Production Cross Research Articles

Dynamics over cocycle double cross product

Dynamics over cocycle double cross product

Perfusion Process Intensification for Lentivirus Production Using a Novel Scale-Down Model.

Process intensification has become an important strategy to lower production costs and increase manufacturing capacities for biopharmaceutical products. In particular for the production of viral vectors like lentiviruses (LVs), the transition from (fed-)batch to perfusion processes is a key strategy to meet the increasing demands for cell and gene therapy applications. However, perfusion processes are associated with higher medium consumption. Therefore, it is necessary to develop appropriate small-scale models to reduce development costs. In this work, we present the use of the acoustic wave separation technology in combination with the Ambr 250 high throughput bioreactor system for intensified perfusion process development using stable LV producer cells. The intensified perfusion process developed in the Ambr 250 model, performed at a harvest rate of 3 vessel volumes per day (VVD) and high cell densities, resulted in a 1.4-fold higher cell-specific functional virus yield and 2.8-fold higher volumetric virus yield compared to the control process at a harvest rate of 1 VVD. The findings were verified at bench scale after optimizing the bioreactor set-up, resulting in a 1.4-fold higher cell-specific functional virus yield and 3.1-fold higher volumetric virus yield.

Engineered Packaging Cell Line for the Enhanced Production of Baboon-Enveloped Retroviral Vectors

Engineered Packaging Cell Line for the Enhanced Production of Baboon-Enveloped Retroviral Vectors

Algebraic and geometric definitions of the cross product: the link

Given two vectors $\overrightarrow u = {({u_1},\,\,{u_2},\,{u_3})^t}$ and $\overrightarrow y = {({v_1},\,{v_2},\,{v_3})^t}$ in ${{\mathcal{R}}^3}$ , the cross product $\overrightarrow u \times \overrightarrow v $ is defined as follows (see [1] or [2]): $$Algebraic{\rm{ }}definition{\rm{:}}\,\,\overrightarrow u \times \overrightarrow v \, = \,\left[ {\matrix{ {{u_2}{v_3}} \hfill & - \hfill & {{u_3}{v_2}} \hfill \cr {{u_3}{v_1}} \hfill & - \hfill & {{u_1}{v_3}} \hfill \cr {{u_1}{v_2}} \hfill & - \hfill & {{u_2}{v_1}} \hfill \cr } } \right].$$

Characterization of the function of Adenovirus L4 gene products and their impact on AAV vector production

Efficient manufacturing of recombinant adenovirus-associated viral vectors is critical to the successful development of genomic medicines. We attempted to optimize AAV vector production in a producer cell line platform. In this system, helper functions required for AAV replication and production are provided via infection with a replication-competent wild-type Adenovirus. To evaluate strategies for reduction of replication and packaging of adenovirus as well as to understand the interplay of recombinant AAV and the helper virus during AAV vector production, wild-type adenovirus was compared to a mutant (Ad5ts149) containing a temperature-sensitive mutation in the DNA polymerase gene. Infection of a producer cell line with Ad5ts149 at the restrictive temperature reduced recombinant AAV titer and altered the pattern of AAV protein expression. Further investigation revealed that the adenoviral late L4-22K/33K gene products regulated both AAV rep/cap gene transcription and splicing of the rep/cap transcripts. Furthermore, the L4-33K gene products were found to impact AAV production in both the producer cell line and transient transfection platforms. Optimization of Adenovirus L4-22K/33K expression to facilitate efficient expression and splicing of AAV rep/cap transcripts therefore represents a unique opportunity to optimize AAV vector production.

Developing Excel VBA Functions for the Mathematical Modeling of Three-Dimensional Vectors

The current computer support for operations involving three-dimensional vectors is insufficient, even in widely used programs like Excel. These programs lack customised features specifically designed for vector operations. However, this limitation can be overcome by using the options provided by Visual Basic for Applications. By creating user functions, we can effectively calculate various results related to the mathematical application of vectors. These functions include determining the magnitude and absolute value of a vector, calculating the angle between two vectors or the cosine of that angle, finding the scalar product and vector product of two vectors, and evaluating the mixed product of three vectors. By incorporating these custom functions into the spreadsheet program, users can easily perform mathematical calculations pertaining to three-dimensional vectors.

