Matrix Loop Research Articles

An AlphaFold Structure Analysis of COQ2 as Key a Component of the Coenzyme Q Synthesis Complex.

Coenzyme Q (CoQ) is a lipidic compound that is widely distributed in nature, with crucial functions in metabolism, protection against oxidative damage and ferroptosis and other processes. CoQ biosynthesis is a conserved and complex pathway involving several proteins. COQ2 is a member of the UbiA family of transmembrane prenyltransferases that catalyzes the condensation of the head and tail precursors of CoQ, which is a key step in the process, because its product is the first intermediate that will be modified in the head by the next components of the synthesis process. Mutations in this protein have been linked to primary CoQ deficiency in humans, a rare disease predominantly affecting organs with a high energy demand. The reaction catalyzed by COQ2 and its mechanism are still unknown. Here, we aimed at clarifying the COQ2 reaction by exploring possible substrate binding sites using a strategy based on homology, comprising the identification of available ligand-bound homologs with solved structures in the Protein Data Bank (PDB) and their subsequent structural superposition in the AlphaFold predicted model for COQ2. The results highlight some residues located on the central cavity or the matrix loops that may be involved in substrate interaction, some of which are mutated in primary CoQ deficiency patients. Furthermore, we analyze the structural modifications introduced by the pathogenic mutations found in humans. These findings shed new light on the understanding of COQ2's function and, thus, CoQ's biosynthesis and the pathogenicity of primary CoQ deficiency.

Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis

Organelle transporters define metabolic compartmentalization, and how this metabolite transport process can be modulated is poorly explored. Here, we discovered that human SLC25A39, a mitochondrial transporter critical for mitochondrial glutathione uptake, is a short-lived protein under dual regulation at the protein level. Co-immunoprecipitation mass spectrometry and CRISPR knockout (KO) in mammalian cells identified that mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1. SLC25A39 senses mitochondrial iron-sulfur cluster using four matrix cysteine residues and inhibits its degradation. SLC25A39 protein regulation is robust in developing and mature neurons. This dual transporter regulation, by protein quality control and metabolic sensing, allows modulating mitochondrial glutathione level in response to iron homeostasis, opening avenues for exploring regulation of metabolic compartmentalization. Neuronal SLC25A39 regulation connects mitochondrial protein quality control, glutathione, and iron homeostasis, which were previously unrelated biochemical features in neurodegeneration.

Sleep spindles in primates: Modeling the effects of distinct laminar thalamocortical connectivity in core, matrix, and reticular thalamic circuits.

Sleep spindles are associated with the beginning of deep sleep and memory consolidation and are disrupted in schizophrenia and autism. In primates, distinct core and matrix thalamocortical (TC) circuits regulate sleep spindle activity through communications that are filtered by the inhibitory thalamic reticular nucleus (TRN); however, little is known about typical TC network interactions and the mechanisms that are disrupted in brain disorders. We developed a primate-specific, circuit-based TC computational model with distinct core and matrix loops that can simulate sleep spindles. We implemented novel multilevel cortical and thalamic mixing, and included local thalamic inhibitory interneurons, and direct layer 5 projections of variable density to TRN and thalamus to investigate the functional consequences of different ratios of core and matrix node connectivity contribution to spindle dynamics. Our simulations showed that spindle power in primates can be modulated based on the level of cortical feedback, thalamic inhibition, and engagement of model core versus matrix, with the latter having a greater role in spindle dynamics. The study of the distinct spatial and temporal dynamics of core-, matrix-, and mix-generated sleep spindles establishes a framework to study disruption of TC circuit balance underlying deficits in sleep and attentional gating seen in autism and schizophrenia.

New Insights Regarding Hemin Inhibition of the Purified Rat Brain 2-Oxoglutarate Carrier and Relationships with Mitochondrial Dysfunction.

