WHAT IS THIS SUMMARY ABOUT?:In this article, we summarize results from a clinical study called LOTIS-2, in which researchers looked at patients with a type of blood cancer called diffuse large B-cell lymphoma, or DLBCL for short. Patients received the drug loncastuximab tesirine, or Lonca for short, which targets a marker on the surface of tumor cells called CD19.Patient information from the LOTIS-2 study, other studies of Lonca, and information from scientific publications was used to develop a quantitative systems pharmacology (QSP) model, which can predict how Lonca works in the body. The goal was to use the QSP model to see if CD19 levels can predict tumor size changes after Lonca treatment and if Lonca can still work to treat DLBCL when CD19 levels are very low. The prior LOTIS-1 and LOTIS-2 trials demonstrated an acceptable safety profile for Lonca, and therefore the current study did not evaluate safety data. WHAT WERE THE RESULTS?:Researchers used immunohistochemistry, a common technique to evaluate CD19 expression. They found that there was no association between patients who responded to Lonca treatment and levels of CD19 on their tumor cells. Some patients with low or even undetectable levels of CD19 on their tumor cells had observable decreases in tumor size after Lonca treatment. WHAT DO THE RESULTS OF THE STUDY MEAN?:While Lonca uses the CD19 target to find and destroy cancer cells, Lonca does not require a large amount of CD19 to kill tumor cells. These results mean that Lonca may be an effective treatment for patients with DLBCL, even if CD19 expression in tumors is undetectable by immunohistochemistry.

CD19-targeting treatments have shown promise in relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL). Loncastuximab tesirine (loncastuximab tesirine-lpyl [Lonca]) is a CD19-targeting antibody-drug conjugate indicated for R/R DLBCL after at least two systemic treatments. CD19 expression was evaluated in patients receiving Lonca in the LOTIS-2 clinical trial with available tissue samples obtained after last systemic therapy/before Lonca treatment. Lonca cytotoxicity was evaluated in a panel of six lymphoma cell lines with various CD19 expression levels. Quantitative systems pharmacology (QSP) modelling was used to predict Lonca responses. Lonca responses were seen in patients across all CD19 expression levels, including patients with low/no detectable CD19 expression and H-scores at baseline. Similarly, Lonca induced cytotoxicity in cell lines with different levels of CD19 expression, including one with very low expression. QSP modelling predicted that CD19 expression by immunohistochemistry alone does not predict Lonca response, whereas inclusion of CD19 surface density improved response prediction. Virtual patients responded to Lonca with estimated CD19 as low as 1000 molecules/cell of CD19, normally below the immunohistochemistry detection level. We found Lonca is an effective treatment for R/R DLBCL regardless of CD19 expression by immunohistochemistry. These results provide the basis for future studies addressing CD19-targeted agent sequencing.

A comparative study (Sun et al., eLife, 2019) showed that the abundance of proteins at sites of endocytosis in fission and budding yeast is more similar in the two species than previously thought, yet membrane invaginations in fission yeast elongate two-fold faster and are nearly twice as long as in budding yeast. Here we use a three-dimensional model of a motile endocytic invagination (Nickaeen et al., MBoC, 2019) to investigate factors affecting elongation of the invaginations. We found that differences in turgor pressure in the two yeast species can largely explain the paradoxical differences observed experimentally in endocytic motility.

