Cyclic Sequence Research Articles

High Affinity Recognition of a Selected Amino Acid Epitope within a Protein by Cucurbit[8]uril Complexation.

Supramolecular interactions between the host cucurbit[8]uril (CB[8]) and amino acids have been widely interrogated, but recognition of specific motifs within a protein domain have never been reported. A phage display approach was herein used to select motifs with the highest binding affinity for the heteroternary complex with methyl viologen and CB[8] (MV⋅CB[8]) within a vast pool of cyclic peptide sequences. From the selected motifs, an epitope consisting of three amino acid was extrapolated and incorporated into a solvent-exposed loop of a protein domain; the protein exhibited micromolar binding affinity for the MV⋅CB[8] complex, matching that of the cyclic peptide. By achieving selective CB[8]-mediated conjugation of a small molecule to a recombinant protein scaffold we pave the way to biomedical applications of this simple ternary system.

High Affinity Recognition of a Selected Amino Acid Epitope within a Protein by Cucurbit[8]uril Complexation

AbstractSupramolecular interactions between the host cucurbit[8]uril (CB[8]) and amino acids have been widely interrogated, but recognition of specific motifs within a protein domain have never been reported. A phage display approach was herein used to select motifs with the highest binding affinity for the heteroternary complex with methyl viologen and CB[8] (MV⋅CB[8]) within a vast pool of cyclic peptide sequences. From the selected motifs, an epitope consisting of three amino acid was extrapolated and incorporated into a solvent‐exposed loop of a protein domain; the protein exhibited micromolar binding affinity for the MV⋅CB[8] complex, matching that of the cyclic peptide. By achieving selective CB[8]‐mediated conjugation of a small molecule to a recombinant protein scaffold we pave the way to biomedical applications of this simple ternary system.

An Approximate Analysis of the Inner Wall Loading of a Bimetallic Camera Shell of Reusable Rocket Engine

В различных технических устройствах в качестве конструктивных элементов достаточно широко используют биметаллические оболочки. Характерным примером применения биметаллических оболочек является конструкция камеры сгорания жидкостного ракетного двигателя (ЖРД). В процессе работы ЖРД оболочка камеры сгорания подвержена интенсивным тепловым и механическим воздействиям, что приводит к необходимости ее охлаждения. Охлаждающий тракт оболочки образован зазором между ее внутренней и наружной стенками, скрепленными между собой гофрированными проставками или фрезерованными ребрами. Наружная стенка выполняет роль силового элемента оболочки, а внутренняя стенка непосредственно контактирует с высокотемпературными продуктами сгорания и подвержена интенсивному нагреву. Различие функций стенок оболочки вызывает необходимость их изготовления из разных материалов с различающимися теплофизическими и механическими характеристиками.

Isotopic fingerprints of Milankovitch cycles in Pennsylvanian carbonate platform‐top deposits: the Valdorria record, Northern Spain

AbstractSedimentary cyclic sequences deposited during the Late Palaeozoic Ice Age are widespread. Glacio‐eustatic control of the cyclic patterns is commonly accepted, and the durations of the cyclothems generally match the short‐ and long‐eccentricity Milankovitch orbital parameters. Nevertheless, geochemical fingerprints of orbital parameters are poorly documented in deep‐time sedimentary records. Here, we report on well‐exposed Bashkirian cyclothems of c. 123 ka and c. 400 ka durations from the Valdorria platform. The shorter‐term cyclothems can be grouped into longer‐term composite sequences that are consistent with generally accepted durations of c. 125 ka and c. 400 ka for Milankovitch eccentricity cycles. The stratigraphic pattern is mirrored by the isotope geochemical signals, which show distinct recurring trends. These trends are confirmed by statistical tests. Whereas intrinsic factors and/or subaerial exposure related to sea‐level lowstands might have truncated cycle patterns in tectonically stable basins, rapid subsidence of the Valdorria platform's foreland basin appears to have contributed to a faithful recording of cyclothems of different orders. The patterns and biostratigraphic constraint revealed in this study demonstrate the power of orbital forcing in imprinting sedimentary and geochemical signals in the rock record.