A kinetic analysis of the transport assays on the purified rat brain 2-oxoglutarate/malate carrier (OGC) was performed starting from our recent results reporting about a competitive inhibitory behavior of hemin, a physiological porphyrin derivative, on the OGC reconstituted in an active form into proteoliposomes. The newly provided transport data and the elaboration of the kinetic equations show evidence that hemin exerts a mechanism of partially competitive inhibition, coupled with the formation of a ternary complex hemin-carrier substrate, when hemin targets the OGC from the matrix face. A possible interpretation of the provided kinetic analysis, which is supported by computational studies, could indicate the existence of a binding region responsible for the inhibition of the OGC and supposedly involved in the regulation of OGC activity. The proposed regulatory binding site is located on OGC mitochondrial matrix loops, where hemin could establish specific interactions with residues involved in the substrate recognition and/or conformational changes responsible for the translocation of mitochondrial carrier substrates. The regulatory binding site would be placed about 6 Å below the substrate binding site of the OGC, facing the mitochondrial matrix, and would allow the simultaneous binding of hemin and 2-oxoglutarate or malate to different regions of the carrier. Overall, the presented experimental and computational analyses help to shed light on the possible existence of the hemin-carrier substrate ternary complex, confirming the ability of the OGC to bind porphyrin derivatives, and in particular hemin, with possible consequences for the mitochondrial redox state mediated by the malate/aspartate shuttle led by the mitochondrial carriers OGC and AGC.

Research on three-dimensional visualization system of Natech events triggered domino accidents in oil-gas depots

Natech events and domino accidents happen worldwide and usually lead to severe consequences, especially in hazardous areas such as Oil-Gas depots. With the continuous development of the Oil-Gas industry and information technology, it is essential to realize the three-dimensional management and monitoring of hazardous substances. To evaluate the consequences caused by Natech events triggered domino accidents (accident chain), a matrix loop method was proposed to calculate the probability and evolution path of the accident chain. The actual layout and the real-time data of the Oil-Gas depot are input into the evaluation method in matrices, thus making the results reliable and updated. Besides, a B/S architecture system is developed to present the evaluation consequences of the proposed method. The three-dimensional visualization effects of natural disasters, technological accidents and the dynamic propagation process of the accident chain are also realized in the system to enhance the user's experience. A system application regarding lightning-triggered domino accidents was carried out to demonstrate the feasibility and rapidity of the proposed evaluation method and perform the system's operation process and visualization effects. The application results show that the system can provide effective decision-making assistance to safety management workers before the accident and guidance for emergency rescue operations during the accident.

Semisimple Flat F-Manifolds in Higher Genus

In this paper, we generalize the Givental theory for Frobenius manifolds and cohomological field theories to flat F-manifolds and F-cohomological field theories. In particular, we define a notion of Givental cone for flat F-manifolds, and we provide a generalization of the Givental group as a matrix loop group acting on them. We show that this action is transitive on semisimple flat F-manifolds. We then extend this action to F-cohomological field theories in all genera. We show that, given a semisimple flat F-manifold and a Givental group element connecting it to the constant flat F-manifold at its origin, one can construct a family of F-CohFTs in all genera, parameterized by a vector in the associative algebra at the origin, whose genus 0 part is the given flat F-manifold. If the flat F-manifold is homogeneous, then the associated family of F-CohFTs contains a subfamily of homogeneous F-CohFTs. However, unlike in the case of Frobenius manifolds and CohFTs, these homogeneous F-CohFTs can have different conformal dimensions, which are determined by the properties of a certain metric associated to the flat F-manifold.

Function-Related Asymmetry of the Interactions between Matrix Loops and Conserved Sequence Motifs in the Mitochondrial ADP/ATP Carrier.

The ADP/ATP carrier (AAC) plays a central role in oxidative metabolism by exchanging ATP and ADP across the inner mitochondrial membrane. Previous experiments have shown the involvement of the matrix loops of AAC in its function, yet potential mechanisms remain largely elusive. One obstacle is the limited information on the structural dynamics of the matrix loops. In the current work, unbiased all-atom molecular dynamics (MD) simulations were carried out on c-state wild-type AAC and mutants. Our results reveal that: (1) two ends of a matrix loop are tethered through interactions between the residue of triplet 38 (Q38, D143 and Q240) located at the C-end of the odd-numbered helix and residues of the [YF]xG motif located before the N-end of the short matrix helix in the same domain; (2) the initial progression direction of a matrix loop is determined by interactions between the negatively charged residue of the [DE]G motif located at the C-end of the short matrix helix and the capping arginine (R30, R139 and R236) in the previous domain; (3) the two chemically similar residues D and E in the highly conserved [DE]G motif are actually quite different; (4) the N-end of the M3 loop is clamped by the [DE]G motif and the capping arginine of domain 2 from the two sides, which strengthens interactions between domain 2 and domain 3; and (5) a highly asymmetric stable core exists within domains 2 and 3 at the m-gate level. Moreover, our results help explain almost all extremely conserved residues within the matrix loops of the ADP/ATP carriers from a structural point of view. Taken together, the current work highlights asymmetry in the three matrix loops and implies a close relationship between asymmetry and ADP/ATP transport.