Pollen, a neighbor-less cell containing the male gametes, undergoes mechanical challenges during plant sexual reproduction, including desiccation and rehydration. It was previously shown that the pollen-specific mechanosensitive ion channel MscS-like (MSL)8 is essential for pollen survival during hydration and proposed that it functions as a tension-gated osmoregulator. Here, we test this hypothesis with a combination of mathematical modeling and laboratory experiments. Time-lapse imaging revealed that wild-type pollen grains swell, and then they stabilize in volume rapidly during hydration. msl8 mutant pollen grains, however, continue to expand and eventually burst. We found that a mathematical model, wherein MSL8 acts as a simple-tension-gated osmoregulator, does not replicate this behavior. A better fit was obtained from variations of the model, wherein MSL8 inactivates independent of its membrane tension gating threshold or MSL8 strengthens the cell wall without osmotic regulation. Experimental and computational testing of several perturbations, including hydration in an osmolyte-rich solution, hyper-desiccation of the grains, and MSL8-YFP overexpression, indicated that the cell wall strengthening model best simulated experimental responses. Finally, the expression of a nonconducting MSL8 variant did not complement the msl8 overexpansion phenotype. These data indicate that contrary to our hypothesis and to the current understanding of MS ion channel function in bacteria, MSL8 does not act as a simple membrane tension-gated osmoregulator. Instead, they support a model wherein ion flux through MSL8 is required to alter pollen cell wall properties. These results demonstrate the utility of pollen as a cellular scale model system and illustrate how mathematical models can correct intuitive hypotheses.

Introduction: CD19 is a clinically-validated target for the treatment of B-cell malignancies, and several CD19-targeted therapies have received approval, including chimeric antigen receptor T-cell (CAR-T) therapy, antibody-drug conjugates (ADCs), monoclonal antibodies, and bispecific agents. However, the optimal sequencing of these treatments has not yet been clarified. Loncastuximab tesirine (loncastuximab tesirine-lypl; Lonca) is an ADC comprising an anti-CD19 antibody conjugated to a pyrrolobenzodiazepine (PBD) dimer cytotoxin, indicated for relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL) after ≥2 systemic treatments. Prior CAR-T therapy does not preclude a response to Lonca, and responses were also observed in patients who received CAR-T therapy post-Lonca. The present analysis was performed to determine the contribution of CD19 expression to responses in patients treated with Lonca. Methods: CD19 expression determined by immunohistochemistry (IHC) was evaluated in a cohort of patients enrolled in the LOTIS-2 clinical trial (NCT03589469) with available tissue samples obtained after their last anti-cancer systemic therapy and prior to Lonca. IHC was performed using the LE-CD19 antibody (DAKO), and expression was analyzed using the BenchMark ULTRA platform (Ventana). CD19 expression was assessed by semiquantitative scoring of both the percentage of positive tumor cells and the H-Score (semiquantitative assessment of the percentage of CD19 positive cells and staining intensity). Quantitative Systems Pharmacology (QSP) modeling was used to predict response to Lonca and to test hypotheses regarding patient-specific covariates. Results: The cohort included patients with any prior systemic therapies (n = 59), including patients who received CAR-T as the last therapy prior to biopsy (n = 9). Responses to Lonca were seen in patients across all levels of CD19 expression, including patients with extremely low or no detectable CD19 expression at baseline and extremely low H-Scores. On the basis of the QSP modeling, patients are anticipated to achieve disease response to Lonca with CD19 tumor cell-surface densities as low as 1,000 molecules/cell (Figure 2). Conclusions: Response to Lonca was observed in R/R DLBCL patients with very low CD19 tumor expression as measured by IHC. QSP modeling predicts that CD19 expression level by IHC is not predictive of response to Lonca, whereas the addition of CD19 surface density improves the response prediction. Patients responded to Lonca with estimated tumor cell surface densities as low as 1,000 molecules/cell, normally below the level of IHC detection. Our findings indicate that Lonca is an effective treatment option for patients with R/R DLBCL following ≥ 2 lines of treatment, even in patients expected to have a low level of CD19 expression. These results serve as a basis for future studies addressing sequencing of CD19-targeted agents. Funding: ADC Therapeutics SA; medical writing: CiTRUS Health Group. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

We formulated a spatially resolved model to estimate forces exerted by a polymerizing actin meshwork on an invagination of the plasma membrane during endocytosis in yeast cells. The model, which approximates the actin meshwork as a visco-active gel exerting forces on a rigid spherocylinder representing the endocytic invagination, is tightly constrained by experimental data. Simulations of the model produce forces that can overcome resistance of turgor pressure in yeast cells. Strong forces emerge due to the high density of polymerized actin in the vicinity of the invagination and because of entanglement of the meshwork due to its dendritic structure and cross-linking. The model predicts forces orthogonal to the invagination that are consistent with formation of a flask shape, which would diminish the net force due to turgor pressure. Simulations of the model with either two rings of nucleation-promoting factors (NPFs) as in fission yeast or a single ring of NPFs as in budding yeast produce enough force to elongate the invagination against the turgor pressure.

