A primary challenge facing conservationists is reconciling the human needs of forest adjacent communities with the needs of conserving forest biodiversity, especially in tropical regions with growing populations of rural poor. Agroforestry has the potential to simultaneously provide for human needs and enhance forest biodiversity, but the complex interactions and feedbacks between the social and natural dimensions are relatively undescribed and thus systematic implementation is rare. The attributes of trees on farms required for human needs and conservation value may conflict. For example, exotic species in monoculture may provide the most economic value for farmers, while relic or planted indigenous tree mixtures may be more valuable for biological conservation. The objective of this study was to explore whether agroforestry practices in a moist tropical forest ecosystem in Kenya can simultaneously provide timber and fuelwood value to small-holder farmers while extending forest tree biodiversity. We described the agroforestry attributes on farms around a tropical forest, assessed the relationship between number and biomass of timber/fuelwood trees and tree biodiversity, and explored the relationships between forest tree diversity attributes and farm tree diversity attributes on a landscape scale using spatial analysis. We found that the diversity and number of trees on farms in this area are extensive yet variable, but that no significant relationship exists between the number of timber/fuelwood trees and tree diversity. This suggests that the two values of agroforestry may not be in conflict, due mainly to the high diversity of trees used for fuelwood. We also found that trees on farms in the larger landscape add to the conservation value of forest tree biodiversity and could be important components in conservation management. If agroforestry is to play an increasingly active role in conserving biodiversity in human-dominated landscapes, particularly in areas of dense subsistence farmer populations, increase recognition needs to be given to farmer’s perception of the value of trees and their selection of what trees to plant or maintain.

This brief note is aimed to dissociate from quantum physics contextuality, where the latter is standardly defined on the basis of families of compatible observables. In quantum physics, contextuality is just an exhibition of incompatibility of observables and, hence, Bohr's principle of complementarity. At the same time we recognize that contextuality can play the important role outside of physics.

A picture is worth a thousand words. Many branches of Science have been historically benefited with plots and visual analyses (lately, image processing and deep learning) alongside with traditional number crunching. In Molecular Biophysics, one such problem is the structure validation problem in proteins which stands with a history of plot-tools being effectively serving the complex problem to its complete resolution. Spanning across six decades, validation of protein structures (from experimental to modeled) dates back to the legendary Ramachandran Plot (with its never ending growth and modern-day applications) to the relatively recent innovation of the Complementarity Plot (CP), establishing the dual nature of complementarity as the physical basis of both binding and folding of proteins. Lately, CP has been extended to serve as a trustworthy free energy predictor utilizing supervised learning in the form of a comprehensive web-server (EnCPdock: https://www.scinetmol.in/EnCPdock/) that can be directly used in the design of protein interfaces. The commentary recapitulate the history of structure validation with a special emphasis on plot tools, highlighting key features and important discoveries worth re-visiting.

The combined efect of shape and electrostatic complementarities (Sc, EC) at the interface of the interacting protein partners (PPI) serves as the physical basis for such associations and is a strong detterminant of their binding energetics. EnCPdock (https://www.scinetmol.in/EnCPdock/) presents a comprehensive web-platform for the direct conjoint comparative analyses of complementarity and binding energetics in PPIs. It elegantly interlinks the dual nature of local (Sc) and non-local complementarity (EC) in PPIs using the Complementarity Plot. It further derives an AI-based ∆G_binding with a prediction accuracy comparable to the state-of-the-art. This book-chapter presents a practical manual to conceptualize and implement EnCPdock with its various features and functionalities, collectively having the potential to serve as a valuable protein engineering tool in the design of novel protein interfaces.