Lax Operator Algebras and Applications to τ-Symmetries for Multilayer Integrable Couplings

The algebraic structures of zero curvature representations are furnished for multilayer integrable couplings associated with matrix spectral problems, both discrete and continuous. The key elements are a class of matrix loop algebras consisting of block matrices with blocks of the same size. As illustrative examples, isospectral and non-isospectral integrable couplings and the corresponding commutator relations of their Lax operators are computed explicitly in the cases of the Volterra lattice hierarchy and the AKNS hierarchy, along with their τ-symmetry algebras.

Locality-Guided Global-Preserving Optimization for Robust Feature Matching.

Feature matching is a fundamental problem in many computer vision tasks. This paper proposes a novel effective framework for mismatch removal, named LOcality-guided Global-preserving Optimization (LOGO). To identify inliers from a putative matching set generated by feature descriptor similarity, we introduce a fixed-point progressive approach to optimize a graph-based objective, which represents a two-class assignment problem regarding an affinity matrix containing global structures. We introduce a strategy that a small initial set with a high inlier ratio exploits the topology of the affinity matrix to elicit other inliers based on their reliable geometry, which enhances the robustness to outliers. Geometrically, we provide a locality-guided matching strategy, i.e., using local topology consensus as a criterion to determine the initial set, thus expanding to yield the final feature matching set. In addition, we apply local affine transformations based on reference points to determine the local consensus and similarity scores of nodes and edges, ensuring the validity and generality for various scenarios including complex nonrigid transformations. Extensive experiments demonstrate the effectiveness and robustness of the proposed LOGO, which is competitive with the current state-of-the-art methods. It also exhibits favorable potential for high-level vision tasks, such as essential and fundamental matrix estimation, image registration and loop closure detection.

Reduction of dislocation, mean free path, and migration barriers using high entropy alloy: insights from the atomistic study of irradiation damage of CoNiCrFeMn

High entropy alloy has attracted extensive attention in nuclear energy due to outstanding irradiation resistance, partially due to sluggish diffusion. The mechanism from a defect-generation perspective, however, has received much less attention. In this paper, the formation of dislocation loops, and migration of interstitials and vacancies in CoNiCrFeMn high entropy alloy under consecutive bombardments were studied by molecular dynamics simulations. Compared to pure Ni, less defects were produced in the CoNiCrFeMn. Only a few small dislocation loops were observed, and the length of dislocation was small. The dislocation loops in Ni matrix were obviously longer and so was the length of dislocation. The interstitial clusters had much smaller mean free path during migration in the CoNiCrFeMn. The mean free path of 10-interstitial clusters in CoNiCrFeMn was reduced over 40 times compared to that in pure Ni. In addition, CoNiCrFeMn had a smaller difference of migration energy between interstitial and vacancy, which increased the opportunity of recombination of defects, therefore, led to less defects and much fewer dislocation loops. Our results provide insights into the mechanism of irradiation resistance in the high entropy alloy and could be useful in material design for irradiation tolerance and accident tolerance materials in nuclear energy.

Prognostic Factors Five Years After Enucleation for Uveal Melanoma.

PurposeA subgroup of uveal melanoma (UM) gives rise to metastases at a late stage. Our objective was to identify patient and tumor characteristics that are associated with UM-related death in patients who survived 5 years following enucleation.MethodsA retrospective analysis was performed in 583 primary UM cases, enucleated at the Leiden University Medical Center between 1983 and 2013. Univariable and multivariable Cox regression analyses were performed in the total cohort and separately in those surviving more than 5 years (n = 297).ResultsIn the total cohort, the median age was 62.6 years, and the median tumor diameter was 12.0 mm. Monosomy 3 was detected in 53% of cases and gain of 8q in 47%. In the cohort surviving 5 years, the median age was 59.5 years, and the median tumor diameter was 11.0 mm. Monosomy 3 and gain of 8q were detected in 33% and 31% of cases, respectively. In the total cohort, male gender (P = 0.03), tumor diameter (P < 0.001), mitotic count (P < 0.001), extravascular matrix loops (P = 0.03), extraocular growth (P < 0.001), and gain of 8q (P < 0.001) were independently associated with UM-related death. In patients surviving 5 years after enucleation, univariable analysis revealed that age (P = 0.03), tumor diameter (P < 0.001), monosomy 3 (P = 0.04), and 8q gain (P = 0.003) were associated with subsequent UM-related death. Using a multivariable analysis, only male gender (P = 0.03) and gain of 8q (P = 0.01) remained significant.ConclusionsPredictors of UM-related death change over time. Among UM patients who survived the initial 5 years following enucleation, male gender and chromosome 8q status were the remaining factors related to UM-related death later on.

