Matrix Production Research Articles

A20 in hepatic stellate cells suppresses chronic hepatitis by inhibiting DCLK1-JNK pathway-dependent chemokines.

Hepatic stellate cells (HSCs) are responsible for liver fibrosis accompanied by its activation into myofibroblasts and the abundant production of extracellular matrix. However, the HSC contribution to progression of liver inflammation has been less known. We aimed to elucidate the mechanism in HSCs underlying the inflammatory response and the function of tumor necrosis factor α-related protein A20 (TNFAIP3). We established A20 conditional knockout (KO) mice crossing Twist2-Cre and A20 floxed mice. Using these mice, the effect of A20 was analyzed in mouse liver and HSCs. The human HSC line LX-2 was also used to examine the role and underlying molecular mechanism of A20. In this KO model, A20 was deficient in >80% of HSCs. Spontaneous inflammation with mild fibrosis was found in the liver of the mouse model without any exogenous agents, suggesting that A20 in HSCs suppresses chronic hepatitis. Comprehensive RNA sequence analysis revealed that A20-deficient HSCs exhibited an inflammatory phenotype and abnormally expressed chemokines. A20 suppressed JNK pathway activation in HSCs. Loss of A20 function in LX-2 cells also induced excessive chemokine expression, mimicking A20-deficient HSCs. A20 overexpression suppressed chemokine expression in LX-2. In addition, we identified DCLK1 in the genes regulated by A20. DCLK1 activated the JNK pathway and upregulates chemokine expression. DCLK1 inhibition significantly decreased chemokine induction by A20-silencing, suggesting that A20 controlled chemokine expression in HSCs via the DCLK1-JNK pathway. In conclusion, A20 suppresses chemokine induction dependent on the DCLK1-JNK signaling pathway. These findings demonstrate the therapeutic potential of A20 and the DCLK1-JNK pathway for the regulation of inflammation in chronic hepatitis.

Silk fibroin microgrooved zirconia surfaces improve connective tissue sealing through mediating glycolysis of fibroblasts

The use of zirconia has significantly enhanced the aesthetic outcomes of implant restorations. However, peri-implantitis remains a challenge to long-term functionality of implants. Unlike the perpendicularly arranged collagen fibers in periodontal tissue, those in peri-implant tissue lie parallel to the abutment surface and contain fewer fibroblasts, making them more prone to inflammation. Studies have shown that microgroove structures on implant abutments could improve surrounding soft tissue structure. However, creating precise microgrooves on zirconia without compromising its mechanical integrity is technically challenging. In this study, we applied inkjet printing, an additive manufacturing technique, to create stable silk fibroin microgroove (SFMG) coatings of various dimensions on zirconia substrates. SFMG significantly improved the hydrophilicity of zirconia and showed good physical and chemical stability. The SFMG with 90 μm interval and 10 μm depth was optimal in promoting the proliferation, alignment, and extracellular matrix production of human gingival fibroblasts (HGFs). Moreover, the in vitro results revealed that SFMG stimulated key glycolytic enzyme gene expression in HGFs via the PI3K-AKT-mTOR pathway. Additionally, the in vivo results of histological staining of peri-abutments soft tissue showed that SFMG promoted the vertical alignment of collagen fibers relative to the abutment surface, improving connective tissue sealing around the zirconia abutment. Our results indicated that SFMG on zirconia can enhance HGF proliferation, migration and collagen synthesis by regulating glycolysis though PI3K-AKT-mTor pathway, thereby improving connective tissue sealing.

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Resource efficient schemes for the quantum simulation of lattice gauge theories can benefit from hybrid encodings of gauge and matter fields that use the native degrees of freedom, such as internal qubits and motional phonons in trapped-ion devices. We propose to use a parametric scheme to induce a tunneling of the phonons conditioned to the internal qubit state which, when implemented with a single trapped ion, corresponds to a minimal Z2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{\\mathbb{Z}}}_{2}$$\\end{document} gauge theory. To evaluate the feasibility of this scheme, we perform numerical simulations of the state-dependent tunneling using realistic parameters, and identify the leading sources of error in future experiments. We discuss how to generalize this minimal case to more complex settings by increasing the number of ions, moving from a single link to a Z2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{\\mathbb{Z}}}_{2}$$\\end{document} plaquette, and to an entire Z2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{\\mathbb{Z}}}_{2}$$\\end{document} chain. We present analytical expressions for the gauge-invariant dynamics and the corresponding confinement, which are benchmarked using matrix product state simulations.