We examined how combinations of corporate social responsibility (CSR) activities lead to high performance in Korean companies. This study addressed two related questions to expand our limited knowledge in this area. The first was what combinations of CSR activities achieve high performance. The second was to identify how CSR activities form an interdependent system, depending on different corporate situations. Korean Economic Justice Institute index data, from 2012 to 2018, were used with fuzzy set qualitative comparative analysis, and the results revealed several effective CSR activity factor combinations under given strategies and management environments. Companies with high performance exhibit complementarity between social contribution, environmental management, fairness, and employee satisfaction. By contrast, companies with low corporate performance show no complementarity between relatively unrelated activity factors. For companies whose CSR activities lead to low financial performance, most of the causal pathways focused only on activities at the primary stakeholder level, with weak diversity of CSR activities’ combinations at the primary and secondary stakeholder levels. These results indicate not only the appropriateness of CSR activity factor combinations for companies’ strategy and management environment contexts, but also their effectiveness, and are expected to provide companies with significant implications for CSR activities.

The time interval set approach depends on results for radiation propagation from star sources, ie spherically symmetric, where properties relate to propagation sphere surfaces, finite for any realistic event and measurement. In contrast the usual vector and one moment time set approach from Newton’s laws, applies to stationary parallel radiation. A time interval only description necessarily has to start from it's own definitions, and properties for time intervals have to be defined with time intervals. This paper is devoted to deriving time interval only set properties commutation, addition and multiplication and derivative, and to define how these can correspond consistently to one moment time set properties. Time development within the time interval description equilibrium depends on the well-known ‘mean velocity theorem’ (MVT) and the time interval version of the Legendre transform, defined in earlier papers. Radiation propagation ‘away from’ and gravitation ‘towards’ the star source can be part of the description. In the discussion parts these properties are applied within astrophysics. Included is a integral derivation of star source radiation energy for both zero and non zero wave particle mass. The time interval set is not one of the usual sets encountered. However it’s non-linearity or non-commutativity property can be related to Noether charges and structure constants, that equal the radiation wave group-velocity, for photons the light velocity c, and, different from the usual derivative to one moment time, to specifics of the time interval only set derivative to time intervals.

This paper consists of two parts. In part I some new relations for a field theory with time intervals are derived. One concept of field theory evaluated is complementarity, another is field operators both defined within a time interval description. Part II includes specific results and commentary. Discussed are time interval dependent wave propagation surfaces for star source emission waves and derived is a metric propagation surface area requirement. The results allow to consider one same field that like gravitation within General Relativity applies to both non zero and zero mass. The associated field energy is space time dependent for non zero mass, and is related to a space time dependent metric tensor for zero mass wave particles. Defined is internal energy transfer where wave particle numbers increase linearly and mass and momentum diminish, decrease inversely with the distance from the wave emission source. The commentary are applications related to cosmological overall volume and temperature dependence.

This note is a part of my efforts for getting rid of nonlocality from quantum mechanics (QM). Quantum nonlocality is two faced Janus, one face is apparent quantum mechanical nonlocality (assigned with projection postulate), another face is nonlocality of Bell's model with the hidden variables. This paper is directed against the latter. The main casualty of Bell's model is that it contradicts to the Heinsenberg's uncertainty and Bohr's complementarity principles. The aim of this note is to point to the physical seed of the aforementioned principles. This is the {\it quantum postulate}: the existence of indivisible quantum of action given by the Planck constant. Bell's model by contradicting to the basic principles of QM implies rejection of this postulate. Thus, it contradicts not only to the QM-formalism, but also to the fundamental feature of the quantum world that was initially discovered by Planck.