Universal Cycle Packings and Coverings for k-Subsets of an n-Set

A cyclic sequence of elements of [n] is an (n, k)-Ucycle packing (respectively, (n, k)-Ucycle covering) if every k-subset of [n] appears in this sequence at most once (resp. at least once) as a subsequence of consecutive terms. Let $$p_{n,k}$$pn,k be the length of a longest (n, k)-Ucycle packing and $$c_{n,k}$$cn,k the length of a shortest (n, k)-Ucycle covering. We show that, for a fixed $$k,p_{n,k}={n\atopwithdelims ()k}-O(n^{\lfloor k/2\rfloor })$$k,pn,k=nk-O(nźk/2ź). Moreover, when k is not fixed, we prove that if $$k=k(n)\le n^{\alpha }$$k=k(n)≤nź, where $$0<\alpha <1/3$$0<ź<1/3, then $$p_{n,k}={n\atopwithdelims ()k}-o({n\atopwithdelims ()k}^\beta )$$pn,k=nk-o(nkβ) and $$c_{n,k}={n\atopwithdelims ()k}+o({n\atopwithdelims ()k}^\beta )$$cn,k=nk+o(nkβ), for some $$\beta <1$$β<1. Finally, we show that if $$k=o(n)$$k=o(n), then $$p_{n,k}={n\atopwithdelims ()k}(1-o(1))$$pn,k=nk(1-o(1)).

Rank aggregation in cyclic sequences

In this paper we propose the problem of finding the cyclic sequence which best represents a set of cyclic sequences. Given a set of elements and a precedence cost matrix we look for the cyclic sequence of the elements which is at minimum distance from all the ranks when the permutation metric distance is the Kendall Tau distance. In other words, the problem consists of finding a robust cyclic rank with respect to a set of elements. This problem originates from the Rank Aggregation Problem for combining different linear ranks of elements. Next, we also introduce the problem of finding the cyclic sequence with minimum expected cost with respect to a probability measure based on dissimilarity between cyclic sequences on the Kendall Tau metric. Finally, we establish certain relationships among some classical problems and the new problems that we have proposed.

Reliability of non-repairable systems with cyclic-mission switching and multimode failure components

This paper considers a mission-based non-repairable system which has multiple and cyclic mission sequences, and whose components have multimode failures. For example, the valve system with two failure modes cannot only fail to close when required to close but can also fail to open when required to open. A discrete-time semi-Markov chain within the time evolution framework is constructed, which is more properly to model the realistic problems because the sojourn times between the successive missions may be not satisfied Markov property. Using the aggregated stochastic theory and Z-transform, the explicit form of the solution of system reliability is obtained, which can simplify calculations and get some distributions of some sojourn times that the readers relish, including perfect and imperfect operations. In addition, two special valve systems with two-mission and three-mission switching are provided respectively. Finally, numerical examples are presented to illustrate the proposed model and the method.

Putting Order into Our Universe: The Concept of Blended Learning—A Methodology within the Concept-based Terminology Framework

This paper aims at discussing the advantages of a methodology design grounded on a concept-based approach to Terminology applied to the most prominent scenario of current Higher Education: blended learning. Terminology is a discipline that aims at representing, describing and defining specialized knowledge through language, putting order into our universe (Nuopponen, 2011). Concepts, as elements of the structure of knowledge (Sager, 1990) emerge as a complex research object. Can they be found in language? A concept-based approach to Terminology implies a clear-cut view of the role of language in terminological work: though language is postulated as being a fundamental tool to grasp, describe and organize knowledge, an isomorphic relationship between language and knowledge cannot be taken for granted. In other words, the foundational premise of a concept-based approach is that there is no one-to-one correspondence between atomic elements of knowledge and atomic elements of linguistic expression. This is why a methodological approach to Terminology merely based upon specialized text research is regarded as biased (Costa, 2013). As a consequence, we argue that interactional strategies between terminologist and domain expert deserve particular research attention. To our mind, the key to concept-based terminological work is to carry out a concept analysis of data gathered from a specialised text corpora combined with an elicitation process of the tacit knowledge and concept-oriented discursive negotiation. Following such view, we put forward a methodology to answer the question: how is blended learning defined in the Post-Bologna scenario? Even though there are numerous high-quality models and practical descriptions for its implementation (similarly to other concepts related to distance learning), the need to understand, demarcate and harmonize the concept of blended learning against the current Higher Education background results from the premise that the theoretical reflection on this concept is still insufficient. Therefore, we believe it is vital to understand blended learning as the new normal in Higher Education (Norberg et al., 2011), or a negotiable third way (Peres, 2011; Norberg &amp; Jahnke, 2014). Our methodological model is built in three phases: (1) exploratory phase in the area/ object of the study; (2) conceptual analysis phase of discourse and textual documents; (3) modeling and result validation phase. We support the thesis that the experimental nature of this approach discloses productivity in a cyclical sequence between the discursive and textual analysis with conceptual objectives, collaborative interaction and introspection. In other words, even though the nature of this study does not allow for a generalization (apart from a dual relation in the mediation between the terminologist and the specialist), we advocate the relevance of an action-reflection procedure, both introspective and collaborative, one in which the terminologist will become a conceptualizer, a decision-maker and an interventionist.

