Production Cross Research Articles

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.

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.

Factors Affecting Technical Efficiency of Coffee Producers: The Case Dale Woreda, Sidama Region, Ethiopia

Coffee is the major source of income for smallholder farmers and is a leading export crop for Ethiopia. Even though a great proportion of coffee production comes from smallholder farmers with farm sizes below two hectares, productivity in these farms remained very low. To identify the causes of low productivity this study identified the technical efficiency level of smallholder coffee farmers and the factors that influence technical efficiency in coffee production in Dale Woreda, Sidama Region, Ethiopia using the stochastic frontier approach. In addition, this study attempts to determine whether the agricultural and some of the socio-economic characteristics of farmers can influence the efficiency of their technical efficiency coffee production. By exploiting the information that was gathered in a survey of 150 farmers selected randomly from three kebeles using stratified random sampling in the woreda, these farmers' technical efficiency was estimated using a trans-long-type stochastic frontier model and two-limit Tobit model. The mean technical efficiency of the study area is 65.43%. The results suggest that, factors like the land cover, labor in hours, compost used as well as their cross product and the interaction effects of labor with sufficient compost used, labor with proper capital-labor force, and minimum cost for agricultural equipment and composite with proper capital significant determinants of coffee technical efficiency in the area. Furthermore, variables like educational status, age of the coffee tree, membership of cooperative associations, size of livestock holding, presence of additional off-farm incomes, and age of household head are significant predictors of the technical efficiency of farmers in the study area. Thus, by improving their education, improving the frequency of extension service, increasing livestock holdings, improving membership in cooperative associations, and replacing the aged coffee tree, someone can improve his/her technical efficiency directly and coffee production indirectly.

Generation of Murine Chimeric Antigen Receptor-Modified T Cells for In Vivo Studies in Syngeneic Tumor Models.

CAR-T cell therapy has emerged as a potent and effective tool in the immunotherapy of refractory cancers. However, challenges exist in their clinical application, necessitating extensive preclinical research to optimize their function. Various preclinical in vitro and in vivo models have been proposed for such purpose; among which immunocompetent mouse models serve as an invaluable tool in studying host immune interactions within a more realistic simulation of the tumor milieu. We hereby describe a standardized protocol for the generation of high-titer γ-retroviral vectors through transfection of the HEK293T packaging cell line. The virus-containing supernatant is further concentrated using an inhouse concentrator solution, titrated, and applied to mouse T cells purified via a convenient and rapid method by nylon-wool columns. Using the method presented here, we were able to achieve high titer γ-retrovirus and highly pure mouse T cells with desirable CAR transduction efficiency. The mouse CAR T cells produced through this protocol demonstrate favorable CAR expression and viability, thus making them suitable for further in vitro/in vivo assays. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Production of γ-retroviral vectors from retrovirus-backbone plasmids Basic Protocol 2: Concentration of γ-retrovirus-containing supernatants Basic Protocol 3: Titration of concentrated γ-retrovirus Basic Protocol 4: Isolation and activation of mouse T cells Basic Protocol 5: Transduction of activated mouse T cells, assessment of CAR expression, and expansion of CAR T cells for further in vitro/in vivo studies Support Protocol: Surface staining of cells for flow cytometric assessment of CAR expression.

Exploration of microscopic physical processes of Z-pinch by a modified electrostatic direct implicit particle-in-cell algorithm

Abstract For investigating efficiently the stagnation kinetic-process of Z-pinch, we develop a novel modified electrostatic implicit particle-in-cell algorithm in radial one-dimension for Z-pinch simulation in which a small-angle cumulative binary collision algorithm is used. In our algorithm, the electric field in z-direction is solved by a parallel electrode-plate model, the azimuthal magnetic field is obtained by Ampere’s law, and the term for charged particle gyromotion is approximated by the cross product of the averaged velocity and magnetic field. In simulation results of 2 MA deuterium plasma shell Z-pinch, the mass-center implosion trajectory agrees generally with that obtained by one-dimensional MHD simulation, and the plasma current also closely aligns with the external current. The phase space diagrams and radial-velocity probability distributions of ions and electrons are obtained. The main kinetic characteristic of electron motion is thermal equilibrium and oscillation, which should be oscillated around the ions, while that of ion motion is implosion inwards. In the region of stagnation radius, the radial-velocity probability distribution of ions transits from the non-equilibrium to equilibrium state with the current increasing, while of electrons is basically the equilibrium state. When the initial ion density and current peak are not high enough, the ions may not reach their thermal equilibrium state through collisions even in its stagnation phase.