COVID-19 is characterized by an unprecedented abrupt increase in the viral transmission rate (SARS-CoV-2) relative to its pandemic evolutionary ancestor, SARS-CoV (2003). The complex molecular cascade of events related to the viral pathogenicity is triggered by the Spike protein upon interacting with the ACE2 receptor on human lung cells through its receptor binding domain (RBD_Spike). One potential therapeutic strategy to combat COVID-19 could thus be limiting the infection by blocking this key interaction. In this current study, we adopt a protein design approach to predict and propose non-virulent structural mimics of the RBD_Spike which can potentially serve as its competitive inhibitors in binding to ACE2. The RBD_Spike is an independently foldable protein domain, resilient to conformational changes upon mutations and therefore an attractive target for strategic re-design. Interestingly, in spite of displaying an optimal shape fit between their interacting surfaces (attributed to a consequently high mutual affinity), the RBD_Spike–ACE2 interaction appears to have a quasi-stable character due to a poor electrostatic match at their interface. Structural analyses of homologous protein complexes reveal that the ACE2 binding site of RBD_Spike has an unusually high degree of solvent-exposed hydrophobic residues, attributed to key evolutionary changes, making it inherently ‘reaction-prone’. The designed mimics aimed to block the viral entry by occupying the available binding sites on ACE2, are tested to have signatures of stable high-affinity binding with ACE2 (cross-validated by appropriate free energy estimates), overriding the native quasi-stable feature. The results show the apt of directly adapting natural examples in rational protein design, wherein, homology-based threading coupled with strategic ‘hydrophobic ↔ polar’ mutations serve as a potential breakthrough.

This article is devoted to the results of in-depth analysis of the system of binary-oppositional structures in DNA n-plet alphabets and their algebraic-matrix representations. These results show that the molecular complementary replication of DNA strands is accompanied by the presence of an algebraic version of the principle "like begets like" in matrix representations of DNA alphabets having internal structures. This algebraic version is based on binary-oppositional structures in the genetic molecular system, which can be represented by binary numbers and corresponding matrices of DNA alphabets. The received results allow thinking that the phenomenon "like begets like" (or a complementary replication in a wide sense) is systemic in the genetic organization and is connected with algebraic features of biological organization. Correspondingly, the biological principle "like begets like" can be additionally modeled by algebraic-matrix methods and approaches. Such algebra-matrix modeling of the genetic coding system gives new ways for studying and understanding the key role of the named principle in genetic and other inherited physiological complexes. On this way, the author discovered general rules of stochastic organization of information binary sequences of genomic DNAs of eukaryotes and prokaryotes. The presented rules are connected with information dichotomies of probabilities and corresponding fractal-like trees of probabilities, which fundamentally differ from constructional dichotomies in biological bodies. The received phenomenological data and rules lead to new biological ideas.

Currently, there are two approaches to the foundations of thermodynamics. One, associated with the mechanistical Clausius-Boltzmann tradition, is favored by the physics community. The other, associated with the post-mechanical Carnot tradition, is favored by the engineering community. The bold hypothesis is that the conceptual foundation of engineering thermodynamics is the more comprehensive. Therefore, contrary to the dominant consensus, engineering thermodynamics (ET) represents the true foundation of thermodynamics. The foundational issue is crucial to a number of unresolved current and historical issues in thermodynamic theory and practice. ET formally explains the limited successes of the ‘rational mechanical’ approaches as idealizing special cases. Thermodynamic phenomena are uniquely dissymmetric and can never be completely understood in terms of symmetry-based mechanical concepts. Consequently, ET understands thermodynamic phenomena in new way, in terms of the post-mechanical formulation of action. The ET concept of action and the action framework trace back to Maupertuis’s Principle of Least Action, both clarified in the engineering worldview research program of Lazare and Sadi Carnot. Despite the intervening Lagrangian ‘mechanical idealization of action’, the original dualistic, indeterminate engineering understanding of action, somewhat unexpectedly, re-emerged in Planck’s quantum of action. The link between engineering thermodynamics and quantum theory is not spurious and each of our current formulations helps us develop our understanding of the other. Both the ET and quantum theory understandings of thermodynamic phenomena, as essentially dissymmetric (viz. embracing complementary), entail that there must be an irreducible, cumulative historical, qualitatively emergent, aspect of reality.