Effects of cyclic axial loading sequences on piles in sand

The cyclic axial behaviour of piled foundations in sand is studied using centrifuge tests. Model piles are partially jacked in flight. Loads are applied to identify cyclic tension loading effects in stable and meta-stable zones on pile behaviour and physical failure. Failure occurs with larger displacements than those achieved during monotonic loading tests. Sequences of 200 cycles with three different amplitudes are applied in different orders. With the same total amount of cycles, final displacements are different and potentially lead to failure. The order of the cyclic sequences significantly affects pile behaviour; however, this is not taken into account or even mentioned in standards.

On the Shift Value Set of Cyclic Shifted Sequences for PAPR Reduction in OFDM Systems

Orthogonal frequency division multiplexing (OFDM) signals have high peak-to-average power ratio (PAPR), which causes distortion when OFDM signal passes through a nonlinear high power amplifier. A partial transmit sequence (PTS) scheme is one of the typical PAPR reduction methods. A cyclic shifted sequences (CSSs) scheme is evolved from the PTS scheme to improve the PAPR reduction performance, where OFDM signal subsequences are cyclically shifted and combined to generate alternative OFDM signal sequences. The shift value (SV) sets in the CSS scheme should be carefully selected because those are closely related to the PAPR reduction performance of the CSS scheme. In this letter, we propose some criteria to select the good SV sets and verify its validness through simulations.

Some cyclic codes with prime length from cyclotomy of order 4

Cyclic codes are a subclass of linear codes and are widely used in many applications as they have efficient encoding and decoding algorithms. In this paper, we investigate two classes of cyclic codes over źźq$\mathbb {F}_{q}$ with prime length using cyclotomy of order 4. Both the dimensions and the generator polynomials are explicitly determined. The method serves as a connection between cyclic codes and sequences over źźq$\mathbb {F}_{q}$ whose supports are the unions of certain cyclotomic classes of order 4. The main results thus partially answer two open problems in Ding (2015).

Wavelet Analysis on Symbolic Sequences and Two-Fold de Bruijn Sequences

The concept of symbolic sequences play important role in study of complex systems. In the work we are interested in ultrametric structure of the set of cyclic sequences naturally arising in theory of dynamical systems. Aimed at construction of analytic and numerical methods for investigation of clusters we introduce operator language on the space of symbolic sequences and propose an approach based on wavelet analysis for study of the cluster hierarchy. The analytic power of the approach is demonstrated by derivation of a formula for counting of {\it two-fold de Bruijn sequences}, the extension of the notion of de Bruijn sequences. Possible advantages of the developed description is also discussed in context of applied p

