Linear Strands Research Articles

Merck bets $250 million on circular RNA

Merck & Co. has entered a collaboration with circular RNA company Orna Therapeutics to develop several programs, including vaccines and therapeutics for infectious diseases and oncology. Merck will pay Orna $150 million up front and invest $100 million of equity in Orna’s series B financing round, which initially closed Aug. 16 with $221 million. Orna could receive up to $3.5 billion in milestone payments. The company’s technology stems from research done at the Massachusetts Institute of Technology by cofounder Alex Wesselhoeft and molecular geneticist Daniel G. Anderson, who is on Orna’s board of directors. To make circular RNA, which the firm has dubbed oRNA, Orna brings together the two ends of a strand of linear messenger RNA (mRNA). Because the loose ends can be targeted by RNA-degrading enzymes, RNA circles are stabler in the body than linear strands, CEO Tom Barnes says. That greater stability helps the circles produce more

Physicochemical and morphological characteristics of potato pectin with in-situ acid-induced gelation.

Pectin in the potato cell wall plays an important role in strengthening connections of intercellular junctions during thermal processing through in-situ acid-induced gelation (in-situ acid-induced gelation [AIG]). Thus, the variation in the physicochemical and structural characteristics of potato pectin with in-situ AIG was focused in this study. The intra- and intermolecular hydrogen bonding among (d-galacturonic acid) GalA units around 3400cm-1 (absorbance intensity was increased from 50.9 to 70.7) in Fourier transform infrared spectra were enhanced in the pectin with in-situ AIG. The crystallinity of pectin with in-situ AIG increased from 4.02% to 36.63%. Atomic force microscopy revealed that pectin with in-situ AIG was made up of wide linear strands with the length from 0.5 to 4.6µm. Thermogravimetric and rheological analysis showed that the structure of potato pectin was more stable and resistant to heat processing after in-situ AIG. These observations proved that the complex structure of potato pectin with in-situ AIG linked with its thermal stability. PRACTICAL APPLICATION: In-situ gelated pectin in the intercellular space caused a helpful structure modification of vegetable to maintain its hardness with heat process. This study will provide novel insights into the physicochemical properties of in-situ gelated pectin in the potato cell and useful knowledge on the behavior of pectin during the preparation of potato products.

On the linear strand of edge ideals of some zero-divisor graphs

Let I(G) be the edge ideal associated to a simple graph G. Given a prime number p and an integer, we study the -graded Betti numbers that appear in the linear strand of the minimal free resolution of , where is the zero-divisor graph of the ring . In particular, we compute the extremal Betti number of . As a consequence, we find the Castelnuovo-Mumford regularity and projective dimension of these ideals. Moreover, we exhibit formulae that determine all -graded Betti numbers in the linear strand of the minimal free resolution of for certain values of n.

Koszul homology of quotients by edge ideals

We show that the Koszul homology algebra of a quotient of a polynomial ring by the edge ideal of a forest is generated by the lowest linear strand. This provides a large class of Koszul algebras whose Koszul homology algebras satisfy this property. We obtain this result by constructing the minimal graded free resolution of a quotient by such an edge ideal via the so called iterated mapping cone construction and using the explicit bases of Koszul homology given by Herzog and Maleki. Using these methods we also recover a result of Roth and Van Tuyl on the graded Betti numbers of quotients by edge ideals of trees.

Bioinformatics analysis and pharmacological effect of Stevia rebaudiana in the prevention of type-2 diabetes

Different groups of enzymes and regulatory elements are involved in the synthesis of Ribodioside A, which is one of the most important sweetening compounds in stevia. The UGT family (UDP-glycosyltransferase) is a group of regulatory genes that are very effective in converting steviol glycoside to Ribodioside A. Bioinformatics analyses on this gene family, which included the UGT74G1, UGT76G1, and UGT85C2 genes, showed that the protein encoded by these genes had a UDPGT protected protein domain. Also, the study of the secondary structure of these proteins showed that the total corrosion of these proteins is mainly from alpha-helix and random screws or loops that are connected with linear strands. Also, the study of the secondary structure of these proteins showed that the total corrosion of these proteins is mainly from alpha-helix and random screws or loops that are connected with linear strands. The results of studying the three-dimensional structure of the studied proteins confirmed the previous findings of high genomic similarity between these proteins. The results of the ProtScale program showed that the abundance of amino acids with negative hydropathicity in the sequence of these proteins is high, which is effective in creating plant resistance to drought stress. Finally, the codon preference trend of these proteins was investigated using the sequence manipulation suite database. This information can be used for other research, including the transfer of these proteins.

