Regulation of 2D DNA Nanostructures by the Coupling of Intrinsic Tile Curvature and Arm Twist

The overwinding and underwinding of duplex segments between junctions have been used in designing both left-handed and right-handed DNA origami nanostructures. For a variety of DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the DNA tile (specified as the intrinsic tile curvature) has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile curvature and its evolution in DNA tubes by the coupling of the twist of the inter-tile arm (specified as the arm twist) have never been addressed. In this work, we designed three types of tile cores built around a circular 128 nucleotide scaffold by using longitudinal weaving (LW), bridged longitudinal weaving (bLW) and transverse weaving (TW). Joining the tiles with inter-tile arms having the length of an odd number of DNA half-turns (termed O-tiling) almost resulted into planar 2D lattices, whereas joining the tiles with the arms having the length of an even number of DNA half-turns (termed E-tiling) nearly generated tubes. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the E-tiling tubes and thereby the conformations of their component tiles with addressable concave and convex curvatures. When the arms have the normal winding at the relaxed B-form of DNA, the intrinsic tile curvature deter-mines the chirality of the E-tiling tubes. By regulating the arm length and the sticky end length of the bLW-Ep/q (E-tiling of the bLW cores with the arm length of p-bp and the sticky end length of q-nt) assemblies, the arm can be overwound, resulting in a left-handed twist, and can also be underwound, resulting in a right-handed twist. Chiral bLW-Ep/q tubes with either a right-handed curvature or a left-handed curvature can also be formed by the coupling of the intrinsic tile curvature and the arm twist. We were able to assign the chiral indices (n,m) to each tube using high-resolution AFM images, and therefore were able to estimate the tile curvature using a regular polygon model that approximated the transverse section of the tube. A deeper understanding of the integrated actions of dif-ferent types of twisting forces on the DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.

Thorns amongst Roses? Lived Experience of Philippine Male College Students Aspiring to Become Professional Elementary Teachers

There is a noticeable under-representation of the male gender particularly in the field of elementary teacher education. The main aim of this paper is to understand the lived experience of male college students aspiring to become professional elementary teachers. As phenomenological research, it involved six purposively selected male students enrolled in a predominantly female elementary teacher education program in a Philippine university. The data were gathered through online interviews and analyzed based on a phenomenological analysis framework. The following themes emerged: 1.) We hear discouraging stereotypes about teaching; 2.) We are passionate about educating the young ones; 3.) We feel that awkward moment in a room of females; and 4.) We have an inclusive learning environment. These themes are based on the individual textural and structural descriptions and form the basis for the composite textural and structural descriptions of the phenomenon of interest. This paper confirms the experiences encountered by males in the formal teaching career stage as relative to experiences received by males in the early stage of the teacher preparation. It also identifies factors that encourage males to enter elementary teacher education as a field of study, providing practical insights for designing a more inclusive program.

Mixed computation

Proof-theoretic models of grammar are based on the view that an explicit characterization of a language comes in the form of the recursive enumeration of strings in that language. That recursive enumeration is carried out by a procedure which strongly generates a set of structural descriptions Σ and weakly generates a set of strings S; a grammar is thus a function that pairs an element of Σ with elements of S. Structural descriptions are obtained by means of Context-Free phrase structure rules or via recursive combinatorics and structure is assumed to be uniform: binary branching trees all the way down. In this work we will analyse natural language constructions for which such a rigid conception of phrase structure is descriptively inadequate and propose a solution for the problem of phrase structure grammars assigning too much or too little structure to natural language strings: we propose that the grammar can oscillate between levels of computational complexity in local domains, which correspond to elementary trees in a lexicalised Tree Adjoining Grammar.