The Design of Fast Type-V Discrete Cosine Transform Algorithms for Short-Length Input Sequences

Fast algorithms for type-five discrete cosine transform (DCT-V) for sequences of input data of short length in the range of two to eight are elaborated in the paper. A matrix–vector product representation of the DCT-V is the starting point for designing the algorithms. In each specific case, the DCT-V matrices have remarkable structural properties that follow from the localization of identical entries within the matrices. Each matrix of the DCT-V has only a few distinct entries that are repeated at different positions in its structure. Using simple transformations such as permutations of the rows and/or columns of this matrix or its favorable decomposition into two or more matrix components, it is possible to obtain efficient matrix structures that lead to useful factorization schemes. Based on the suitable factorization schemes we obtained, we developed fast algorithms that reduce the number of arithmetic operations when calculating the DCT-V. The correctness of the obtained algorithmic solutions was justified theoretically using a strict mathematical background of each of them. The developed algorithms were then further tested using MATLAB R2023b software to finally confirm their correctness. Finally, an evaluation of the computational complexity for each obtained solution is presented. The evaluation results were compared with the computational complexity of the direct calculation of matrix–vector products. The resulting factorizations of the matrices of the DCT-V reduce the average number of multiplications by 57% but increase the number of additions by 29%.

Two-gluon one-photon vertex in a magnetic field and its explicit one-loop approximation in the intermediate field strength regime

We find the general structure for the two-gluon one-photon vertex in the presence of a constant magnetic field. We show that, when accounting for the symmetries satisfied by the strong and electromagnetic interactions under parity, charge conjugation and gluon interchange, and for gluons and photons on mass-shell, there exist only three possible tensor structures that span the vertex. These correspond to external products of the polarization vectors for each of the particles in the vertex. We also explicitly compute the one-loop approximation to this vertex in the intermediate field strength regime, which is the most appropriate one to describe possible effects of the presence of a magnetic field to enhance photon emission during preequilibrium in peripheral relativistic heavy-ion collisions. We show that the most favored direction for the photon to propagate is in the plane transverse to the field, which is consistent with a positive contribution to ν2 and may help to understand the larger than expected elliptic flow coefficient measured in this kind of reaction. Published by the American Physical Society 2024

Casimirs of the Virasoro algebra

We explicitly solve a recurrence relation due to Feigin and Fuchs to obtain the Casimirs of the Virasoro algebra in terms of the inverse of the Shapovalov form. Combined with our recent result for the inverse Shapovalov form, this allows us to write the Casimir operators as linear combinations of products of singular vectors.

AAV2 can replicate its DNA by a rolling hairpin or rolling circle mechanism, depending on the helper virus.

AAV is a small helper virus-dependent, non-pathogenic parvovirus. The AAV genome replication mechanism was extensively studied in the presence of AdV as the helper virus and described to proceed using RHR. Surprisingly, HSV-1 co-infection facilitates RCR of the AAV2 DNA. We directly compared AdV5 and HSV-1 supported AAV2 DNA replication and showed that AAV2 can adapt its replication mechanism to the helper virus. A detailed understanding of the AAV replication mechanism expands our knowledge of virus biology and can contribute to increase gene therapy vector production.

Introducing a G-Makassar variant in HSCs by in vivo base editing treats sickle cell disease in mice