Dense QCD2 with matrix product states

We study one-flavor SU(2) and SU(3) lattice QCD in (1 + 1) dimensions at zero temperature and finite density using matrix product states and the density matrix renormalization group. We compute physical observables such as the equation of state, chiral condensate, and quark distribution function as functions of the baryon number density. As a physical implication, we discuss the inhomogeneous phase at nonzero baryon density, where the chiral condensate is inhomogeneous, and baryons form a crystal. We also discuss how the dynamical degrees of freedom change from hadrons to quarks through the formation of quark Fermi seas.

Matrix product state approximations to quantum states of low energy variance

We show how to efficiently simulate pure quantum states in one dimensional systems that have both finite energy density and vanishingly small energy fluctuations. We do so by studying the performance of a tensor network algorithm that produces matrix product states whose energy variance decreases as the bond dimension increases. Our results imply that variances as small as ∝1/log⁡N can be achieved with polynomial bond dimension. With this, we prove that there exist states with a very narrow support in the bulk of the spectrum that still have moderate entanglement entropy, in contrast with typical eigenstates that display a volume law. Our main technical tool is the Berry-Esseen theorem for spin systems, a strengthening of the central limit theorem for the energy distribution of product states. We also give a simpler proof of that theorem, together with slight improvements in the error scaling, which should be of independent interest.

Characterizing the upper bound on the transparency order of (n, m)-functions

Abstract Transparency order ( TO {\mathcal{TO}} ) is one of the indicators used to measure the resistance of ( n , m ) \left(n,m) -function to differential power analysis. At present, there are three definitions: TO {\mathcal{TO}} , redefined transparency order ( ℛTO {\mathcal{ {\mathcal R} TO}} ), and modified transparency order ( ℳTO {\mathcal{ {\mathcal M} TO}} ). For the first time, we give one necessary and sufficient condition for ( n , m ) \left(n,m) -function reaching TO = m {\mathcal{TO}}=m and completely characterize ( n , m ) \left(n,m) -functions reaching TO = m {\mathcal{TO}}=m for any n n and m m . We find that any ( n , 1 ) \left(n,1) -function cannot reach TO = m {\mathcal{TO}}=m for odd n n . Based on the matrix product, the necessary conditions for ( n , m ) \left(n,m) -function reaching ℳTO = m {\mathcal{ {\mathcal M} TO}}=m or ℛTO = m {\mathcal{ {\mathcal R} TO}}=m are given, respectively. Finally, it is proved that any balanced ( n , m ) \left(n,m) -function cannot reach the upper bound on TO {\mathcal{TO}} (or ℛTO {\mathcal{ {\mathcal R} TO}} , ℳTO {\mathcal{ {\mathcal M} TO}} ).

Time-Dependent Variational Principle with Controlled Bond Expansion for Matrix Product States.

We present a controlled bond expansion (CBE) approach to simulate quantum dynamics based on the time-dependent variational principle (TDVP) for matrix product states. Our method alleviates the numerical difficulties of the standard, fixed-rank one-site TDVP integrator by increasing bond dimensions on the fly to reduce the projection error. This is achieved in an economical, local fashion, requiring only minor modifications of standard one-site TDVP implementations. We illustrate the performance and accuracy of CBE-TDVP with several numerical examples on finite quantum lattices, including new results on bipolaron formation in the Peierls-Hubbard model and spin pumping via adiabatic flux insertion in a chiral spin liquid.

