Next‐generation sequencing (NGS) technologies have revolutionised the analysis of genomic structural variants (SVs), providing significant insights into SV de novo formation based on analyses of rearrangement breakpoint junctions. The short DNA reads generated by NGS, however, have also created novel obstacles by biasing the ascertainment of SVs, an aspect that we refer to as the ‘short‐read dilemma’. For example, recent studies have found that SVs are often complex, with SV formation generating large numbers of breakpoints in a single event (...) (multi‐breakpoint SVs) or structurally polymorphic loci having multiple allelic states (multi‐allelic SVs). This complexity may be obscured in short reads, unless the data is analysed and interpreted within its wider genomic context. We discuss how novel approaches will help to overcome the short‐read dilemma, and how integration of other sources of information, including the structure of chromatin, may help in the future to deepen the understanding of SV formation processes. (shrink)

The process of antigenic variation in parasitic African trypanosomes is a remarkable mechanism for outwitting the immune system of the mammalian host, but it requires a delicate balancing act for the monoallelic expression, folding and transport of a single variant surface glycoprotein (VSG). Only one of hundreds of VSG genes is expressed at time, and this from just one of ≈15 dedicated expression sites. By switching expression of VSGs the parasite presents a continuously shifting antigenic facade leading to prolonged (...) chronic infections lasting months to years. The basics of VSG structure and switching have been known for several decades, but recent studies have brought higher resolution to many aspects this process. New VSG structures, in silico modeling of infections, studies of VSG codon usage, and experimental ablation of VSG expression provide insights that inform how this remarkable system may have evolved. (shrink)

This article argues that the much-maligned ‘notational variants’ of a given formal linguistic theory play a role similar to alternative numerical measurement scales. Thus, they can be used to identify the invariant components of the grammar; i.e., those features that do not depend on the choice of empirically equivalent representation. Treating these elements as the ‘meaningful’ structure of language has numerous consequences for the philosophy of science and linguistics. I offer several such examples of how linguistic theorizing can profit from (...) adopting a measurement-theoretic viewpoint. The first concerns a measurement-theoretic response to a famous criticism of Quine's. Others follow from issues of simplicity in the current biolinguistics program. An unexpected similarity with behaviorist practices is also uncovered. I then argue that managable and useful steps can be taken in this area. (shrink)

This paper is a contribution to the study of the rôle of disjunction inAlgebraic Logic. Several kinds of (generalized) disjunctions, usually defined using a suitable variant of the proof by cases property, were introduced and extensively studied in the literature mainly in the context of finitary logics. The goals of this paper are to extend these results to all logics, to systematize the multitude of notions of disjunction (both those already considered in the literature and those introduced in this (...) paper), and to show several interesting applications allowed by the presence of a suitable disjunction in a given logic. (shrink)

Physics appears to be in a unique position to withstand antirealist attacks, especially ‘pessimistic induction’ arguments. Such resilience provides an incentive for embracing a ‘structural’ variant of scientific realism. Nevertheless, an examination of the physics-mathematics relationship suggests that whatever determines the success of modelling endeavours lends scant support to structural realism. A closer look at conceptual prerequisites of joint ab initio derivations of (i) Galilean and ‘special’ relativity theories and (ii) classical and ‘quantal’ probabilistic frameworks also fosters (...) scepticism about a major claim of structural realists: that mathematical features of theoretical frameworks – those, in particular, which determine their predictive efficiency – are ultimately rooted in ‘structural’ aspects of the natural world. Further concerns with the central tenets of structural realism are finally briefly addressed, and the question of possible non-instrumentalist alternatives is raised. (shrink)