We formulated a spatially resolved model to estimate forces exerted by a polymerizing actin meshwork on an invagination of the plasma membrane during endocytosis in yeast cells. The model is a continuous approximation tightly constrained by experimental data. Simulations of the model produce forces that can overcome resistance of turgor pressure in yeast cells. Strong forces emerge due to the high density of polymerized actin in the vicinity of the invagination and because of entanglement of the meshwork due to its dendritic structure and crosslinking. The model predicts forces orthogonal to the invagination that would result in a flask shape that diminishes the net force due to turgor pressure. Simulations of the model with either two rings of nucleation promoting factors as in fission yeast or a single ring of nucleation promoting factors as in budding yeast produce enough force to elongate the invagination against the turgor pressure.

Cytokinesis is the fundamental and ancient cellular process by which one cell physically divides into two. Cytokinesis in animal and fungal cells is achieved by contraction of an actomyosin cytoskeletal ring assembled in the cell cortex, typically at the cell equator. Cytokinesis is essential for the development of fertilized eggs into multicellular organisms and for homeostatic replenishment of cells. Correct execution of cytokinesis is also necessary for genome stability and the evasion of diseases including cancer. Cytokinesis has fascinated scientists for well over a century, but its speed and dynamics make experiments challenging to perform and interpret. The presence of redundant mechanisms is also a challenge to understand cytokinesis, leaving many fundamental questions unresolved. For example, how does a disordered cytoskeletal network transform into a coherent ring? What are the long-distance effects of localized contractility? Here, we provide a general introduction to 'modeling for biologists', and review how agent-based modeling and continuum mechanics modeling have helped to address these questions.

In the present contribution, we compare (quantitatively) different mixed least-squares finite element methods (LSFEMs) with respect to computational costs and accuracy. Various first-order systems are derived based on the residual forms of the equilibrium equation and the continuity condition. The first formulation under consideration is a div-grad first-order system resulting in a three-field formulation with total stresses, velocities, and pressure (S-V-P) as unknowns. Here, the variables are approximated in H(div) × H1 × L2 on triangles and in H1 × H1 × L2 on quadrilaterals. In addition to that a reduced stress-velocity (S-V) formulation is derived and investigated. S-V-P and S-V formulations are promising approaches when the stresses are of special interest, e.g., for non-Newtonian, multiphase or turbulent flows. The main focus of the work is drawn to performance and accuracy aspects on the one side for finite elements with different interpolation orders and on the other side on the usage of efficient solvers, for instance of Krylov-space or multigrid type.

We present a three-dimensional computational study of the transient heat transfer and turbulent fluid flow inside an arc-welding electrode continuous furnace. The model is implemented in FLUENT, a finite volume commercial code. Large difference in the length scales of the electrodes and the furnace, movement of the electrodes, and existence of various modes of heat transfer are the major factors influencing the accuracy and efficiency of the simulation. Two modeling strategies are used to overcome these difficulties. First, the electrode geometry and material composition are simplified using a thermally equivalent model. Second, the electrode movement inside the furnace is avoided by implementing dine dependent boundary conditions applied to a fixed domain. A fairly close agreement is obtained in comparing the load's temperature history against the experimental data with an absolute relative difference below 2.7%. The space between the electrode trays in the furnace is very limited. The analysis shows that the input air does not circulate effectively between the trays. This lowers the thermal efficiency of the furnace and leads to uneven treatment of the electrodes. The present study provides guidelines to improve future furnace designs. (C) 2017 Elsevier Ltd. All rights reserved.