Precise repair of the pathogenic mutation in hematopoietic stem cells (HSCs) represents an ideal cure for patients with sickle cell disease (SCD). Here, we demonstrated correction of the SCD phenotype by converting the sickle mutation codon (GTG) into a benign G-Makassar variant (GCG) using in vivo base editing in HSCs. We demonstrated successful production of helper-dependent adenoviral vectors expressing an all-in-one base editor mapping to the sickle mutation site. In HSC-enriched cells from SCD patients, transduction with the base editing vector in vitro resulted in 35% GTG > GCG conversion and phenotypic improvements of derived red blood cells. After ex vivo transduction of HSCs from a SCD mouse model and subsequent transplantation, we achieved an average of 88% editing at the target site in transplanted mice. Importantly, in vivo HSC base editing followed by selection generated 24.5% Makassar variant in long-term repopulating HSCs of SCD mice. The treated animals demonstrated correction of disease hallmarks without showing noticeable side effects. Off-target analyses at top-scored genomic sites revealed no off-target editing. This in vivo approach requires only one non-integrating vector, only intravenous/subcutaneous injections, and minimal in vivo selection. This technically simple approach has the potential for scalable applications in resource-limiting regions where SCD is prevalent.

Reduced form of statistical equilibrium equations and radiative transfer equations

Abstract An extension of the vector algebra for irreducible spherical tensor operators (ITOs) is proposed, which involves coupling two ITOs into a third one (V (kv)= T (kt)× U (ku)*), with the additional condition that one of the operators is a complex conjugate and therefore is not an ITO. The correctness condition is considered for this extension. The new coupling rule treats the density matrices ρ(Kl) and all tensors related to light polarization (J (Kr) or Τ (K)) equally.
This approach has been applied to rewrite the fundamental statistical equilibrium equations and radiation transfer equations relevant to astrophysical polarimetry. The revised equations are more concise and eliminate the need for the nj symbols. Instead, they utilize vector and scalar products of ITOs. All rate coefficients in the equations consist of two independent factors, the reduced matrix element from dipole moments and the product (vector or scalar) of the tensors ρ(Kl) and J (Kr) (or Τ (K)).

Fed-batch strategies for intensified rVSV vector production in high cell density cultures of suspension HEK293 cells.

Vesicular stomatitis virus (VSV) has been increasingly demonstrated as a promising viral vector platform. As the interest over this modality for vaccine and gene therapy applications increases, the need for intensified processes to produce these vectors emerge. In this study, we develop fed-batch-based operations to intensify the production of a recombinant VSV-based vaccine candidate (rVSV-SARS-CoV-2) in suspension cultures of HEK293 cells. A feeding strategy, in which a commercial concentrated medium was added to cultures based on cell growth through a fixed cell specific feeding rate (CSFR), was applied for the development of two different processes using Ambr250 modular bioreactors. Cultures operated in hybrid fed-batch/perfusion (FB/P) or fed-batch (FB) were able to sustain infections performed at 8.0 × 106 cells/mL, respectively resulting in 3.9 and 5.0-fold increase in total yield (YT) and 1.7 and 5.6-fold increase in volumetric productivity (VP) when compared with a batch reference. A maximum viral titer of 4.5 × 1010 TCID50/mL was reached, which is comparable or higher than other processes for VSV production in different cell lines. Overall, our study reports efficient fed-batch options to intensify the production of a rVSV-based vaccine candidate in suspension HEK293 cells.

MATHEMATICAL APPROACH OF THE BACKPROPAGATION METHOD FOR CONSTRUCTING ARTIFICIAL NEURAL NETWORKS

Backpropagation isthe core part of a neural network. This method is used to efficiently train a network using a chain rule that allows differentiation of complex functions. In other words, after each pass through the network, the backpropagation method performs a backward pass to adjust the model parameters, such as weights and biases. This article highlights the importance of using the backpropagation method from the point of view of mathematical formulas for neural networks. The importance of using the backpropaga-tion learning algorithm to calculate the gradient (gradient descent) and the need to use the activation function to minimize the loss function is mathematically described and calculated by formulas, and also proven by calculating the matrix products of vectors for each layer of parameters - weights and biases and applying complex differential equations.

Auto-transduction in lentiviral vector bioprocessing: A quantitative assessment and a novel inhibition strategy.