Models of optimum discrete signals on the ring combinatorial configurations

The innovative techniques for improving the quality indices of radio-signals for communications and radars with non-uniform structure (e.g. code sequences) with respect to error protection, using novel combinatorial configurations such as cyclic difference sets and Ideal Ring Bundles (IRB)s was regarded. Method for construction of optimum discrete signals, based on these models is proposed. IRBs are cyclic sequences of positive integers, which form perfect partitions of a finite interval [1,N]. The sums of connected sub-sequences of an IRB enumerate the set of integers [1,N-1] exactly R-times. This property makes IRBs useful in applications, which need to partition sets with the smallest possible number of intersections. The models of optimum discrete signals, having previously unknown favorable property, which hold for the same set of the IRBs in varieties permutations of its terms, named the "Glory to Ukraine Stars” have been indicated as a cluster of combinatorial configurations. Some algorithms and useful examples for constructing of optimum cyclic error-correcting codes presented. It shows that remarkable properties of IRBs have encoded in fine structure of circular symmetry and asymmetry ensembles. There are great classes of new two- and multidimensional IRBs, which being in excess classic models of optimum discrete signals with respect to number and combinatorial varieties. Indicate that the IRBs to be in exceed of classic perfect difference sets multiply.

A class of binary cyclic codes and sequence families

For two odd integers l, k with \(0<l<k\) and \(\gcd (l,k)=1\), let \(m=2k\) and \(d=\frac{2^{lk}+1}{2^l+1}+\frac{2(2^m-1)}{3}\). In this paper, we determine the value distribution of the exponential sum \(\sum _{x\in \mathbb {F}_{2^m}}(-1)^{\mathrm {Tr}_1^m(ax+bx^d)}\). As applications, the weight distribution of a class of binary cyclic codes is settled. Second, we determine the correlation distribution among sequences in a sequence family.

4-tert-butylphenoxy substituted phthalocyanine with RGD motif as highly selective one-photon and two-photon imaging probe for mitochondria and cancer cell

An unsymmetrical phthalocyanine based one- and two-photon fluorescence imaging probe that substituted with 4-tert-butylphenoxy and RDGyK moieties was developed and characterized by UV-vis and high-resolution MALDI-TOF/MS. The conjugate is non-aggregated in [Formula: see text],[Formula: see text]-dimethylformamide, with relatively weak fluorescence emission ([Formula: see text] 0.023) and high singlet oxygen quantum yield ([Formula: see text] 0.55). Conjugation of the cyclic peptide sequence c(RGDyK) can enhance the cellular uptake towards the DU145 and PC3 cells. While the fluorescence is greatly enhanced in mitochondria, the conjugate is non-cytotoxicity either in dark or upon exposure to red-light with dose up to 12 J.cm[Formula: see text]. The results suggest that this conjugate is a promising multifunctional imaging probe for mitochondria and cancer.

Improving the roller shaping of large-diameter pipe from strip

Current geometric requirements on pipe—especially thin-walled pipe for gas pipelines—set strict limits on the deviation of the cross section in shaping. A special control algorithm for the drives in the sheetbending machine minimizes local geometric errors in the cross section during the roller shaping of largediameter pipe from strip. Analysis of the nonuniformity in deformation permits the formulation of a cyclic operating sequence for the drives. Experiments confirm its effectiveness. On the basis of this research, automatic control of the drives in the sheet-bending machine is possible.

How Bad Are Vandermonde Matrices?

Estimation of the condition numbers of Vandermonde matrices, motivated by applications to interpolation and quadrature, can be traced back to at least the 1970s. Empirical study has consistently shown that Vandermonde matrices tend to be badly ill-conditioned, with a narrow class of exceptions, such as the matrices of the discrete Fourier transform (hereafter we use the acronym DFT). So far, however, formal support for this empirical observation has been limited to the matrices defined by the real set of knots. We prove that, more generally, any Vandermonde matrix of a large size is badly ill-conditioned unless its knots are more or less equally spaced on or about the circle $\{x:~|x|=1\}$. The matrices of the DFT are unitary up to scaling and therefore perfectly conditioned. They are defined by a cyclic sequence of knots, equally spaced on that circle, but we prove that even a slight modification of the knots into the so-called quasi-cyclic sequence on this circle defines badly ill-conditioned Vandermonde matrices. Likewise, we prove that the half-size leading (that is, northwestern) block of a large DFT matrix is badly ill-conditioned. (This result was motivated by an application to preconditioning of an input matrix for Gaussian elimination with no pivoting and for block Gaussian elimination.) Our analysis involves the Ekkart--Young theorem, the Vandermonde-to-Cauchy transformation of matrix structure, our new inversion formula for a Cauchy matrix, and low-rank approximation of its large submatrices.