Inorganic Structural Chemistry of Titanium Dioxide Polymorphs

Apart from rutile, which crystallizes in the rutile-type structure characteristic of many metal dioxides, three major polymorphs of titanium dioxide (TiO2) are known: anatase, brookite, and the α-lead dioxide (α-PbO2)-type high-pressure form. Ti ions are commonly found in octahedra composed of six oxide ions, and their crystal structures are distinguished according to the linkage pattern of the TiO6 octahedra. Inorganic structural chemistry considers that, in the rutile and α-PbO2 types, Ti ions occupy half of the octahedral voids in the hexagonal close packing of oxide ions, and the TiO6 octahedra in each layer are joined via edge sharing to form linear and zigzag strands, respectively. Anatase and brookite, on the other hand, exhibit more complex three-dimensional edge-sharing octahedral connections, although their origins are not fully explained. I show that these configurations can be interpreted as distinct stacking structures of layers with α-PbO2-type zigzag strands. Additionally, I characterize the crystal structures of four TiO2 polymorphs in detail using stacking sequence descriptions based on anion close packings and explore their relationships in terms of inorganic structural chemistry. I note that the moderate covalent nature of the Ti-O bond and the local structural instability of d0 ions result in an unusual variety of polymorphs in TiO2.

Intersecting Linear Light Strands: a Particle Explanation for the Fresnel Central Spot

The Fresnel central spot in a shadow, theorized to be generated from wave interference, has given strong support for wave models of light. Using extended exposure macro imaging in various media, the shadow is shown to be more complex with multiple lines of light intersecting in the center. Using the particle concept of discrete light strands perpendicularly reflecting from a diffraction source, these observations can be more accurately explained. Another quantized aspect of light is shown where linear light strands become rings when an energy threshold is reached.

Linear strands of initial ideals of determinantal facet ideals

We construct an explicit linear strand for the initial ideal of any determinantal facet ideal (DFI) with respect to any diagonal term order. We show that if the clique complex of Δ has no 1-nonfaces larger than a certain cardinality, then the Betti numbers of the linear strand of and its initial ideal coincide. This confirms a conjecture of Ene–Herzog–Hibi for closed graphs with at most 2 maximal cliques. Additionally, we show that the linear strand of the initial ideal of any DFI is supported on an induced subcomplex of the complex of boxes introduced by Nagel–Reiner.

T1 invasive lung adenocarcinoma: Thin-section CT solid score and histological periostin expression predict tumor recurrence.

Adenocarcinoma is the most common histological type of non-small cell lung cancer (NSCLC), and various biomarkers for predicting its prognosis after surgical resection have been suggested, particularly in early-stage lung adenocarcinoma. Periostin (also referred to as POSTN, PN or osteoblast-specific factor) is an extracellular matrix protein, the expression of which is associated with tumor invasiveness in patients with NSCLC. In the present study, the novel approach, in which the thin-section CT findings prior to surgical resection and periostin expression of resected specimens were analyzed in combination, was undertaken to assess whether the findings could be a biomarker for predicting the outcomes following resection of T1 invasive lung adenocarcinoma. A total of 73 patients who underwent surgical resection between January 2000 and December 2009 were enrolled. A total of seven parameters were assessed in the thin-section CT scans: i) Contour; ii) part-solid ground-glass nodule or solid nodule; iii) percentage of solid component (the CT solid score); iv) presence of air-bronchogram and/or bubble-like lucencies; v) number of involved vessels; vi) shape linear strands between the nodule and the visceral pleura; and vii) number of linear strands between the nodule and the visceral pleura. Two chest radiologists independently assessed the parameters. Periostin expression was evaluated on the basis of the strength and extent of staining. Univariate and multivariate analyses were subsequently performed using the Cox proportional hazards model. There was a substantial to almost perfect agreement between the two observers with regard to classification of the seven thin-section CT parameters (κ=0.64-0.85). In the univariate analysis, a CT solid score >80%, pathological lymphatic invasion, tumor and lymph node status and high periostin expression were significantly associated with recurrence (all P<0.05). Multivariate analysis demonstrated that a CT solid score >80% and high periostin expression were risk factors for recurrence (P=0.002 and P=0.011, respectively). The cumulative recurrence rates among the three groups (both negative, CT solid score >80% or high periostin expression, or both positive) were significantly different (log-rank test, P<0.001). Although the solid component is already known to be a major predictor of outcome in lung adenocarcinomas according to previous studies, the combined analysis of CT solid score and periostin expression might predict the likelihood of tumor recurrence more precisely.

