region in the corona where polymer chains are stretched under significant confinement, but orientation of these chains has never been measured because conventional nanoscale-resolved measurements lack sensitivity to polymer orientation in amorphous regions. Here, we directly measure local chain orientation in polystyrene grafted gold nanoparticles using polarized resonant soft X-ray scattering (P-RSoXS).

Computational investigation of left ventricular hemodynamics following bioprosthetic aortic and mitral valve replacement.

The left ventricle of the heart is a fundamental structure in the human cardiac system that pumps oxygenated blood into the systemic circulation. Several valvular conditions can cause the aortic and mitral valves associated with the left ventricle to become severely diseased and require replacement. However, the clinical outcomes of such operations, specifically the postoperative ventricular hemodynamics of replacing both valves, are not well understood.

A Deep Learning Framework for Design and Analysis of Surgical Bioprosthetic Heart Valves.

Bioprosthetic heart valves (BHVs) are commonly used as heart valve replacements but they are prone to fatigue failure; estimating their remaining life directly from medical images is difficult. Analyzing the valve performance can provide better guidance for personalized valve design. However, such analyses are often computationally intensive.

Optimization Framework for Patient-Specific Cardiac Modeling.

Purpose: Patient-specific models of the heart can be used to improve the diagnosis of cardiac diseases, but practical application of these models can be impeded by the computational costs and numerical uncertainties of fitting mechanistic models to clinical measurements from individual patients. Reliable and efficient tuning of these models within clinically appropriate error bounds is a requirement for practical deployment in the time-constrained environment of the clinic.

Methods: We developed an optimization framework to tune parameters of patient-specific mechanistic models using routinely-acquired non-invasive patient data more efficiently than manual methods.

A framework for biomechanics simulations using four-chamber cardiac models.

Computational cardiac models have been extensively used to study different cardiac biomechanics; specifically, finite-element analysis has been one of the tools used to study the internal stresses and strains in the cardiac wall during the cardiac cycle. Cubic-Hermite finite element meshes have been used for simulating cardiac biomechanics due to their convergence characteristics and their ability to capture smooth geometries compactly-fewer elements are needed to build the cardiac geometry-compared to linear tetrahedral meshes. Such meshes have previously been used only with simple ventricular geometries with non-physiological boundary conditions due to challenges associated with creating cubic-Hermite meshes of the complex heart geometry.

Rapid B-rep model preprocessing for immersogeometric analysis using analytic surfaces.

Computational fluid dynamics (CFD) simulations of flow over complex objects have been performed traditionally using fluid-domain meshes that conform to the shape of the object. However, creating shape conforming meshes for complicated geometries like automobiles require extensive geometry preprocessing. This process is usually tedious and requires modifying the geometry, including specialized operations such as defeaturing and filling of small gaps.

Comparative Study of Community Acquired and Nosocomial Spontaneous Bacterial Peritonitis and its Variants in 150 Patients.

Background: Nosocomial acquisition of spontaneous bacterial peritonitis (SBP) is debated as having a different microbial etiology and prognosis. Identification of clinical, laboratory predictors of mortality and appropriate empirical antimicrobial selection is necessary to prevent early mortality and morbidity. We aimed to find the clinical and bacteriological profile in nosocomial and community acquired SBP and its variants, and the predictors of mortality.

Model of Human Fetal Growth in Hypoplastic Left Heart Syndrome: Reduced Ventricular Growth Due to Decreased Ventricular Filling and Altered Shape.

Introduction: Hypoplastic left heart syndrome (HLHS) is a congenital condition with an underdeveloped left ventricle (LV) that provides inadequate systemic blood flow postnatally. The development of HLHS is postulated to be due to altered biomechanical stimuli during gestation. Predicting LV size at birth using mid-gestation fetal echocardiography is a clinical challenge critical to prognostic counseling.

Biomechanics Simulations Using Cubic Hermite Meshes with Extraordinary Nodes for Isogeometric Cardiac Modeling.

Cubic Hermite hexahedral finite element meshes have some well-known advantages over linear tetrahedral finite element meshes in biomechanical and anatomic modeling using isogeometric analysis. These include faster convergence rates as well as the ability to easily model rule-based anatomic features such as cardiac fiber directions. However, it is not possible to create closed complex objects with only regular nodes; these objects require the presence of extraordinary nodes (nodes with 3 or >= 5 adjacent elements in 2D) in the mesh.