Variation in mild context-sensitivity

Aravind Joshi famously hypothesized that natural language syntax was characterized (in part) by mildly context-sensitive generative power. Subsequent work in mathematical linguistics over the past three decades has revealed surprising convergences among a wide variety of grammatical formalisms, all of which can be said to be mildly context-sensitive. But this convergence is not absolute. Not all mildly context-sensitive formalisms can generate exactly the same stringsets (i.e. they are not all weakly equivalent), and even when two formalisms can both generate a certain stringset, there might be differences in the structural descriptions they use to do so. It has generally been difficult to find cases where such differences in structural descriptions can be pinpointed in a way that allows linguistic considerations to be brought to bear on choices between formalisms, but in this paper we present one such case. The empirical pattern of interest involves wh-movement dependencies in languages that do not enforce the wh-island constraint. This pattern draws attention to two related dimensions of variation among formalisms: whether structures grow monotonically from one end to another, and whether structure-building operations are conditioned by only a finite amount of derivational state. From this perspective, we show that one class of formalisms generates the crucial empirical pattern using structures that align with mainstream syntactic analysis, and another class can only generate that same string pattern in a linguistically unnatural way. This is particularly interesting given that (i) the structurally-inadequate formalisms are strictly more powerful than the structurally-adequate ones from the perspective of weak generative capacity, and (ii) the formalism based on derivational operations that appear on the surface to align most closely with the mechanisms adopted in contemporary work in syntactic theory (merge and move) are the formalisms that fail to align with the analyses proposed in that work when the phenomenon is considered in full generality.

Generating contrastive explanations for inductive logic programming based on a near miss approach

In recent research, human-understandable explanations of machine learning models have received a lot of attention. Often explanations are given in form of model simplifications or visualizations. However, as shown in cognitive science as well as in early AI research, concept understanding can also be improved by the alignment of a given instance for a concept with a similar counterexample. Contrasting a given instance with a structurally similar example which does not belong to the concept highlights what characteristics are necessary for concept membership. Such near misses have been proposed by Winston (Learning structural descriptions from examples, 1970) as efficient guidance for learning in relational domains. We introduce an explanation generation algorithm for relational concepts learned with Inductive Logic Programming (GeNME). The algorithm identifies near miss examples from a given set of instances and ranks these examples by their degree of closeness to a specific positive instance. A modified rule which covers the near miss but not the original instance is given as an explanation. We illustrate GeNME with the well-known family domain consisting of kinship relations, the visual relational Winston arches domain, and a real-world domain dealing with file management. We also present a psychological experiment comparing human preferences of rule-based, example-based, and near miss explanations in the family and the arches domains.

Lexicalised Locality: Local Domains and Non-Local Dependencies in a Lexicalised Tree Adjoining Grammar

Contemporary generative grammar assumes that syntactic structure is best described in terms of sets, and that locality conditions, as well as cross-linguistic variation, is determined at the level of designated functional heads. Syntactic operations (merge, MERGE, etc.) build a structure by deriving sets from lexical atoms and recursively (and monotonically) yielding sets of sets. Additional restrictions over the format of structural descriptions limit the number of elements involved in each operation to two at each derivational step, a head and a non-head. In this paper, we will explore an alternative direction for minimalist inquiry based on previous work, e.g., Frank (2002, 2006), albeit under novel assumptions. We propose a view of syntactic structure as a specification of relations in graphs, which correspond to the extended projection of lexical heads; these are elementary trees in Tree Adjoining Grammars. We present empirical motivation for a lexicalised approach to structure building, where the units of the grammar are elementary trees. Our proposal will be based on cross-linguistic evidence; we will consider the structure of elementary trees in Spanish, English and German. We will also explore the consequences of assuming that nodes in elementary trees are addresses for purposes of tree composition operations, substitution and adjunction.