Reversible Stepwise Condensation Polymerization with Cyclization: Strictly Alternating Co-polymerization and Homopolymerization Based upon Two Orthogonal Reactions

In a preceding work [M. Lang, K. Kumar, A simple and general approach for reversible condensation polymerization with cyclization, Macromolecules 54 (2021) 7021], we have introduced a simple recursive scheme that allows to treat stepwise linear reversible polymerizations of any kind with cyclization. This approach is used to discuss the polymerization of linear Gaussian strands (LGS) with two different reactive groups $A$ and $B$ on either chain end that participate in two orthogonal reactions and the strictly alternating copolymerization of LGS that carry $A$ reactive groups with LGS equipped with type $B$ reactive groups. The former of these cases has not been discussed theoretically in literature, the latter only regarding some special cases. We provide either analytical expressions or exact numerical solutions for the general cases with and without cyclization. Weight distributions, averages, polydispersity, and the weight fractions of cyclic and linear species are computed. All numerical solutions were tested by Monte-Carlo simulations.

Numerical investigation on compressive arch action of prestressed concrete beam-column assemblies against progressive collapse

To investigate the compressive arch action (CAA) of prestressed concrete beam-column assemblies, bonded prestressed concrete (BPC) assembly models were established and validated using previous experimental data. The beneficial effect of CAA on the progressive collapse resistance of BPC structures is quantified by the load increase factor η, and the CAA of BPC assemblies with four layout schemes of prestressed tendons is investigated. Furthermore, the effect of seven parameters on the progressive collapse resistance of BPC assemblies with parabolic strands is determined. A model is proposed to evaluate the CAA of BPC assemblies. The results indicate that the CAA capacity of BPC assemblies differs with different strand layout schemes. Parabolic strands aggravate the failure of the area near the middle column; the contribution of linear strands is the smallest; the resistance of parallel strands is similar to that of X-shaped strands. Moreover, the ratio of prestressed tendons, the ratio of non-prestressed reinforcement at the top and bottom of the beam, and the section dimensions of the column have a significant impact on the load increase factor. The proposed models were validated against both experimental and simulation results with a mean error of less than 5%.

Certain homological invariants of bipartite kneser graphs

In this paper, we obtain a combinatorial formula for computing the Betti numbers in the linear strand of edge ideals of bipartite Kneser graphs. We deduce lower and upper bounds for regularity of powers of edge ideals of these graphs in terms of associated combinatorial data and show that the lower bound is attained in some cases. Also, we obtain bounds on the projective dimension of edge ideals of these graphs in terms of combinatorial data.

Rolling-circle and strand-displacement mechanisms for non-enzymatic RNA replication at the time of the origin of life

It is likely that RNA replication began non-enzymatically, and that polymerases were later selected to speed up the process. We consider replication mechanisms in modern viruses and ask which of these is possible non-enzymatically, using mathematical models and experimental data found in the literature to estimate rates of RNA synthesis and replication. Replication via alternating plus and minus strands is found in some single-stranded RNA viruses. However, if this occurred non-enzymatically it would lead to double-stranded RNA that would not separate. With some form of environmental cycling, such as temperature, salinity, or pH cycling, double-stranded RNA can be melted to form single-stranded RNA, although re-annealing of existing strands would then occur much faster than synthesis of new strands. We show that re-annealing blocks this form of replication at a very low concentration of strands. Other kinds of viruses synthesize linear double strands from single strands and then make new single strands from double strands via strand-displacement. This does not require environmental cycling and is not blocked by re-annealing. However, under non-enzymatic conditions, if strand-displacement occurs from a linear template, we expect the incomplete new strand to be almost always displaced by the tail end of the old strand through toehold-mediated displacement. A third kind of replication in viruses and viroids is rolling-circle replication which occurs via strand-displacement on a circular template. Rolling-circle replication does not require environmental cycling and is not prevented by toehold-mediated displacement. Rolling-circle replication is therefore expected to occur non-enzymatically and is a likely starting point for the evolution of polymerase-catalysed replication.