Structural realism as developed by John Worrall and others can claim philosophical roots as far back as the late 19th century, though the discussion at that time does not unambiguously favor the contemporary form, or even its realism. After a critical examination of some aspects of the historical background some severe critical challenges to both Worrall's and Ladyman's versions are highlighted, and an alternative empiricist structuralism proposed. Support for this empiricist version is provided in part by the different way (...) in which we can do justice to Worrall's original demands and in part by the viewpoint it provides (in contrast to e.g. Michael Friedman's) on the stability maintained through scientific theory change. Planck against the heretics 1.1 Poincaré on the meaning of Maxwell's equations 1.2 Two responses: reification and structuralism On the road to structuralism 2.1 The microscope 2.2 Mathematization of the world picture 2.3 The 18th–20th century The new structural realism 3.1 From scientific realism to structuralism 3.2 The Ladyman variant: objectivity and invariance 3.3 How is structural realism supported? An empiricist structuralism 4.1 Royal succession in science 4.2 Defence of the empiricist version 4.3 Structure: an empiricist view. (shrink)

In recent years, dependency grammars have established themselves as valuable tools in theoretical and computational linguistics. To many linguists, dependency grammars and the more standard constituency-based formalisms are notational variants. We argue that, beyond considerations of formal equivalence, cognition may also serve as a background for a genuine comparison between these different views of syntax. In this paper, we review and evaluate some of the most common arguments and evidence employed to advocate for the cognitive or neural reality of dependency (...) grammars in linguistics, psycholinguistics, or neurolinguistics. We then raise the possibility that the abilities to represent and track, alternatively or in parallel, constituency and dependency structures co-exist in human cognition and are constitutive of syntactic competence. (shrink)

Pathogenic variants occurring in protein‐coding regions underlie human genetic disease through various mechanisms. They can lead to a loss of function (LOF) such as in recessive conditions or in dominant conditions due to haploinsufficiency. Dominant‐negative (DN) effects, counteracting the activity of the normal gene‐product, and gain of function (GOF) are also mechanisms driving dominance. Here, I discuss a few papers on these specific mechanisms. In short, there is accumulating evidence pointing to differences between LOF versus non‐LOF variants (DN and GOF). (...) The latter are thought to have milder effects on protein structure and, as expected, DN variants are enriched at protein interfaces. This tendency to cluster in 3D space can help improve the ability of computational tools to predict the pathogenicity of DN variants, which is currently a challenging issue. More recent results support the hypothesis whereby cotranslational assembly of macromolecular complexes can buffer deleterious consequences of variants that would otherwise lead to DN effects (DNEs). Indeed, subunits the variants of which are responsible for DNEs tend to elude cotranslational assembly, thus poisoning complexes involving wild‐type subunits. The constraints explaining why the buffering of DNEs is not universal require further investigation. (shrink)

The aim of this paper is to prove strong completeness theorems for several Anderson-like variants of Gödels theory wrt. classes of modal structures, in which: (i). 1st order terms order receive only rigid extensions in the constant objectual 1st order domain; (ii). 2nd order terms receive non-rigid extensions in preselected world-relative objectual domains of 2nd order and rigid intensions in the constant conceptual 2nd order domain.

Behavioural variant frontotemporal dementia (bvFTD) is characterized by an absence of obvious cognitive impairment and presence of symptoms such as disinhibition, social inappropriateness, personality changes, hyper-sexuality, and hyper-orality. Affected individuals do not feel concerned enough about their actions to be deterred from violating social norms, and their antisocial behaviours are most likely caused by the neurodegenerative processes in the frontal and anterior temporal lobes. BvFTD patients present a challenge for the traditional notion of autonomy and the medical and criminal (...) justice systems. Antisocial behaviour is often the earliest recognized manifestation of bvFTD. Given that the symptoms are not specific and that atrophy of the frontal lobes is only observable with structural neuroimaging in the later stages of the disease, it is hard to ascertain their autonomy. Recently proposed re-conceptualizations of autonomy (Dworkin’s, Jaworska’s, and Dubljević’s) can, however, be sufficiently redefined to provide explicit rules and offer nuanced guidance in such cases. A combination of notions of autonomy gives the most nuanced guidance with three modifications: 1) including socio-moral judgement in the notion of “normal cognitive competence,” 2) excluding in-principle un-endorsable ideals from the notion of “capacity to value,” and 3) redefining ideal-typical degrees of compulsion (mild, severe, and total). (shrink)