Life of Pi: Exploring functions of Pi16+ fibroblasts

Fibroblasts are mesenchymal cells that are responsible for creating and maintaining tissue architecture through the production of extracellular matrix. These cells also play critical roles in processes such as wound repair and immune modulation in normal tissues and various disease states including fibrosis, autoimmunity, and cancer. Fibroblasts have a complex repertoire of functions that vary by organ, inflammatory state, and the developmental stage of an organism. How fibroblasts manage so many functions in such a context-dependent manner represents a gap in our understanding of these cells. One possibility is that a tissue-resident precursor cell state exists that provides the fibroblast lineage with flexibility during growth, inflammation, or other contexts that require dynamic tissue changes. Recent work has suggested that a precursor fibroblast cell state is marked by expression of Peptidase inhibitor 16 (Pi16). This review aims to concatenate and compare studies on fibroblasts that express Pi16 to clarify the roles of this cell state in fibroblast lineage development and other functions.

Biogenic amine tryptamine in human vaginal probiotic isolates mediates matrix inhibition and thwarts uropathogenic E. coli biofilm

Probiotics offer a promising prophylactic approach against various pathogens and represent an alternative strategy to combat biofilm-related infections. In this study, we isolated vaginal commensal microbiota from 54 healthy Indian women to investigate their probiotic traits. We primarily explored the ability of cell-free supernatant (CFS) from Lactobacilli to prevent Uropathogenic Escherichia coli (UPEC) colonization and biofilm formation. Our findings revealed that CFS effectively reduced UPEC’s swimming and swarming motility, decreased cell surface hydrophobicity, and hindered matrix production by downregulating specific genes (fimA, fimH, papG, and csgA). Subsequent GC–MS analysis identified Tryptamine, a monoamine compound, as the potent bioactive substance from Lactobacilli CFS, inhibiting UPEC biofilms with an MBIC of 4 µg/ml and an MBEC of 8 µg/ml. Tryptamine induced significant changes in E. coli colony biofilm morphology, transitioning from the Red, Dry, and Rough (RDAR) to the Smooth and White phenotype, indicating reduced extracellular matrix production. Biofilm time-kill assays demonstrated a four-log reduction in UPEC viability when treated with Tryptamine, highlighting its potent antibacterial properties, comparable to CFS treatment. Biofilm ROS assays indicated a significant elevation in ROS generation within UPEC biofilms, suggesting a potential antibacterial mechanism. Gene expression studies with Tryptamine-treated samples showed a reduction in expression of curli gene (csgA), consistent with CFS treatment. This study underscores the potential of Tryptamine from probiotic Lactobacilli CFS as a promising antibiofilm agent against UPEC biofilms.

Some self-dual codes and isodual codes constructed by matrix product codes

Some self-dual codes and isodual codes constructed by matrix product codes

Interleukin-1α inhibits transforming growth factor-β1 and β2-induced extracellular matrix production, remodeling and signaling in human lung fibroblasts: Master regulator in lung mucosal repair

BackgroundLung fibroblasts play a central role in maintaining lung homeostasis and facilitating repair through the synthesis and organization of the extracellular matrix (ECM). This study investigated the cross-talk between interleukin-1 alpha (IL-1α) and transforming growth factor-β (TGF-β) signaling, two key regulators in tissue repair and fibrosis, in the context of lung fibroblast repair in the healthy lung. ResultsStimulation of lung fibroblasts with TGF-β1 and TGF-β2 induced collagen-I and fibronectin protein expression (p < 0.05), a response inhibited with co-treatment with IL-1α (p < 0.05). Additionally, TGF-β1 and TGF-β2 induced myofibroblast differentiation, and collagen-I gel contraction, which were both suppressed by IL-1α (p < 0.05). In contrast, interleukin (IL)-6, IL-8 and thymic stromal lymphopoietin induced by IL-1α, were unaffected by TGF-β1 or TGF-β2. Mechanistically, IL-1α administration led to the suppression of TGF-β1 and TGF-β2 signaling, through downregulation of mRNA and protein for TGF-β receptor II and the downstream adaptor protein TRAF6, but not through miR-146a that is known to be induced by IL-1α. DiscussionIL-1α acts as a master regulator, modulating TGF-β1 and TGF-β2-induced ECM production, remodeling, and myofibroblast differentiation in human lung fibroblasts, playing a vital role in balancing tissue repair versus fibrosis. Further research is required to understand the dysregulated cross-talk between IL-1α and TGF-β signaling in chronic lung diseases and the exploration of therapeutic opportunities. MethodsPrimary human lung fibroblasts (PHLF) were treated with media control, or 1 ng/ml IL-1α with or without 50 ng/ml TGF-β1 or TGF-β2 for 1, 6 and 72 h. Cell lysates were assessed for the expression of ECM proteins and signaling molecules by western blot, miRNA by qPCR, mRNA by RNA sequencing and cell supernatants for cytokine production by ELISA. PHLFs were also seeded in non-tethered collagen-I gels to measure contraction, and myofibroblast differentiation using confocal microscopy.