Validation of the plasmid study to relate DNA damaging effects of radionuclides to those from external beam radiotherapy

IntroductionThe biological consequences of absorbed radiation doses are ill-defined for radiopharmaceuticals, unlike for external beam radiotherapy (EBRT). A reliable assay that assesses the biological consequences of any radionuclide is much needed. Here, we evaluated the cell-free plasmid DNA assay to determine the relative biological effects of radionuclides such as Auger electron-emitting [67Ga]GaCl3 or [111In]InCl3 compared to EBRT. MethodsSupercoiled pBR322 plasmid DNA (1.25 or 5 ng/μL) was incubated with 0.5 or 1 MBq [67Ga]GaCl3 or [111In]InCl3 for up to 73 h or was exposed to EBRT (137Cs; 5 Gy/min; 0–40 Gy). The induction of relaxed and linear plasmid DNA, representing single and double strand breaks, respectively, was assessed by gel electrophoresis. Chelated forms of 67Ga were also investigated using DOTA and THP. Topological conversion rates for supercoiled-to-relaxed (ksrx) or relaxed-to-linear (krlx) DNA were obtained by fitting a kinetic model. ResultsDNA damage increased both with EBRT dose and incubation time for [67Ga]GaCl3 and [111In]InCl3. Damage caused by [67Ga]GaCl3 decreased when chelated. [67Ga]GaCl3 proved more damaging than [111In]InCl3; 1.25 ng/μL DNA incubated with 0.5 MBq [67Ga]GaCl3 for 2 h led to a 70% decrease of intact plasmid DNA as opposed to only a 19% decrease for [111In]InCl3. For both EBRT and radionuclides, conversion rates were slower for 5 ng/μL than 1.25 ng/μL plasmid DNA. DNA damage caused by 1 Gy EBRT was the equivalent to damage caused by 0.5 MBq unchelated [67Ga]GaCl3 and [111In]InCl3 after 2.05 ± 0.36 and 9.3 ± 0.77 h of incubation, respectively. ConclusionsThis work has highlighted the power of the plasmid DNA assay for a rapid determination of the relative biological effects of radionuclides compared to external beam radiotherapy. It is envisaged this approach will enable the systematic assessment of imaging and therapeutic radionuclides, including Auger electron-emitters, to further inform radiopharmaceutical design and application.

Revisiting the problem of crystallisation and melting of selenium

In this paper, we study the structure of the solid selenium (Se) formed by the vapor deposition method. We provide direct visual evidence that faceted crystal-like shapes obtained from vapor phase deposition are a self-assembly of linear strands that have a persistence length of 10 μm. These strands are held together by weak forces and can easily be separated. These chains occasionally get entangled to form chiral structures and often meander about destroying long range orientation and translation order in a continuous manner. Moreover, it is easy for the long strands of linear chains to slide past the neighboring ones, and hence the system has a large concentration of disinclination like defects in addition to the defects caused by the entanglement of the chains. Like organic polymers, the obtained Se structures also exhibit a spread in the melting temperature. This spread is closely related to the density of the sub-structures present in the system. The infrared imaging shows that these structures heat up in an inhomogeneous manner and the cross polarized images show that the process of melting initiates in the bulk.

Electrochemical biosensor for the detection of a sequence of the TP53 gene using a methylene blue labelled DNA probe

The development of an electrochemical biosensor utilising a hairpin DNA probe labelled with methylene blue for the detection of the TP53 gene is described. Structural rearrangement of the hairpin probe into a linear double DNA strand induced different rates of electron transfer that enabled an increase in current upon hybridization. The increase in current observed upon hybridization was studied at different surface probe densities, hybridization times, concentration and length of target DNA sequences. The biosensor selectively detected a single nucleotide polymorphism in the TP53 gene affecting residue 175 of the p53 protein, with the response more pronounced at shorter hybridization times. Detection of target DNA sequences at nanomolar concentrations was achieved and the sensor possessed good operational and storage stability.

