Order In Coupling Research Articles

Prediction of Antibody-Antigen Binding via Machine Learning: Development of Data Sets and Evaluation of Methods

Background The mammalian immune system is able to generate antibodies against a huge variety of antigens, including bacteria, viruses, and toxins. The ultradeep DNA sequencing of rearranged immunoglobulin genes has considerable potential in furthering our understanding of the immune response, but it is limited by the lack of a high-throughput, sequence-based method for predicting the antigen(s) that a given immunoglobulin recognizes. Objective As a step toward the prediction of antibody-antigen binding from sequence data alone, we aimed to compare a range of machine learning approaches that were applied to a collated data set of antibody-antigen pairs in order to predict antibody-antigen binding from sequence data. Methods Data for training and testing were extracted from the Protein Data Bank and the Coronavirus Antibody Database, and additional antibody-antigen pair data were generated by using a molecular docking protocol. Several machine learning methods, including the weighted nearest neighbor method, the nearest neighbor method with the BLOSUM62 matrix, and the random forest method, were applied to the problem. Results The final data set contained 1157 antibodies and 57 antigens that were combined in 5041 antibody-antigen pairs. The best performance for the prediction of interactions was obtained by using the nearest neighbor method with the BLOSUM62 matrix, which resulted in around 82% accuracy on the full data set. These results provide a useful frame of reference, as well as protocols and considerations, for machine learning and data set creation in the prediction of antibody-antigen binding. Conclusions Several machine learning approaches were compared to predict antibody-antigen interaction from protein sequences. Both the data set (in CSV format) and the machine learning program (coded in Python) are freely available for download on GitHub.

3S-LEADERSHIP MODEL AS A TOOL OF USING DESIGN THINKING IN THE SYSTEM OF PUBLIC GOVERNANCE

The problem of integrated implementation of technology and techniques of design thinking, design management and design leadership into public administration should be considered a priority, as this area is the institutional component that determines the level of either innovative development of a society or its stagnation and decline. The dynamic changes in the intellect, mentality, experience, life values and orientations of modern people set new requirements for leaders in the age of intellectual economy, therefore traditional theories and models of leadership no longer meet the needs of group design-thinking. The purpose of this study is to determine a leadership model most adequate to the principles and criteria of design thinking so as to adapt it to the priority use in the processes and procedures of public administration. The tasks of the study are to analyze the expediency of changes in traditional leadership models and tools oriented to new requirements for design leaders; to outline the conditions for the effective management in the “leader-follower” pair in order to substantiate the role of a leader in design-thinking process and identify the leader’s influence on the group’s performance depending on the level of his/her mastery of using design thinking methodology; to assess the level of adequacy of the 3S leadership model to the criteria and methods of design thinking. To reach the objectives of the article the method of comparative analysis was used. The results of the analysis of the known models of design thinking processes revealed that this process is a fundamental condition and basis for leaders to create an atmosphere of effective use of their own intellect and the intellect of their followers in “leader-follower” pair for joint creativity and innovation. The conclusions of the study draw attention to the feasibility of and conditions for integrating the intellect of “leader-follower” pair and using for this purpose a model of 3S-leadership, based on common behavioral phenomena of synarchy, syntelect and synergy of its members. The main condition for the group to use design thinking technology efficiently has been defined as the mastery of design thinking methodology by its leader with the simultaneous use of the 3S-leadership model to influence followers, which will allow all group members to re-orient to the criteria of the 3S-model, their intellectual activity to be organized according to the recommendations of design thinking, and the leader to transform into a real design-leader who ensures a collective synergistic effect, i.e. a joint innovative product. Authors believe that the results of this study will contribute to the development of programs for training design-thinking leaders for the national system of public administration.