P-600 Development of human ovarian spheroids as an innovating 3D model to study female hormone-related disorders

Abstract Study question Can spheroids of theca and granulosa cells serve as a new model to explore the cellular and molecular mechanisms involved in female hormone-related disorders? Summary answer Layered theca-granulosa cell spheroids can be successfully assembled with preserved cellular viability, β-estradiol production, and significant upregulation of extracellular matrix (ECM) components. What is known already Spheroid models can revolutionize reproductive biology research, faithfully replicating the ovarian microenvironment for insights into hormonal regulation, cell-cell interactions, and pathologies like polycystic ovarian syndrome (PCOS) and premature ovarian insufficiency (POI). These models can replicate the spatial configuration of the theca cells (TCs) and granulosa cells (GCs), which are the primary components of the follicle’s somatic compartment. Studies using rodent spheroids demonstrate improved estradiol and progesterone secretion, suggesting potential applicability. Though challenging to obtain, recent studies have successfully derived TCs through the differentiation of stromal cells (SCs), introducing new possibilities for spheroid reproductive research in the context of human models. Study design, size, duration The study included GCs from around 15 IVF patients and SCs from postmortem ovaries of 3 postmenopausal women were used to be differentiated into TCs. Participants/materials, setting, methods TCs and GCs were used to construct three spheroid types: layered theca-collagen-granulosa (TCG), layered theca-granulosa (TG), and non-layered. In TCG, GCs formed granulosa-spheroids, which were coated with collagen-I and combined with TCs. TG-spheroids were produced similarly without the collagen layer. Non-layered spheroids were assembled using isolated GCs and TCs. All embedded in PEGylated fibrin hydrogel. Media estradiol synthesis was measured via enzyme-linked immune assay (ELISA), and immunofluorescence was employed to characterize cellular functionality and ECM. Main results and the role of chance In GCs, positive expressions for AMHR, CYP19A1, and FHSR were observed, while following differentiation, TCs exhibited positivity for CYP17A1, LHR and CD13. A notable distinction emerged when comparing TCs within the spheroids to those in 2D cultures, as the former demonstrated an improvement in longevity. Layered TG-spheroids exhibited significant increases in collagen-IV, EMILIN-1, and collagen type I compared to G-spheroids. Interestingly, TCG-spheroids exhibited a distinct decrease in collagen type IV. Across all spheroid types, collagen type VI and laminin were notably absent from their ECM. Moreover, all spheroids had a significant increase in β-estradiol production. Non-layered spheroids showed a significant viability decrease inside the PEGylated fibrin over 30 days, in contrast to the sustained viability observed in the layered TG- and TCG-spheroids. Limitations, reasons for caution Utilizing primary cells, particularly specific patient-derived cells, poses a limitation due to their short availability, which could impact the study’s size. Wider implications of the findings Theca-granulosa spheroids deepen our understanding of reproductive health, offering insights into conditions such as POI and menopausal symptoms. By investigating the nuanced endocrine interplay, this 3D model paves the way for new toxicity studies, provides insights into PCOS, and hints at potential applications in hormone replacement therapy (HRT). Trial registration number Not applicable