Innovative fixed bed bioreactor platform: Enabling linearly scalable adherent cell biomanufacturing with real-time biomass prediction from nutrient consumption.

Scalable single-use adherent cell-based biomanufacturing platforms are essential for unlocking the full potential of cell and gene therapies. The primary objective of this study is to design and develop a novel fixed bed bioreactor platform tailored specifically for scaling up adherent cell culture. The bioreactor comprises a packed bed of vertically stacked woven polyethylene terephthalate mesh discs, sandwiched between two-fluid guide plates. Leveraging computational fluid dynamics modeling, we optimized bioreactor design to achieve uniform flow with minimal shear stress. Residence time distribution measurements demonstrated excellent flow uniformity with plug flow characteristics. Periodic media sampling coupled with offline analysis revealed minimal gradients of crucial metabolites (glucose, glutamine, lactate, and ammonia) across the bioreactor during cell growth. Furthermore, the bioreactor platform demonstrated high performance in automated cell harvesting, with ≈96% efficiency and ≈98% viability. It also exhibited linear scalability in both operational parameters and performance for cell culture and adeno-associated virus vector production. We developed mathematical models based on oxygen uptake rates to accurately predict cell growth curves and estimate biomass in real-time. This study demonstrates the effectiveness of the developed fixed-bed bioreactor platform in enabling scalable adherent cell-based biomanufacturing with high productivity and process control.

Gene therapy for retinal diseases: From genetics to treatment.

The gene therapy approach for retinal disorders has been considered largely over the last decade owing to the favorable outcomes of the US Food and Drug Administration-approved commercial gene therapy, Luxturna. Technological advances in recent years, such as next-generation sequencing, research in molecular pathogenesis of retinal disorders, and precise correlations with their clinical phenotypes, have contributed to the progress of gene therapies for various diseases worldwide, and more recently in India as well. Thus, considerable research is being conducted for the right choice of vectors, transgene engineering, and accessible and cost-effective large-scale vector production. Many retinal disease-specific clinical trials are presently being conducted, thereby necessitating the collation of such information as a ready reference for the scientific and clinical community. In this article, we present an overview of existing gene therapy research, which is derived from an extensive search across PubMed, Google Scholar, and clinicaltrials.gov sources. This contributes to prime the understanding of basic aspects of this cutting-edge technology and information regarding current clinical trials across many different conditions. This information will provide a comprehensive evaluation of therapies in existing use/research for personalized treatment approaches in retinal disorders.

In-Depth Comparison of Adeno-Associated Virus Containing Fractions after CsCl Ultracentrifugation Gradient Separation.

Recombinant adeno-associated viruses (rAAVs) play a pivotal role in the treatment of genetic diseases. However, current production and purification processes yield AAV-based preparations that often contain unwanted empty, partially filled or damaged viral particles and impurities, including residual host cell DNA and proteins, plasmid DNA, and viral aggregates. To precisely understand the composition of AAV preparations, we systematically compared four different single-stranded AAV (ssAAV) and self-complementary (scAAV) fractions extracted from the CsCl ultracentrifugation gradient using established methods (transduction efficiency, analytical ultracentrifugation (AUC), quantitative and digital droplet PCR (qPCR and ddPCR), transmission electron microscopy (TEM) and enzyme-linked immunosorbent assay (ELISA)) alongside newer techniques (multiplex ddPCR, multi-angle light-scattering coupled to size-exclusion chromatography (SEC-MALS), multi-angle dynamic light scattering (MADLS), and high-throughput sequencing (HTS)). Suboptimal particle separation within the fractions resulted in unexpectedly similar infectivity levels. No single technique could simultaneously provide comprehensive insights in the presence of both bioactive particles and contaminants. Notably, multiplex ddPCR revealed distinct vector genome fragmentation patterns, differing between ssAAV and scAAV. This highlights the urgent need for innovative analytical and production approaches to optimize AAV vector production and enhance therapeutic outcomes.