PEACE AND PERFORMANCE (2P) PARADIGM ON ICT PROFESSIONALS

The two core dependencies of any employee to work happily or even excel in career are Performance and Peace . Peace is defined here as the mental state or stress-free condition for one to use the mind and brain to perform at the optimum level. No one likes to be labeled as a non-performer and no one wants to lose their peace of mind. The need for performance and peace is a natural need in every employee, thus in the new era of human development, following the 2P thirst will be a more suitable and effective method as opposed to forcing and pushing through. The 2P Paradigm wishes to reveal a new vision. The performer and performance should never be separated. Personal Peace and work performance should go together so that the performer performs well. The ultimate aim of Performance is and Peace is an effective means to sustainable Performance In the 2P Paradigm. Both are means and ends. Each is needed and knitted with each other. They are the natural synergizing opposite pairs of order. They should not be separated, like how the protons should not be separated from the electrons in an atom. With the current emphasis on digital economy by the government, ICT organization performance need to be focused. Hence, the 2P paradigm is critically important in ICT organization and department

Runge–Kutta pairs of orders 8(7) with extended stability regions for addressing linear inhomogeneous systems

The non‐stiff Initial Value Problem is a wider subject classified in Mathematics. Here, we consider an interesting subclass. Namely, the Linear Inhomogeneous system that shares constant coefficients. Runge–Kutta pairs of high orders are chosen in order to achieve stringent accuracies when solving these systems numerically. It is theoretically interesting to equip these methods with large stability intervals for addressing the problems at hand. Thus, at first, we present an explicit algorithm for deriving the coefficients of such pairs of orders eight and seven. Then we adjust this in an optimization precess for extending the stability region and simultaneously keep the principal truncation error as low as possible. The resulting pair outperforms other standard pairs in a series of relevant problems.

Pengendalian Persediaan Material Heel Counter A1004 Pada Sepatu Predator P2-P3 Family Dengan Metode Material Requirement Planning (Studi Kasus di Perusahaan Sepatu)

Raw materials are a very important point for a company. Raw materials owned by a company to support the smooth production process, because with good raw material management will be able to save raw material costs so as to minimize costs. All shoe models are developed in advance in the Development department using the required materials and components according to the concept from Adidas as their buyer. In the supply of materials, the Development department purchases the Heel Counter (HC) A1004 in pairs and in its use, there is often a shortage of stock on the Predator P2 and P3 models in size 6T, resulting in delays in making shoes for delivery to Adidas. This study aims to determine the analysis of material inventory with the Material Requirement Planning (MRP) method so that there is no shortage of stock again. This study uses lot sizing EOQ and POQ techniques, Safety Stock, Re-order Point and looking for ordering frequency in order to solve the problem of existing stock shortages. The results showed that orders made to avoid stock shortages were ordering using the POQ method with an average purchase of 140 pairs per purchase, 41 pairs of safety stock, 71 pairs of re-order points and frequency order once a month. Keywords : MRP, EOQ, POQ, Safety Stock, ROP, Frequency

Competing instabilities of the extended Hubbard model on the triangular lattice: Truncated-unity functional renormalization group and application to moiré materials

A simple yet paradigmatic model for the interplay of strong electronic correlations and geometric frustration is the triangular lattice Hubbard model. Recently it was proposed that moir\'e structures of transition metal dichalcogenides can be used to simulate extended versions that include non-local density-density interactions. We study competing instabilities of interacting electrons in such an extended Hubbard model on the triangular lattice near a filling where the density of states has a Van Hove singularity. We employ a truncated-unity functional renormalization group approach to investigate two cases: a paradigmatic minimally extended Hubbard model and a specific model with parameters that are applicable to hetero-bilayers of transition metal dichalcogenides. We unravel rich phase diagrams, including tendencies to spin-density-wave order and unconventional pairing, which can give rise to topological superconductivity. We classify the symmetry of the superconducting instabilities according to their irreducible representations and show that higher lattice harmonics are dominant when the nearest-neighbor interaction is sizable indicating pair formation between second-nearest neighbors. The phenomenological consequences can be enhanced spin and thermal quantum Hall responses in a topological superconductor.

Density-induced BCS-Bose evolution in gated two-dimensional superconductors: The role of the interaction range in the Berezinskii-Kosterlitz-Thouless transition

We discuss the evolution from Bardeen-Cooper-Schrieffer (BCS) to Bose superconductivity vs. carrier density n in two-dimensional (2D) gated superconductors and address the fundamental role that the interaction range plays in the Berezinskii-Kosterlitz-Thouless transition. We investigate the density dependence of the critical temperature (T c ), superfluid density, order parameter modulus, chemical potential and pair size. Our most important finding is that it is absolutely essential to include classical and quantum phase fluctuations, as well as finite-ranged interactions to explain the non-monotonic behavior of T c vs. n and to guarantee that the upper bound on T c is not exceeded in 2D superconductors, as experimentally observed in (Nakagawa Y. et al., Science, 372 (2021) 190), a lithium-intercalated layered nitride, and in magic-angle twisted trilayer graphene (Park J. M. et al., Nature, 590 (2021) 249). Furthermore, we show that we can extract, from measurements of T c and the order parameter modulus, the effective mass of charge carriers and their interaction strength and range.