A multiscale model for the study of cardiac biomechanics in single-ventricle surgeries: a clinical case.

Complex congenital heart disease characterized by the underdevelopment of one ventricular chamber (single ventricle (SV) circulation) is normally treated with a three-stage surgical repair. This study aims at developing a multiscale computational framework able to couple a patient-specific three-dimensional finite-element model of the SV to a patient-specific lumped parameter (LP) model of the whole circulation, in a closed-loop fashion. A sequential approach was carried out: (i) cardiocirculatory parameters were estimated by using a fully LP model; (ii) ventricular material parameters and unloaded geometry were identified by means of the stand-alone, three-dimensional model of the SV; and (iii) the three-dimensional model of SV was coupled to the LP model of the circulation, thus closing the loop and creating a multiscale model.

Left Ventricular Diastolic and Systolic Material Property Estimation from Image Data: LV Mechanics Challenge.

Cardiovascular simulations using patient-specific geometries can help researchers understand the mechanical behavior of the heart under different loading or disease conditions. However, to replicate the regional mechanics of the heart accurately, both the nonlinear passive and active material properties must be estimated reliably. In this paper, automated methods were used to determine passive material properties while simultaneously computing the unloaded reference geometry of the ventricles for stress analysis.

A review and current perspective on Wilson disease.

Wilson disease is a rare, inherited autosomal recessive disease of copper metabolism and may be more common where consanguinity is prevalent. Much has been known about the disease after it was first described by Kinnier Wilson as 'progressive lenticular degeneration in 1912. Over 500 mutations of the ATP7B gene has been identified with no clear genotype to phenotype correlation.

Patient-Specific Models of Cardiac Biomechanics.

Patient-specific models of cardiac function have the potential to improve diagnosis and management of heart disease by integrating medical images with heterogeneous clinical measurements subject to constraints imposed by physical first principles and prior experimental knowledge. We describe new methods for creating three-dimensional patient-specific models of ventricular biomechanics in the failing heart. Three-dimensional bi-ventricular geometry is segmented from cardiac CT images at end-diastole from patients with heart failure.

Myofiber prestretch magnitude determines regional systolic function during ectopic activation in the tachycardia-induced failing canine heart.

Electrical dyssynchrony leads to prestretch in late-activated regions and alters the sequence of mechanical contraction, although prestretch and its mechanisms are not well defined in the failing heart. We hypothesized that in heart failure, fiber prestretch magnitude increases with the amount of early-activated tissue and results in increased end-systolic strains, possibly due to length-dependent muscle properties. In five failing dog hearts with scars, three-dimensional strains were measured at the anterolateral left ventricle (LV).

A three-dimensional finite element model of human atrial anatomy: new methods for cubic Hermite meshes with extraordinary vertices.

High-order cubic Hermite finite elements have been valuable in modeling cardiac geometry, fiber orientations, biomechanics, and electrophysiology, but their use in solving three-dimensional problems has been limited to ventricular models with simple topologies. Here, we utilized a subdivision surface scheme and derived a generalization of the "local-to-global" derivative mapping scheme of cubic Hermite finite elements to construct bicubic and tricubic Hermite models of the human atria with extraordinary vertices from computed tomography images of a patient with atrial fibrillation. To an accuracy of 0.

Novel role for vinculin in ventricular myocyte mechanics and dysfunction.

Vinculin (Vcl) plays a key structural role in ventricular myocytes that, when disrupted, can lead to contractile dysfunction and dilated cardiomyopathy. To investigate the role of Vcl in myocyte and myocardial function, cardiomyocyte-specific Vcl knockout mice (cVclKO) and littermate control wild-type mice were studied with transmission electron microscopy (TEM) and in vivo magnetic resonance imaging (MRI) tagging before the onset of global ventricular dysfunction. MRI revealed significantly decreased systolic strains transverse to the myofiber axis in vivo, but no changes along the muscle fibers or in fiber tension in papillary muscles from heterozygous global Vcl null mice.