Lentiviral vectors are highly efficient gene delivery vehicles used extensively in the rapidly growing field of cell and gene therapy. Demand for efficient, large-scale, lentiviral vector bioprocessing is growing as more therapies reach late-stage clinical trials and are commercialized. However, despite substantial progress, several process inefficiencies remain. The unintended auto-transduction of viral vector-producing cells by newly synthesized lentiviral vector particles during manufacturing processes constitutes one such inefficiency which remains largely unaddressed. In this study, we determined that over 60% of functional lentiviral vector particles produced during an upstream production process were lost to auto-transduction, highlighting a major process inefficiency likely widespread within the industry. Auto-transduction of cells by particles pseudotyped with the widely used vesicular stomatitis virus G protein was inhibited via the adoption of a reduced extracellular pH during vector production, impairing the ability of the vector to interact with its target receptor. Employing a posttransfection pH shift to pH 6.7-6.8 resulted in a sevenfold reduction in vector genome integration events, arising from lentiviral vector-mediated transduction, within viral vector-producing cell populations and ultimately resulted in improved lentiviral vector production kinetics. The proposed strategy is scalable and cost-effective, providing an industrially relevant approach to improve lentiviral vector production efficiencies.

Calculation of the Point of Application (Centre of Pressure) of Force and Torque Imparted on a Spherical Object from Gyroscope Sensor Data, Using Sports Balls as Practical Examples.

This study investigates the determination of the centre of pressure (COP) on spherical sports objects such as cricket balls and footballs using gyroscope data from Inertial Measurement Units (IMUs). Conventional pressure sensors are not suitable for capturing the tangential forces responsible for torque generation. This research presents a novel method to calculate the COP solely from gyroscope data and avoids the complexity of isolating user-induced accelerations from IMU data. The COP is determined from the cross-product of consecutive torque vectors intersecting the surface of the sphere. Effective noise management techniques, including filtering and data interpolation, were employed to improve COP visualisation. Experiments were conducted using a smart cricket ball and a smart football. Validation tests using spin rates between 7.5 and 12 rps and torques ranging from 0.08 to 0.12 Nm confirmed consistent COP clustering around the expected positions. Further analysis extended to various spin bowling deliveries recorded using a smart cricket ball, and a curved football kick recorded using a smart football demonstrated the wide applicability of the method. The COPs of various spin bowling deliveries showed adjacent positions on the surface of the ball, traversing through backspin, sidespin and topspin, excluding the flipper and doosra deliveries. The calculation of the COP on the surface of the soccer ball could only be achieved by increasing the data sampling frequency sevenfold using curve fitting. Knowledge and use of the COP position offers significant advances in understanding and analysing ball dynamics in sports.

Enhanced ER protein processing gene expression increases rAAV yield and full capsid ratio in HEK293 cells

The recombinant adeno-associated virus (rAAV) vector is among the most promising viral vectors in gene therapy. However, the limited manufacturing capacity in human embryonic kidney (HEK) cells is a barrier to rAAV commercialization. We investigated the impact of endoplasmic reticulum (ER) protein processing and apoptotic genes on transient rAAV production in HEK293 cells. We selected four candidate genes based on prior transcriptomic studies: XBP1, GADD34 / PPP1R15A, HSPA6, and BCL2. These genes were stably integrated into HEK293 host cells. Traditional triple-plasmid transient transfection was used to assess the vector production capability and the quality of both the overexpressed stable pools and the parental cells. We show that the overexpression of XBP1, HSPA6, and GADD34 increases rAAV productivity by up to 100% and increases specific rAAV productivity by up to 78% in HEK293T cells. Additionally, more prominent improvement associated with ER protein processing gene overexpression was observed when parental cell productivity was high, but no substantial variation was detected under low-producing conditions. We also confirmed genome titer improvement across different serotypes (AAV2 and AAV8) and different cell lines (HEK293T and HEK293); however, the extent of improvement may vary. This study unveiled the importance of ER protein processing pathways in viral particle synthesis, capsid assembly, and vector production.Key points• Upregulation of endoplasmic reticulum (ER) protein processing (XBP1, HSPA6, and GADD34) leads to a maximum 100% increase in rAAV productivity and a maximum 78% boost in specific rAAV productivity in HEK293T cells• The enhancement in productivity can be validated across different HEK293 cell lines and can be used for the production of various AAV serotypes, although the extent of the enhancement might vary slightly• The more pronounced improvements linked to overexpressing ER protein processing genes were observed when parental cell productivity was high, with minimal variation noted under low-producing conditions