An Underwater Cooperative Spectrum Sharing Protocol for a Centralized Underwater Cognitive Acoustic Network.

To efficiently utilize nonexclusive underwater acoustic frequencies, we propose an Underwater Cooperative Spectrum Sharing (UCSS) protocol for a centralized underwater cognitive acoustic network that mainly consists of two parts. In the first part, to check the random occurrence of interferers periodically, the time domain is divided into frames that consist of a sensing and a non-sensing sub-frame. Then, we set the ratio of the two sub-frames to enhance the sensing rate via simulations. As a result, there exists the upper limit of the ratio, which can be used for determining the proportion of the sensing time within a frame. The second part is to design two heuristic resource allocation (RA) algorithms. One is a multiround RA (MRRA), where a central entity allocates a data channel (i.e., resource) to a CU each round so that multiple rounds are executed until no CUs need to be allocated or there is a lack of data channels. The other is a single-round RA (SRRA), where a CU is allocated to as many data channels as its QoS within a round. We also specify four rules to determine the allocation order of the CUs: random, fixed, high-QoS-based, and low-channel allocation-rate-based. In this study, we investigate the best RA allocation order pair supporting the highest channel allocation rate and fairness index via extensive simulations. It is shown that the MRRA outperformed the SRRA, regardless of allocation orders at any conditions, and the random and low-channel allocation-rate-based allocation orders with MRRA supported the best performance. In particular, even without the optimization process, the MRRA guarantees more than 95% fairness.

AFFINE LOGIC FOR CONSTRUCTIVE MATHEMATICS

AbstractWe show that numerous distinctive concepts of constructive mathematics arise automatically from an “antithesis” translation of affine logic into intuitionistic logic via a Chu/Dialectica construction. This includes apartness relations, complemented subsets, anti-subgroups and anti-ideals, strict and non-strict order pairs, cut-valued metrics, and apartness spaces. We also explain the constructive bifurcation of some classical concepts using the choice between multiplicative and additive affine connectives. Affine logic and the antithesis construction thus systematically “constructivize” classical definitions, handling the resulting bookkeeping automatically.

Discrete adjoint implicit Peer methods in optimal control

It is well known that in the first-discretize-then-optimize approach in the control of ordinary differential equations the discrete adjoint method may converge under additional order conditions only. For Peer two-step methods we derive such adjoint order conditions and pay special attention to different formulations and boundary steps. For s-stage methods, we prove convergence of order s for the state variables if the adjoint method satisfies the conditions for order s−1, at least. We remove some bottlenecks at the boundaries encountered in an earlier paper of Schröder et al. (2014) and discuss the construction of 3-stage methods for the order pair (3,2) in detail. The impact of nodes having equal differences is highlighted. It turns out that the most attractive methods are related to backward differentiation formulas. Three 3-stage methods are constructed, which show the expected orders in numerical tests.

On discrete coherent pairs of measures

In Castillo and Mbouna [On another extension of coherent pairs of measures, Indag. Math. 31 (2020), pp. 223–234], the concept of -coherent pairs of order with index M is introduced. This definition, implicitly related with the standard derivative operator, automatically leaves out the so-called discrete orthogonal polynomials. The purpose of this note is twofold: first, we use the (discrete) Hahn difference operator and rewrite the known results in this framework; second, as an application, we describe exhaustively the (discrete) self-coherent pairs in the situation whether M = 0, , and . This is proved by describing in a unified way the classical orthogonal polynomials with respect to Jackson's operator as special or limiting cases of a four parametric family of q-polynomials.

Fitted modifications of Runge–Kutta–Nyström pairs of orders 7(5) for addressing oscillatory problems

Runge–Kutta–Nyström pair of orders 7(5) using six stages per step have been discovered very recently. Here we modify four of its weights. The resulting method integrates exactly the harmonic oscillator , which serves as model problem. The new weights are perturbations of the original ones. Order reduction which is usually present in such modifications is avoided. Numerical results over standard six stages pairs justify our efforts.