Subaerial exposure and drowning processes in a carbonate platform during the Mesozoic Tethyan rifting: The case of the Jurassic succession of Western Sicily (central Mediterranean)

The Liassic carbonate platform succession outcropping at Monte Maranfusa (central Western Sicily) consists of a shallowing-upward sequence of peritidal carbonates, with Jurassic to Paleogene pelagic limestone and siliciclastic Tertiary covers above. The cyclic sequences of subtidal wackestones/packstones, intertidal microcrystalline carbonates with bird's-eye pores, and supratidal bioclastic grainstones are interbedded with dark layers of the following composition: 1) dark-gray, compact, and well-cemented limestone with blackish clasts, interpreted as calcretes (a type of carbonate soil) and 2) reddish calcite laminae, deformed by elongated cavities, filled with vadose silt, interpreted as paleokarst. This succession is crossed by almost vertical faults, of the Late Liassic to Miocene, which often coincides with neptunian dykes, filled by several generations of Toarcian–Early Miocene pelagic sediments. Another system of dykes, known as neptunian sills, filled by injected Upper Lias–Dogger pelagic sediments, lies parallel to the stratification. The parallel dykes were caused by the flexure of the platform during the Jurassic and presumably by a planar slip in the carbonate rocks, whereas neptunian dykes are caused by faulting episodes. Here, we present evidence that the dark layers in the Liassic succession of Monte Maranfusa, previously described by many authors only as parallel dykes, can actually be interpreted as a) neptunian sills, b) pedogenic calcretes, and c) paleospeleothems. Therefore, we found evidence of exposure/flooding intervals in the evolution of the carbonate platform during the Liassic, linked to different pulses in both the subsidence/tectonic activity and the sea-level oscillations. At the top, Fe–Mn crusts (hardgrounds) seal the carbonate platform succession, which is in turn overlain by condensed pelagic deposits, confirming its drowning during rifting processes.

Computerized Tomography Noise Reduction by CICT Optimized Exponential Cyclic Sequences (OECS) Co-domain

Computerized Tomography Noise Reduction by CICT Optimized Exponential Cyclic Sequences (OECS) Co-domain

Antibody recognition in multiple sclerosis and Rett syndrome using a collection of linear and cyclic N-glucosylated antigenic probes.

Antibody detection in autoimmune disorders, such as multiple sclerosis (MS) and Rett syndrome (RTT) can be achieved more efficiently using synthetic peptides. The previously developed synthetic antigenic probe CSF114(Glc), a type I' β-turn N-glucosylated peptide structure, is able to recognize antibodies in MS and RTT patients' sera as a sign of immune system derangement. We report herein the design, synthesis, conformational analysis, and immunological evaluation of a collection of glycopeptide analogs of CSF114(Glc) to characterize the specific role of secondary structures in MS and RTT antibody recognition. Therefore, we synthesized a series of linear and cyclic short glucosylated sequences, mimicking different β-turn conformations, which were evaluated in inhibition enzyme-linked immunosorbent assays (ELISA). Calculated IC50 ranking analysis allowed the selection of the candidate octapeptide containing two (S)-2-amino-4-pentynoic acid (L-Pra) residues Ac-Pra-RRN(Glc)GHT-Pra-NH2 , with an IC50 in the nanomolar range. This peptide was adequately modified for solid-phase ELISA (SP-ELISA) and surface plasmon resonance (SPR) experiments. Pra-RRN(Glc)GHT-Pra-NH2 peptide was modified with an alkyl chain linked to the N-terminus, favoring immobilization on solid phase in SP-ELISA and differentiating IgG antibody recognition between patients and healthy blood donors with a high specificity. However, this peptide displayed a loss in IgM specificity and sensitivity. Moreover, an analog was obtained after modification of the octapeptide candidate Ac-Pra-RRN(Glc)GHT-Pra-NH2 to favor immobilization on SPR sensor chips. SPR technology allowed us to determine its affinity (KD = 16.4 nM), 2.3 times lower than the affinity of the original glucopeptide CSF114(Glc) (KD = 7.1 nM).