Here, we present a category ${\mathbf {pEff}}$ which can be considered a predicative variant of Hyland's Effective Topos ${{\mathbf {Eff} }}$ for the following reasons. First, its construction is carried in Feferman’s predicative theory of non-iterative fixpoints ${{\widehat {ID_1}}}$. Second, ${\mathbf {pEff}}$ is a list-arithmetic locally cartesian closed pretopos with a full subcategory ${{\mathbf {pEff}_{set}}}$ of small objects having the same categorical structure which is preserved by the embedding in ${\mathbf {pEff}}$ ; furthermore subobjects in ${{\mathbf {pEff}_{set}}}$ are classified (...) by a non-small object in ${\mathbf {pEff}}$. Third ${\mathbf {pEff}}$ happens to coincide with the exact completion of the lex category defined as a predicative rendering in ${{\widehat {ID_1}}}$ of the subcategory of ${{\mathbf {Eff} }}$ of recursive functions and it validates the Formal Church’s thesis. Hence pEff turns out to be itself a predicative rendering of a full subcategory of ${{\mathbf {Eff} }}$. (shrink)

A number of significant contributions in the last four decades show that non-normal modal logics can be fruitfully employed in several applied fields. Well-known domains are epistemic logic, deontic logic, and systems capturing different aspects of action and agency such as the modal logic of agency, concurrent propositional dynamic logic, game logic, and coalition logic. Semantics for such logics are traditionally based on neighbourhood models. However, other model-theoretic semantics can be used for this purpose. Here, we systematically study multi-relational structures, (...) whose investigation is still relatively underdeveloped. After a brief introduction to two different versions of multi-relational semantics – which we call strong and weak multi-relational semantics – we proceed to study several modal schemata. Special attention is paid to the schemata CON and D. Finally we offer completeness proofs for several systems using both strong and weak semantic tools: The proofs thus cover both classical system.. (shrink)

High‐throughput genomic technologies are revolutionizing human genetics. So far the focus has been on the 1.5% of the genome, which is coding, in spite of the fact that the great majority of genomic variants fall outside the coding regions. Recent efforts to annotate the non‐coding sequence show that over 80% of the genome is biochemically active. The genome is divided into regulatory domains consisting of sequence regions that enhance and/or silence the expression of nearby genes and are, in some cases, (...) separated by boundaries with insulator activity. In this paper, we review the recent advances in the identification of variations that influence gene regulation and their consequences for human disease. We hypothesize that structural variations outside of the coding genome can interfere with normal gene regulation by disrupting the regulatory landscape. Therefore, the regulatory landscape of the genome has also to be taken into consideration when investigating the pathology of human disease. (shrink)

We are used to talking about the “structure” posited by a given theory of physics, such as the spacetime structure of relativity. What is “structure”? What does the mathematical structure used to formulate a theory tell us about the physical world according to the theory? What if there are different mathematical formulations of a given theory? Do different formulations posit different structures, or are they merely notational variants? I consider the case of Lagrangian and Hamiltonian classical mechanics. I argue that, (...) contrary to standard wisdom, these are not genuinely equivalent theories: they differ in statespace structure. I suggest that we should be realists about statespace structure. (shrink)

Cognitive-linguistic theories commonly model speakers’ grammatical knowledge as a network of constructions related by a variety of associative links. The present study proposes that structural priming can provide psycholinguistic evidence of such links, and crucially, that the method can be extended to non-alternating constructions. In a comprehension priming experiment using the “maze” variant of self-paced reading, English caused-motion sentences were found to have an inhibitory effect by slowing down participants’ subsequent processing of resultatives, and vice versa, providing evidence (...) that speakers store distinct but related representations for the constructions. Priming effects of a similar magnitude emerged in both directions, suggesting that the constructions are bidirectionally related, while not supporting previous claims about a metaphorical asymmetry between the patterns. Moreover, priming was only marginally affected when prime and target contained the same rather than different verbs, demonstrating that cross-constructional priming in comprehension can be observed in the absence of a “lexical boost”. The results raise questions for follow-up research on the role of inhibition in the grammatical network and the extension of structural priming to other types of constructional links. (shrink)