Learning About Allosteric Drugs and Ways to Design Them

While the accelerating quest for precision medicine requires new individually targeting and selective drugs, and the ability to work with so-called undruggable targets, the realm of allosteric drugs meeting this need remains largely uncharted. Generalizing the observations on two major drug targets with widely observed inherent allostery, GPCRs and kinases, we describe and discuss basic allosteric modes of action that are universally applicable in all types of structures and functions. Using examples of Class A GPCRs and CMGC protein kinases, we show how Allosteric Signalling and Probing Fingerprints can be used to identify potential allosteric sites and reveal effector-leads that may serve as a starting point for the development of allosteric drugs targeting these regulatory sites. A set of distinct characteristics of allosteric ligands was established, which highlights the versatility of their design and make them advantageous before their orthosteric counterparts in personalized medicine. We argue that rational design of allosteric drugs should begin with the search for latent sites or design of non-natural binding sites followed by fragment-based design of allosteric ligands and by the mutual adjustment of the site-ligand pair in order to achieve required drug efficacy. On the basis of the perturbative nature and reversibility of allosteric communication, we propose a generic protocol for computational design of allosteric effectors, enabling also the allosteric tuning of biologics, in obtaining allosteric control over protein functions.

Speech recognition rates and acoustic analyses of English vowels produced by Korean students

English vowels play an important role in verbal communication. However, Korean students tend to experience difficulty pronouncing a certain set of vowels despite extensive education in English. The aim of this study is to apply speech recognition software to evaluate Korean students’ pronunciation of English vowels in minimal pair words and then to examine acoustic characteristics of the pairs in order to check their pronunciation problems. Thirty female Korean college students participated in the recording. Speech recognition rates were obtained to examine which English vowels were correctly pronounced. To compare and verify the recognition results, such acoustic analyses as the first and second formant trajectories and durations were also collected using Praat. The results showed an overall recognition rate of 54.7%. Some students incorrectly switched the tense and lax counterparts and produced the same vowel sounds for qualitatively different English vowels. From the acoustic analyses of the vowel formant trajectories, some of these vowel pairs were almost overlapped or exhibited slight acoustic differences at the majority of the measurement points. On the other hand, statistical analyses on the first formant trajectories of the three vowel pairs revealed significant differences throughout the measurement points, a finding that requires further investigation. Durational comparisons revealed a consistent pattern among the vowel pairs. The author concludes that speech recognition and analysis software can be useful to diagnose pronunciation problems of English-language learners.

Dynamic transition from insulating state to η -pairing state in a composite non-Hermitian system

The dynamics of Hermitian many-body quantum systems has long been a challenging subject due to the complexity induced by the particle-particle interactions. In contrast, this difficulty may be avoided in a well-designed non-Hermitian system. The exceptional point (EP) in a non-Hermitian system admits a peculiar dynamics: the final state being a particular eigenstate, coalescing state. In this work, we study the dynamic transition from a trivial insulating state to an $\ensuremath{\eta}$-pairing state in a composite non-Hermitian Hubbard system. The system consists of two subsystems, A and B, which are connected by unidirectional hoppings. We show that the dynamic transition from an insulating state to an $\ensuremath{\eta}$-pairing state occurs by the probability flow from A to B: the initial state is prepared as an insulating state of A, while B is left empty. The final state is an $\ensuremath{\eta}$-pairing state in B but empty in A. Analytical analyses and numerical simulations show that the speed of relaxation of the off-diagonal long-range order pair state depends on the order of the EP, which is determined by the number of pairs and the fidelity of the scheme is immune to the irregularity of the lattice.

Method of increasing students' activity through physical culture

The research work is devoted to the problem of reducing the overall activity of students in academic and extracurricular activities. The study of the reasons for the reduced activity Ъof university students, ways to increase motivation to lead a healthy lifestyle by interviewing students of 1 - 3 courses of different training areas in SSUGT. Based on the analyzed survey, methodological recommendations were compiled for educational institutions on actions aimed at popularizing an active lifestyle to reduce the number of inactive students. The main recommendations are to improve the conditions for comfortable physical education, the creation of student sports clubs among students who are not professionally involved in sports and conducting five-minute breaks for physical warm-up during training pairs in order to increase the assimilation of educational material.