Climate neutrality of the French energy system: overview and impacts of sustainable aviation fuel production

CO2 emission reduction of sectors such as aviation, maritime shipping, road haulage, and chemical production is challenging but necessary. Although these sectors will most likely continue to rely on carbonaceous energy carriers, they are expected to gradually shift away from fossil fuels. In order to do so, the prominent option is to utilize alternative carbon sources—like biomass and CO2 originating from carbon capture—for the production of non-fossil carbonaceous vectors (biofuels and e-fuels). However, the limited availability of biomass and the varying nature of other carbon sources necessitate a comprehensive evaluation of trade-offs between potential carbon uses and existing sources. Then, it is primordial to understand the origin of carbon used in sustainable aviation fuel (SAF) to understand the implications of defossilizing aviation for the energy system. Moreover, the production of SAF implies deep changes to the energy system that are quantified in this work. This study utilizes the linear programming cost optimization tool EnergyScope TD to analyze the holistic French energy system, encompassing transport, industry, electricity, and heat sectors while ensuring net greenhouse gas neutrality. A novel method to model and quantify carbon flows within the system is introduced, enabling a comprehensive assessment of greenhouse gas neutrality. This study highlights the significance of fulfilling clean energy requirements and implementing carbon dioxide removal measures as crucial steps toward achieving climate neutrality. Indeed, to reach climate neutrality, a production of 1,046 TWh of electricity by non-fossil sources is needed. Furthermore, the findings underscore the critical role of efficient carbon and energy valorization from biomass, providing evidence that producing fuels by combining biomass and hydrogen is optimal. The study also offers valuable insights into the future cost and impact of SAF production for air travel originating from France. That is, the European law ReFuelEU would increase the price of plane tickets by +33% and would require 126 TWh of hydrogen and 50 TWh of biomass to produce the necessary 91 TWh of jet fuel. Finally, the implications of the assumption behind the production of SAF are discussed.

On the Leonardo quaternions sequence

In the present work, a new sequence of quaternions related to the Leonardo numbers -- named the Leonardo quaternions sequence -- is defined and studied. Binet's formula and certain sum and binomial-sum identities, some of which derived from the mentioned formula, are established. Tagiuri-Vajda's identity and, as consequences, Catalan's identity, d'Ocagne's identity and Cassini's identity are presented. Furthermore, applying Catalan's identity, and the connection between composition algebras and vector cross product algebras, Gelin-Cesàro's identity is also stated and proved. Finally, the generating function, the exponential generating function and the Poisson generating function are deduced. In addition to the results on Leonardo quaternions, known results on Leonardo numbers and on Fibonacci quaternions are extended.

An efficient eigenvalue bounding method: CFL condition revisited

Direct and large-eddy simulations of turbulence are often solved using explicit temporal schemes. However, this imposes very small time-steps because the eigenvalues of the (linearized) dynamical system, re-scaled by the time-step, must lie inside the stability region. In practice, fast and accurate estimations of the spectral radii of both the discrete convective and diffusive terms are therefore needed. This is virtually always done using the so-called CFL condition. On the other hand, the large heterogeneity and complexity of modern supercomputing systems are nowadays hindering the efficient cross-platform portability of CFD codes. In this regard, our leitmotiv reads: relying on a minimal set of (algebraic) kernels is crucial for code portability and maintenance! In this context, this work focuses on the computation of eigenbounds for the above-mentioned convective and diffusive matrices which are needed to determine the time-step à la CFL. To do so, a new inexpensive method, that does not require to re-construct these time-dependent matrices, is proposed and tested. It just relies on a sparse-matrix vector product where only vectors change on time. Hence, both implementation in existing codes and cross-platform portability are straightforward. The effectiveness and robustness of the method are demonstrated for different test cases on both structured Cartesian and unstructured meshes. Finally, the method is combined with a self-adaptive temporal scheme, leading to significantly larger time-steps compared with other more conventional CFL-based approaches.