To understand shapes and movements of cells undergoing lamellipodial motility, we systematically explore minimal free-boundary models of actin-myosin contractility consisting of the force-balance and myosin transport equations. The models account for isotropic contraction proportional to myosin density, viscous stresses in the actin network, and constant-strength viscous-like adhesion. The contraction generates a spatially graded centripetal actin flow, which in turn reinforces the contraction via myosin redistribution and causes retraction of the lamellipodial boundary. Actin protrusion at the boundary counters the retraction, and the balance of the protrusion and retraction shapes the lamellipodium. The model analysis shows that initiation of motility critically depends on three dimensionless parameter combinations, which represent myosin-dependent contractility, a characteristic viscosity-adhesion length, and a rate of actin protrusion. When the contractility is sufficiently strong, cells break symmetry and move steadily along either straight or circular trajectories, and the motile behavior is sensitive to conditions at the cell boundary. Scanning of a model parameter space shows that the contractile mechanism of motility supports robust cell turning in conditions where short viscosity-adhesion lengths and fast protrusion cause an accumulation of myosin in a small region at the cell rear, destabilizing the axial symmetry of a moving cell.

Modeling of migrating cells often requires sophisticated numerical tools necessary for solving highly nonlinear partial and ordinary differential equations in domains with moving boundaries. We have recently developed a novel conservative method [1] for simulating reactions and transport in moving domains, which combines an Eulerian approach with tracking an explicit boundary. The latter is implemented by employing FronTier, a robust front-tracking technique [2]. Local mass conservation is ensured by finite-volume spatial discretization and natural-neighbor interpolation. Tests with exact kinematics indicated precise mass conservation and an order of convergence in space between one and two. The 'moving boundary' algorithm is currently being implemented in Virtual Cell (VCell), a general-purpose computational framework for simulating cellular phenomena in realistic geometries [3]. The algorithm was extended by coupling cell kinematics and intracellular dynamics and was validated using a set of benchmark problems. The COMSOL Multiphysics® software was extensively used to obtain alternative numerical solutions that served as reference solution where no exact analytic/closed-form solution was available. The first test case was diffusion inside and expanding circle with the expansion velocity as a function of local concentration. An equivalent advection-diffusion problem was obtained by mapping onto a fixed domain, which was then solved with high precision using the Transport of Diluted Species interface of the COMSOL® software. Quantitative agreement was obtained in comparing the results of the two methods, see Figure 1(a-c). Furthermore, using the simulation result as a reference solution, we have shown that accuracy of our original algorithm is preserved if extrapolation near the boundary and the front-tracking routines are at least second-order accurate, see Figure 1(d). In the second test case, we used a translating and (slightly) deforming cell example from the minimal models of actin-based motility. Briefly, the models included a viscoelastic equation for actin velocity and an advection-diffusion equation for myosin. Effect of cellsubstrate adhesion on cell migration was also considered. We developed an equivalent numerical solution using the coefficient form PDE framework in the COMSOL Multiphysics® software. The moving domain problem was implemented in the moving mesh framework of the COMSOL® software that is based on Arbitrary Lagrangian-Eulerian (ALE) finite element methods. Several snapshots of the solution are shown in the top row of Figure 2. Great agreement was obtained in comparisons against the simulation results, see bottom row of Figure 2, with relative solution and interface position errors below 0.3%. Given the fundamental differences between the two numerical methods, and the various spatial and temporal discretization schemes used in each one, these results validate both solutions.

Electroporation is of interest for many drug-delivery and gene-therapy applications. Prior studies have shown that a two-pulse-electroporation protocol consisting of a short-duration, high-voltage first pulse followed by a longer, low-voltage second pulse can increase delivery efficiency and preserve viability. In this work the effects of the field strength of the first and second pulses and the inter-pulse delay time on the delivery of two different-sized Fluorescein–Dextran (FD) conjugates are investigated. A series of two-pulse-electroporation experiments were performed on 3T3-mouse fibroblast cells, with an alternating-current first pulse to permeabilize the cell, followed by a direct-current second pulse. The protocols were rationally designed to best separate the mechanisms of permeabilization and electrophoretic transport. The results showed that the delivery of FD varied strongly with the strength of the first pulse and the size of the target molecule. The delivered FD concentration also decreased linearly with the logarithm of the inter-pulse delay. The data indicate that membrane resealing after electropermeabilization occurs rapidly, but that a non-negligible fraction of the pores can be reopened by the second pulse for delay times on the order of hundreds of seconds. The role of the second pulse is hypothesized to be more than just electrophoresis, with a minimum threshold field strength required to reopen nano-sized pores or defects remaining from the first pulse. These results suggest that membrane electroporation, sealing, and re-poration is a complex process that has both short-term and long-term components, which may in part explain the wide variation in membrane-resealing times reported in the literature.