3D modelling of ground magnetic-source airborne TEM data for anisotropic media based on the rational Krylov method

With the rapid development of the transient electromagnetic method (TEM), the numerical simulations of three-dimensional anisotropic media have garnered attention. This study used the rational Krylov method to realise the three-dimensional modelling of the ground magnetic-source airborne transient electromagnetic data for arbitrary anisotropic media. First, based on Maxwell's equations, a time-domain electromagnetic equation was derived for anisotropic media. The finite difference method was employed to discretise the equation, and the electromagnetic field was then expressed as the product of an exponential matrix and a vector related to the source. Subsequently, the rational Arnoldi algorithm was adopted to construct the rational Krylov subspace orthogonal basis vectors, and the electromagnetic fields at different times were obtained based on a model reduction strategy. The accuracy of the proposed algorithm was verified through the comparisons of its results with those of other software packages. We calculated the response for different anisotropic parameters of the typical three-dimensional anisotropic models, and analysed the influence of the anisotropic media on the ground magnetic-source airborne transient electromagnetic data. The proposed three-dimensional forward TEM algorithm provides important technical support for identifying the anisotropic geological bodies and lays the foundation for further inversion research.

Infinite Grassmann time-evolving matrix product operator method in the steady state

Infinite Grassmann time-evolving matrix product operator method in the steady state

Duality for the multispecies stirring process with open boundaries

We study the stirring process with N − 1 species on a generic graph G=(V,E) with reservoirs. The multispecies stirring process generalizes the symmetric exclusion process, which is recovered in the case N = 2. We prove the existence of a dual process defined on an extended graph G~=(V~,E~) which includes additional sites in V~∖V where dual particles get absorbed in the long-time limit. We thus obtain a characterization of the non-equilibrium steady state of the boundary-driven system in terms of the absorption probabilities of dual particles. The process is integrable for the case of the one-dimensional chain with two reservoirs at the boundaries and with maximally one particle per site. We compute the absorption probabilities by relying on the underlying gl(N) symmetry and the matrix product ansatz. Thus one gets a closed-formula for (long-ranged) correlations and for the non-equilibrium stationary measure. Extensions beyond this integrable set-up are also discussed.

Discrete higher Berry phases and matrix product states

Discrete higher Berry phases and matrix product states

Temporal entropy and the complexity of computing the expectation value of local operators after a quench

We study the computational complexity of simulating the time-dependent expectation value of a local operator in a one-dimensional quantum system by using temporal matrix product states(MPSs) and argue that it is intimately related to that of encoding temporal transition matrices and their partial traces. We show that we can upper-bound the rank of these reduced transition matrices by one of the Heisenberg evolution of local operators, thus making aconnection between two apparently different quantities, the temporal entanglement and the local operator entanglement(OE). As a result, whenever the local OE grows slower than linearly in time, we show that computing time-dependent expectation values of local operators using temporal MPSs is likely advantageous with respect to computing the same quantities using standard MPS techniques. Published by the American Physical Society 2024

Approximate encoding of quantum states using shallow circuits

Quantum algorithms and simulations often require the preparation of complex states through sequences of 2-qubit gates. For a generic quantum state, the number of required gates grows exponentially with the number of qubits, becoming unfeasible on near-term quantum devices. Here, we aim at creating an approximate encoding of the target state using a limited number of gates. As a first step, we consider a quantum state that is efficiently represented classically, such as a one-dimensional matrix product state. Using tensor network techniques, we develop and implement an efficient optimization algorithm that approaches the optimal implementation, requiring a polynomial number of iterations. We, next, consider the implementation of the proposed optimization algorithm directly on a quantum computer and overcome inherent barren plateaus by employing a local cost function. Our work offers a universal method to prepare target states using local gates and represents a significant improvement over known strategies.

Bootstrapping cascaded random matrix models: Correlations in permutations of matrix products.