Bi-Integrable Couplings Associated with so $$(3,{\mathbb R})$$ ( 3 , R )

By a class of zero curvature equations over a non-semisimple matrix loop algebra, we generate a new hierarchy of bi-integrable couplings for a soliton hierarchy associated with so(3, $$\mathbb {R}$$ ). The bi-Hamiltonian structures are found by the associated variational identity, which imply that all the presented coupling systems possess infinitely many commuting symmetries and conserved functionals and, thus, are Liouville integrable.

Doping effect of aminopyridine analogous in supramolecular quasi-solid polymer electrolyte for DSSCs: improvement in ionic diffusion leading to superior efficiency

In the present work, hydroxy butyl methyl cellulose-based quasi-solid-state polymer gel electrolyte has been prepared by incorporating I−/I3 − couple in ethylene carbonate and propylene carbonate. This bare electrolyte’s properties have been investigated first time by additional doping of amino pyridine analogous moieties such as pyridin-4-amine, di(pyridin-4-yl)amine, and tri(pyridin-4-yl)amine moiety. Effect on ionic conductivity, triiodide diffusion, glass transition temperature, rheology, and photovoltaic performance in dye-sensitized solar cells (DSSC) was briefly evaluated. Addition of dopant creates amorphous loops in the gel matrix, and dopant has lone pair of electrons at the N of pyridile, which attracts the Li+ species of LiI making smooth and fast diffusion of triiodides. Tg and XRD characterizations were performed to prove the immense effect on physical properties. TPA-doped electrolyte shows 4.3 mS/cm conductivity and has explored 3.67% power conversion efficiency in DSSC with N719 sensitizer. This non-volatile type of electrolyte-based DSSCs performs efficiently up 600 h in one sun illumination.

Natural and Induced Mitochondrial Phosphate Carrier Loss: DIFFERENTIAL DEPENDENCE OF MITOCHONDRIAL METABOLISM AND DYNAMICS AND CELL SURVIVAL ON THE EXTENT OF DEPLETION

The relevance of mitochondrial phosphate carrier (PiC), encoded by SLC25A3, in bioenergetics is well accepted. However, little is known about the mechanisms mediating the cellular impairments induced by pathological SLC25A3 variants. To this end, we investigated the pathogenicity of a novel compound heterozygous mutation in SLC25A3. First, each variant was modeled in yeast, revealing that substituting GSSAS for QIP within the fifth matrix loop is incompatible with survival on non-fermentable substrate, whereas the L200W variant is functionally neutral. Next, using skin fibroblasts from an individual expressing these variants and HeLa cells with varying degrees of PiC depletion, PiC loss of ∼60% was still compatible with uncompromised maximal oxidative phosphorylation (oxphos), whereas lower maximal oxphos was evident at ∼85% PiC depletion. Furthermore, intact mutant fibroblasts displayed suppressed mitochondrial bioenergetics consistent with a lower substrate availability rather than phosphate limitation. This was accompanied by slowed proliferation in glucose-replete medium; however, proliferation ceased when only mitochondrial substrate was provided. Both mutant fibroblasts and HeLa cells with 60% PiC loss showed a less interconnected mitochondrial network and a mitochondrial fusion defect that is not explained by altered abundance of OPA1 or MFN1/2 or relative amount of different OPA1 forms. Altogether these results indicate that PiC depletion may need to be profound (>85%) to substantially affect maximal oxphos and that pathogenesis associated with PiC depletion or loss of function may be independent of phosphate limitation when ATP requirements are not high.