ANALYSIS OF FUNCTIONAL REFERENCE ARCHITECTURE THROUGH AN INDUSTRY LENS

There is an inherent tension between functional descriptions of products and structural descriptions. Traditionally system architecture combine the two, by mapping system elements to functions. In this process fundamental decisions about the embodiment of a product are often taken without proper scrutiny. Axiomatic design advocates a zigzag between functional decomposition and system break down. While this approach makes sense for ab initio design these are rare and most products are developed incrementally., This paper takes up the idea of a functional reference architecture.Conventional functional modelling advocates a hierarchical decomposition into sub function. By contrast FRAs decompose function into function chain, i.e., dependent sequences of sub function required to carry out an overall function. This allows the identification of common sub-functions in different chains, and thereby generates a lattice structure of functions rather than a tree. This enables a detailed but solution neutral description of the product.This concept has attracted interest in industry but does not have many tools and methods to develop FRA. The paper discusses some of the areas that require research

Involvement of Parents in Remote Learning of Children amid COVID-19 Crisis in the Philippines: A Transcendental Phenomenology

This paper aimed to explore how parents give meaning to their involvement in the remote learning of their children amid the COVID-19 crisis. Based on Husserlian transcendental approach in phenomenology, the researcher sought to explore the world of 12 parents, specifically mothers, from Mindanao, Philippines through online interviews. The result revealed 36 significant statements forming four emergent themes. These themes underscore the experience of parental involvement in the remote learning of their children amid crisis as 1.) journeying through a myriad of changes; 2.) connecting with the child physically and emotionally; 3.) experiencing multifaceted difficulties in the process; and 4.) responding to the call of new challenges of parenting. These themes are further elaborated through textural and structural descriptions. A statement of the essence of the lived experience of parents as a result of intuitive integration is offered. Aside from theoretical contributions, the outcomes gained in this paper offer several future practical insights for crisis planning in education.

Regulation of 2D DNA Nanostructures by the Coupling of Tile Curvatures and Arm Twists

DNA overwinding and underwinding between adjacent Holliday junctions have been applied in DNA origami constructs to design both left-handed and right-handed nanostructures. For a variety of DNA tubes assembled from small tiles, only a theoretical approach of the intrinsic tile curvature was previously used to explain their formation. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its evolution in DNA tubes by coupling with arm twists were missing. In this work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile arms with a distance of an odd or even number of DNA half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and outside surfaces and thus their component tile conformation with addressable concave and convex curvatures. Both chiral tubes possessing left-handed and right-handed curvatures could be generated by finely tuning p and q in bLW-E_p/q designs (bLW tile cores joined together by inter-tile arms of an even number of half-turns with the arm length of p base pairs (bp) and the sticky end length of q nucleotides (nt)). We were able to assign the chiral indices (n,m) to each specific tube from the high-resolution AFM images, and thus estimated the tile curvature angle with a regular polygon model that approximates each tube’s transverse section. We attribute the curvature evolution of bLW-E_p/q tubes composed of the same tile core to the coupling of the intrinsic tile curvature and different arm twists. A better understanding of the integrated actions of different types of twisting forces on DNA tubes will be much more helpful in engineering DNA nanostructures in the future.

Regulation of 2D DNA Nanostructures by the Coupling of Tile Cur-Vatures and Arm Twists

DNA overwinding and underwinding between adjacent Holliday junctions have been applied in DNA origami constructs to design both left-handed and right-handed nanostructures. For a variety of DNA tubes assembled from small tiles, only an abstract concept of the intrinsic tile curvature was previously used to explain their formation. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its evolution in DNA tubes by coupling with arm twists have been lacking. In this work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile arms with a distance of an odd or even number of DNA half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and outside surfaces and thus their component tile conformation with addressable concave and convex curvatures. Both chiral tubes possessing left-handed and right-handed curvatures could be generated by finely tuning p and q in bLW-E_p/q designs (bLW tile cores joined together by inter-tile arms of even number of half-turns with the arm length of p base pairs (bp) and the sticky end length of q nucleotides (nt)). We were able to assign the chiral indices (n,m) to each specific tube from the high-resolution AFM images, and thus estimated the tile curvature angle with a regular polygon model that approximates each tube’s transverse section. We attribute the curvature evolution of bLW-E_p/q tubes composed of the same tile core to the coupling of the intrinsic tile curvature and different arm twists. A better understanding of integrated actions of different types of twisting forces on DNA tubes will be much more helpful in engineering DNA nanostructures in the future.