Random matrix theory is a useful tool in the study of the physics of multiple scattering systems, often striking a balance between computation speed and physical rigour. Propagation of waves through thick disordered media, as arises, for example, in optical scattering or electron transport, typically necessitates cascading of multiple random matrices drawn from an underlying ensemble for thin media, greatly increasing the computational burden. Here we propose a dual pool based bootstrapping approach to speed up statistical studies of scattering in thick random media. We examine how potential matrix reuse in a pool based approach can impact statistical estimates of population averages. Specifically, we discuss how both bias and additional variance in the sample mean estimator are introduced through bootstrapping. In the diffusive scattering regime, the extra estimator variance is shown to originate from samples in which cascaded transfer matrices are permuted matrix products. Through analysis of the combinatorics and cycle structure of permutations we quantify the resulting correlations. Proofs of several analytic formulas enumerating the frequency with which correlations of different strengths occur are derived. Extension to the ballistic regime is briefly considered.

Extended Laterals and Hydraulic Fracturing Redevelop Tight Fractured Carbonates

_ This article, written by JPT Technology Editor Chris Carpenter, contains highlights of paper SPE 216292, “Redevelopment of Tight Fractured Carbonates Through Extended Laterals and Hydraulic Fracturing,” by Antonio Buono, Cameron Taylor, and Alyssa Dordan, SPE, ExxonMobil, et al. The paper has not been peer reviewed. _ In the complete paper, the authors compare development scenarios in a fractured carbonate play between historic vertical and short horizontal development and modern hydraulically fractured extended lateral development. Because of its long production history and recent redevelopment efforts, the Austin Chalk was chosen as a natural laboratory to test how recent artificial stimulation techniques can lead to additional production from a wider range of pore systems. Development of the Austin Chalk In recent years, application of modern unconventional multistage hydraulic fracturing techniques, coupled with adding proppant to support induced fracture networks, mitigated the steep decline seen in historic production profiles. These improvements were exemplified in a recent Austin Chalk redevelopment where modern completions led to an increase in estimated ultimate recovery (EUR) by 250% on average. In the targeted area of development, historic, short Austin Chalk laterals without modern completions exhibited a wide range of well performance. Some outlier wells achieved high recoveries from accessing an existing natural fracture network with the original completion, whereas others, after only a few months of economic production, were unable to achieve continuous flow without a propped stimulation. The differences in performance partially can be explained by the fact that the reservoir quality of different intervals within the Austin Chalk is likely highly variable. This is exemplified in the B-2 Zone, which contains a well-developed vertical fracture network with variable lengths. Data suggest that the natural fractures are confined within the B-2 and it is geomechanically less-susceptible to wellbore collapse than zones with higher clay concentrations. The B-2 is likely a stiffer interval than the E Zone. This implies that differences exist in the properties of these units that are caused by changes in mineralogy and cementation. The authors aim to characterize reservoir quality and hydrocarbon distributions of the fractured relatively clean zones compared with the hydraulically stimulated reservoir in relatively “dirty” chalky zones, and evaluate geomechanical properties and production expectations from each zone. Depositionally, these units can be characterized broadly as carbonate-rich with subordinate siliciclastic detritus composed of clay minerals and silt-sized quartz and plagioclase grains. These units all contain distinctive stylolite seams. The most-favorable hydrocarbon shows typically are in the lower members of the Austin Chalk. Production data show that natural-fracture-only production (heritage) generally has lower total EUR with highly variable well-to-well production profiles vs. fracture and matrix production, which the authors write that they believe is achieved when unconventional technology is applied to these reservoirs. To project from heritage chalk production to expected EUR using modern completions, the authors used a risked EUR scaling factor of 1.5×. Consequently, the potential uplift in economic viability was recognized through a multiwell Austin Chalk appraisal to assess well-to-well communication with Eagle Ford codevelopment. The authors’ appraisal evaluated reservoir-quality differences between the main landing zones in the Austin Chalk with those from the E Zone of the Austin Chalk and Upper Eagle Ford, respectively, to demonstrate how significant economic uplift can be realized in mature, tight carbonate fields with unconventional technology.