An RTS–CTS based medium access control protocol for full-duplex wireless local area networks

In-band full-duplex (IB-FD) wireless is a promising next generation communication technology which can double the spectral efficiency with respect to the conventional in-band half-duplex (IB-HD) radio. Hidden stations degrade the performances of any practical wireless networks, but unlike IB-HD networks, hidden station scenarios are different in IB-FD wireless networks. In this paper, we have presented a novel energy-efficient medium access control protocol exploiting the network allocation vector, whereby mitigating the hidden station problem in an IB-FD wireless network. Moreover, an analytical model has been devised to unveil the impact of the distance between a primary–secondary transceiver pair in order to select a secondary receiver to initiate a successful relay like IB-FD link, thereby diminishing the inter-station interference problem. In addition, we have shown that the number of IB-FD transmission link increases if the secondary transmitter uses adaptive transmission power. We have evaluated the performance of the proposed protocol through detailed simulations using a modified version of NS-3 in which the wireless module has been re-designed to accommodate the concept of IB-FD radio. Results show that our proposed protocol achieves at least 61% and 41% throughput gain and consumes 58% and 60% lower energy than IEEE 802.11 DCF RTS–CTS and FD-MAC protocols, respectively. Our proposed protocol outperforms the baseline protocols with respect to throughput, energy consumption, average re-transmission rate, average packet drop rate, etc. The proposed scheme can be very useful to IB-FD wireless networks which contain bandwidth-hungry applications.

New family for Runge‐Kutta‐Nyström pairs of orders 6(4) with coefficients trained to address oscillatory problems

In this paper, we consider the integration of the special second‐order initial value problem (IVP) by Runge‐Kutta‐Nyström (RKN) pairs of algebraic orders 6 and 4. For achieving this, we have to solve a certain set of order conditions. The main contribution of the present work is that we introduce a new methodology of solving them that possesses nine free parameters instead of four used by similar pairs until now. This family uses the FSAL (first stage as last) devise. Selecting these extra coefficients properly we may construct methods with better properties. Here, we exploit the free parameters in order to derive a pair with coefficients trained to furnish better results on problems with periodic solutions. Extensive numerical tests justify our approach.

Fast computation of matrix function-based centrality measures for layer-coupled multiplex networks.

Centrality measures identify and rank the most influential entities of complex networks. In this paper, we generalize matrix function-based centrality measures, which have been studied extensively for single-layer and temporal networks in recent years to layer-coupled multiplex networks. The layers of these networks can reflect different relationships and interactions between entities or changing interactions over time. We use the supra-adjacency matrix as network representation, which has already been used to generalize eigenvector centrality to temporal and multiplex networks. With a suitable choice of edge weights, the definition of single-layer matrix function-based centrality measures in terms of walks on networks carries over naturally to the multilayer case. In contrast to other walk-based centralities, matrix function-based centralities are parameterized measures, which have been shown to interpolate between (local) degree and (global) eigenvector centrality in the single-layer case. As the explicit evaluation of the involved matrix function expressions becomes infeasible for medium to large-scale networks, we present highly efficient approximation techniques from numerical linear algebra, which rely on Krylov subspace methods, Gauss quadrature, and stochastic trace estimation. We present extensive numerical studies on synthetic and real-world multiplex transportation, communication, and collaboration networks. The comparison with established multilayer centrality measures shows that our framework produces meaningful rankings of nodes, layers, and node-layer pairs. Furthermore, our experiments corroborate the linear computational complexity of the employed numerical methods in terms of the network size that is theoretically indicated under the assumption of sparsity in the supra-adjacency matrix. This excellent scalability allows the efficient treatment of large-scale networks with the number of node-layer pairs of order 10^{7} or higher.

On a New Family of Runge–Kutta–Nyström Pairs of Orders 6(4)

In this study, Runge–Kutta–Nyström pairs of orders 6(4) using six stages per step are considered. The main contribution of the present work is that we introduce a new family of pairs (i.e., new methodology of solution for order conditions) that possesses seven free parameters instead of four, as used by similar pairs until now. Using these extra coefficients efficiently we may construct methods with better properties. Here, we exploit the free parameters in order to derive a pair with extended imaginary stability interval. This type of method may furnish better results on problems with periodic solutions. Extended numerical tests justify our effort.