We solve the V-V-P, vorticity-velocity-pressure, formulation of the stationary incompressible Navier-Stokes equations based on the least-squares finite element method. For the discrete systems, we use a conjugate gradient (CG) solver accelerated with a geometric multigrid preconditioner for the complete system. In addition, we employ a Krylov space smoother inside of the multigrid which allows a parameter-free smoothing. Combining this linear solver with the Newton linearization, we construct a very robust and efficient solver. We use biquadratic finite elements to enhance the mass conservation of the least-squares method for the inflow-outflow problems and to obtain highly accurate results. We demonstrate the advantages of using the higher order finite elements and the grid independent solver behavior through the solution of three stationary laminar flow problems of benchmarking character. The comparisons show excellent agreement between our results and those of the Galerkin mixed finite element method as well as available reference solutions.

In this contribution we present the least‐squares finite element method (LSFEM) for the incompressible Navier‐Stokes equations. In detail, we consider a non‐Newtonian fluid flow, which is described by a power‐law model, see [1]. The second‐order problem is reformulated by introducing a first‐order div‐grad system consisting of the equilibrium condition, the incompressibility condition and the constitutive equation, which are written in residual forms, see [2]. Here, higher‐order finite elements which are an important aspect regarding accuracy for the present formulation are investigated. (© 2014 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)

AbstractIn the present contribution we propose an improved mixed least‐squares finite element method (LSFEM) and compare it with standard LSFEMs with respect to performance aspects. In detail, we consider an approach for Newtonian fluid flow, which is described by the incompressible Navier‐Stokes equations. The basis for the associated symmetric minimization problem is a reduced stress‐velocity (s‐v) two‐field approach, see e.g. CAI ET AL. [1] and SCHWARZ & SCHRÖDER [2]. The main idea for the proposed formulation is to add an additional equation, which yields an overconstrained first‐order system. This approach does not introduce additional unknowns, so the advantage of two variables (stresses and velocities) remains. Finally, we present a numerical example in order to show the capability of the proposed formulation. (© 2013 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)

AbstractThe focus of this contribution is the examination of the influence of different interpolation orders (especially for the pressure field) by solving the stationary incompressible Navier‐Stokes equations with least‐squares finite elements. We consider two different div‐grad first‐order systems which result in a three‐field formulation with stresses, velocitites and pressure, see e.g. SCHWARZ & SCHRÖDER [1] and BOCHEV & GUNZBURGER [2]. Additionally, a numerical example is presented to show the performance of the considered formulations. (© 2013 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)

The characteristic-based split (CBS) method has been widely used in the finite element community to facilitate the numerical solution of Navier-Stokes (NS) equations. However, this computational algorithm has rarely been employed in the finite volume context and the stabilization of the numerical solution procedure has traditionally been addressed differently in volume-based numerical schemes. In this article, the CBS-based finite volume algorithm is employed to formulate and solve a number of laminar incompressible flow and convective heat transfer problems. Both explicit and implicit versions of the algorithm are first explained and validated in the context of the solution of a lid-driven cavity problem and a backward facing step (BFS) flow problem. The modified algorithm, capable of modelling the coupling between the momentum and energy balance equations, is then introduced and used to solve a buoyancy-driven cavity flow problem. Computational results show that the CBS finite volume algorithm can be reliably used in the solution of laminar incompressible heat and fluid flow problems.