This article is devoted to the problem of genetically coding of inherited cyclic structures in biological bodies, whose life activity is based on a great inherited set of mutually coordinated cyclic processes. The author puts forward and arguments the idea that the genetic coding system is capable of encoding inherited cyclic processes because it itself is a system of cyclic codes connected with Boolean algebra of logic. In other words, the physiological processes in question are cyclical because they are genetically encoded by cyclic codes. In support of this idea, the author presents a set of his results on the connection of the genetic coding system with cyclic Gray codes, which are one of many known types of cyclic codes. This opens up the possibility of using for modeling inherited cyclic biostructures those algebraic and logical theories and constructions that are associated with Gray codes and have long been used in engineering technologies: Karnaugh maps, Hilbert curve, Hadamard matrices, Walsh functions, dyadic analysis, etc. Additionally, the connections of these constructions with statistical rules of genomic DNAs and binary-genomic numbers are considered.

The role of γδ T cells in vertebrate immunity is still an unsolved puzzle. Species such as humans and mice display a low percentage of these T lymphocytes (i.e., “γδ low species”) with a restricted diversity of γδ T cell receptors (TR). Conversely, artiodactyl species (i.e., “γδ high species”) ac-count for a high proportion of γδ T cells with large γ and δ chain repertoires. The genomic organisation of the TR γ (TRG) and δ (TRD) loci has been determined in sheep and cattle, noting that a wide number of germline genes that encode for γ and δ chains characterise their genomes. Taking advantage from the current improved version of the genome assembly, we have investigated the genomic structure and gene content of the dromedary TRD locus, which, as in the other mammalian species, is nested within the TR alpha (TRA) genes. The most remarkable finding was the identification of a very limited number of variable germline genes (TRDV) compared to sheep and cattle, which supports our previous expression analyses for which the somatic hypermutation mechanism is able to enlarge and diversify the primary repertoire of dromedary δ chains. Furthermore, the comparison between genomic and expressed sequences reveals that D genes, up to four incorporated in a transcript, greatly contribute to the increased diversity of the dromedary δ chain antigen binding-site.

The conventional theory of neutron beams interacting with many-body systems treats the beam as a classical system, i.e. with its dynamical variables appearing in the quantum dynamics of the scattering process not as operators but only as c-numbers. Moreover, neutrons are described with plane waves, i.e. the concept of neutron's (finite) coherence length is here irrelevant. The same holds for electron, atom or X-ray scattering. This simplification results in the full decoupling of the probe particle's dynamics from the quantum dynamics of the scatterer---a well-known fact also reflected in the standard formalism of time-correlation functions (see textbooks). Making contact with modern quantum theoretical approaches (e.g., quantum entanglement, 'which-path detection' versus interference, von Neumann measurement, Week Values, etc.) new observable effects may be exposed and/or predicted, for instance, a momentum-transfer deficit and an intensity deficit in neutron scattering from protons of hydrogen-containing samples. 7

The recent Google’s claim on breakthrough in quantum computing is a gong signal for further analysis of foundational roots of (possible) superiority of some quantum algorithms over the corresponding classical algorithms. This note is a step in this direction. We start with critical analysis of rather common reference to entanglement and quantum nonlocality as the basic sources of quantum superiority. We elevate the role of the Bohr’s principle of complementarity¹ (PCOM) by interpreting the Bell-experiments as statistical tests of this principle. (Our analysis also includes comparison of classical vs genuine quantum entanglements.) After a brief presentation of PCOM and endowing it with the information interpretation, we analyze its computational counterpart. The main implication of PCOM is that by using the quantum representation of probability, one need not compute the joint probability distribution (jpd) for observables involved in the process of computation. Jpd’s calculation is exponentially time consuming. Consequently, classical probabilistic algorithms involving calculation of jpd for n random variables can be over-performed by quantum algorithms (for big values of n). Quantum algorithms are based on quantum probability calculus. It is crucial that the latter modifies the classical formula of total probability (FTP). Probability inference based on the quantum version of FTP leads to constructive interference of probabilities increasing probabilities of some events. We also stress the role the basic feature of the genuine quantum superposition comparing with the classical wave superposition: generation of discrete events in measurements on superposition states. Finally, the problem of superiority of quantum computations is coupled with the quantum measurement problem and linearity of dynamics of the quantum state update.