Generating integrable lattice hierarchies by some matrix and operator Lie algebras

Two types of matrix Lie algebras are presented. We make use of the first loop algebra to obtain a new \((1+1)\)-dimensional integrable discrete hierarchy, which generalizes a result given by Gordoa et al., whose reduction is a discrete modified KdV system. Then we produce another new \((2+1)\)-dimensional integrable discrete hierarchy with three fields under a \((2+1)\)-dimensional non-isospectral linear problem. We again generalize the \((1+1)\)- and \((2+1)\)-dimensional discrete hierarchies to obtain a positive and negative integrable discrete hierarchy. In addition, we obtain a discrete integrable coupling system of the \((1+1)\)-dimensional discrete hierarchy presented in the paper by enlarging such the loop algebras. Next, we apply the second matrix loop algebra to introduce an isospectral problem and deduce a new integrable discrete hierarchy, whose quasi-Hamiltonian structure is derived from the trace identity proposed by Tu Guizhang, which can be reduced to some modified Toda lattice equations. A type of Darboux transformation of a reduced discrete system of the latter integrable discrete hierarchy is obtained as well. We introduce two types of operator-Lie algebras according to a given spectral problem by a matrix Lie algebra and apply the r-matrix theory to obtain a few lattice integrable systems, including two \((2+1)\)-dimensional lattice systems.

On the Liouville Integrability of the Periodic Kostant–Toda Flow on Matrix Loops of Level k

In this work, we consider the periodic Kostant–Toda flow on matrix loops in \({\mathfrak{s}\mathfrak{l}(n,\mathbb{C})}\) of level k, which correspond to periodic infinite band matrices with period n with lower bandwidth equal to k and fixed upper bandwidth equal to 1 with 1’s on the first superdiagonal. We show that the coadjoint orbits through the submanifold of such matrix loops can be identified with those of a finite-dimensional Lie group, which appears in the form of a semi-direct product. We then characterize the generic coadjoint orbits and obtain an explicit global cross-section for such orbits. We also establish the Liouville integrability of the periodic Kostant–Toda flow on such orbits via the construction of action-angle variables.

Integrable Couplings of the Boiti-Pempinelli-Tu Hierarchy and Their Hamiltonian Structures

AbstractIntegrable couplings of the Boiti-Pempinelli-Tu hierarchy are constructed by a class of non-semisimple block matrix loop algebras. Further, through using the variational identity theory, the Hamiltonian structures of those integrable couplings are obtained. The method can be applied to obtain other integrable hierarchies.

Integrability of the periodic Kostant–Toda flow on matrix loops of level k

In this note, we announce results on the Liouville integrability of the periodic Kostant–Toda flow on loops of matrices in sl(n,C) of level k.

Valve-Shut off Scheme and Affected Zone Analysis of Multi-Sources Looped-Pipe Network Based on ARCGIS

Based on ArcGIS,Multi-heat sources and multi-loops complex heating network is Modeled and simulated ,and a functional method is put forward, by using Geodatabase data model,it can creat relating matrix and basic loop matrix of heat network quickly,and calculate Hydraulic Regime of heating Network with the Basic Circuit.When pipe-bursting accident occur in heating Network,along with changes in the logical network model.also the entire calculation model is changed.This method is applied to the Study of Valve-shut off scheme after tube-burst accident ,the heating Influence of the accident can be quantitative analyzed , also the degree of influence is compared when tube-burst accident happen at different place.

Proton implantation effect on (SUS-316) stainless steel

Microstructural damage and nano hardness of the industrial grade stainless steel (SUS-316) have been studied under proton (H+) implanted condition applying different doses at room temperature. The implantation scheme such as proton energy, fluence, irradiation time, and penetration depth in the target materials were estimated by Monte Carlo Simulation Code SRIM-2008. In the simulation, the parameters were chosen in such a way that the damage density (displacement per atom or dpa) would be uniform up to certain depth from the surface. X-ray diffraction study of the annealed samples prior to the proton implantation showed the austenitic fcc structure and no significant change was observed after proton implantation in it. Microstructural observation made by Scanning Transmission Electron Microscopy (STEM) revealed that 1dpa of proton-irradiation induced the structural damage extended up to 1μm depth from the surface. The nano hardness study showed that the hardness level of the irradiated samples increased monotonically with the irradiation doses. Proton dose of 1dpa caused 65% increment of hardness level on average in case of uniformly irradiated samples. It was realized that the increment of hardness was a consequence of microstructural damages caused by the formation of interstitial dislocation loops in the sample matrix keeping the lattice structure unaffected.