A Comparative Evaluation of Natural and Synthetic Binder Systems and their Influence on the Thermal and Mechanical Properties of Gallic Acid‐KNO3‐KClO3 Tertiary Pyrotechnic Mixture

AbstractTannic acid is a natural binder that was comparatively investigated against four different types of conventional synthetic binders phenol‐formaldehyde resin, carboxymethyl cellulose sodium salt, ethylcellulose, and hydroxyethylcellulose which are being used in aerosol forming pyrotechnic formulations for firefighting application. It has been found that the nature of the binder in an amount of 3 % significantly influences the fire suppression performance, thermal and mechanical characteristics of gallic acid‐based aerosol‐forming pyrotechnic mixture. The safety and performance characteristics of these formulations were evaluated by conducting analysis specific to pyrotechnic formulations, i. e., calorimetric analysis, linear solid strand burn rate measurement, TGA/DSC thermal analysis, compression test, moisture content, and fire suppression test. These formulations were designed to discharge fire extinguishing aerosol and it can be inferred from the values obtained from these analyses that tannic acid is a preferred binder to the other four binder systems for the Gallic acid‐KNO3‐KClO3 pyrotechnic mixture.

Linear strands of edge ideals of multipartite uniform clutters

We construct the first linear strand of the minimal free resolutions of edge ideals of d -partite d -uniform clutters. We show that the first linear strand of such ideals are supported on relative simplicial complexes . In the case that the edge ideals of such clutters have linear resolutions, we give an explicit and surprisingly simple description of their minimal free resolutions, generalizing known resolutions for edge ideals of Ferrers graphs and hypergraphs and co-letterplace ideals. As an application, we show that the Lyubeznik numbers that appear on the last column of the Lyubeznik table of the cover ideal of such clutters are Betti numbers of certain simplicial complexes. Furthermore, we restate a characterization for edge ideals of d -partite d -uniform clutters which have linear resolutions based on the recent characterization of arithmetically Cohen-Macaulay sets of points in multiprojective spaces.

Stochastic Model of Randomly End-Linked Polymer Network Microregions

Polymerization and formation of crosslinked polymer networks are important processes in manufacturing, materials fabrication, and in the case of hydrated polymer networks, synthesis of biomedical materials, drug delivery, and tissue engineering. While considerable research has been devoted to the modeling of polymer networks to determine averaged, mean-field, global properties, there are fewer studies that specifically examine the variance of the composition across "micro-regions" (composed of a large, but finite, number of polymer network strands) within the larger polymer network.Here, we mathematically model the stochastic formation of polymer networks comprised of linear homobifunctional network strands that undergo an end-linking gelation process. We introduce a master equation that describes the evolution of the probabilities of possible network micro-region configurations as a function of time and extent of reaction. We specifically focus on the dynamics of network formation and the statistical variability of the gel micro-regions, particularly at intermediate extents of reaction. We also consider possible annealing effects and study how cooperative binding between the two end-groups on a single network-strand affects network formation. Our results allow for a more detailed and thorough understanding of polymer network dynamics and variability of network properties.

State Complexity of Overlap Assembly

The state complexity of a regular language [Formula: see text] is the number [Formula: see text] of states in a minimal deterministic finite automaton (DFA) accepting [Formula: see text]. The state complexity of a regularity-preserving binary operation on regular languages is defined as the maximal state complexity of the result of the operation where the two operands range over all languages of state complexities [Formula: see text] and [Formula: see text], respectively. We determine, for [Formula: see text], [Formula: see text], the exact value of the state complexity of the binary operation overlap assembly on regular languages. This operation was introduced by Csuhaj-Varjú, Petre, and Vaszil to model the process of self-assembly of two linear DNA strands into a longer DNA strand, provided that their ends “overlap”. We prove that the state complexity of the overlap assembly of languages [Formula: see text] and [Formula: see text], where [Formula: see text] and [Formula: see text], is at most [Formula: see text]. Moreover, for [Formula: see text] and [Formula: see text] there exist languages [Formula: see text] and [Formula: see text] over an alphabet of size [Formula: see text] whose overlap assembly meets the upper bound and this bound cannot be met with smaller alphabets. Finally, we prove that [Formula: see text] is the state complexity of the overlap assembly in the case of unary languages and that there are binary languages whose overlap assembly has exponential state complexity at least [Formula: see text].