To model behavioral and neural correlates of language comprehension in naturalistic environments, researchers have turned to broad‐coverage tools from natural‐language processing and machine learning. Where syntactic structure is explicitly modeled, prior work has relied predominantly on context‐free grammars (CFGs), yet such formalisms are not sufficiently expressive for human languages. Combinatory categorial grammars (CCGs) are sufficiently expressive directly compositional models of grammar with flexible constituency that affords incremental interpretation. In this work, we evaluate whether a more expressive CCG provides a better (...) model than a CFG for human neural signals collected with functional magnetic resonance imaging (fMRI) while participants listen to an audiobook story. We further test between variants of CCG that differ in how they handle optional adjuncts. These evaluations are carried out against a baseline that includes estimates of next‐word predictability from a transformer neural network language model. Such a comparison reveals unique contributions of CCG structure‐building predominantly in the left posterior temporal lobe: CCG‐derived measures offer a superior fit to neural signals compared to those derived from a CFG. These effects are spatially distinct from bilateral superior temporal effects that are unique to predictability. Neural effects for structure‐building are thus separable from predictability during naturalistic listening, and those effects are best characterized by a grammar whose expressive power is motivated on independent linguistic grounds. (shrink)

Some accounts of mental content represent the objects of belief as structured, using entities that formally resemble the sentences used to express and report attitudes in natural language; others adopt a relatively unstructured approach, typically using sets or functions. Currently popular variants of the latter include classical and neo-classical propositionalism, which represent belief contents as sets of possible worlds and sets of centered possible worlds, respectively; and property self-ascriptionism, which employs sets of possible individuals. I argue against their contemporary proponents (...) that all three views are ineluctably plagued by generation gaps: they either overgenerate beliefs, undergenerate them, or both. (shrink)

In recent philosophy of mathematics avariety of writers have presented ``structuralist''views and arguments. There are, however, a number ofsubstantive differences in what their proponents take``structuralism'' to be. In this paper we make explicitthese differences, as well as some underlyingsimilarities and common roots. We thus identifysystematically and in detail, several main variants ofstructuralism, including some not often recognized assuch. As a result the relations between thesevariants, and between the respective problems theyface, become manifest. Throughout our focus is onsemantic and metaphysical issues, (...) including what is orcould be meant by ``structure'' in this connection. (shrink)

Progressive supranuclear palsy is a movement disorder with prominent tau neuropathology. Brain diseases with abnormal tau deposits are called tauopathies, the most common of which is Alzheimer's disease. Environmental causes of tauopathies include repetitive head trauma associated with some sports. To identify common genetic variation contributing to risk for tauopathies, we carried out a genome-wide association study of 1,114 individuals with PSP and 3,247 controls followed by a second stage in which we genotyped 1,051 cases and 3,560 controls for the (...) stage 1 SNPs that yielded P ≤ 10-3. We found significant previously unidentified signals associated with PSP risk at STX6, EIF2AK3 and MOBP. We confirmed two independent variants in MAPT affecting risk for PSP, one of which influences MAPT brain expression. The genes implicated encode proteins for vesicle-membrane fusion at the Golgi-endosomal interface, for the endoplasmic reticulum unfolded protein response and for a myelin structural component. © 2011 Nature America, Inc. All rights reserved. (shrink)

Perceptual disjunctivism, as I regard it in this paper, is the view that veridical perceptions and hallucinations, while indistinguishable via introspection, are states of fundamentally different kinds. This fundamental difference can be spelled out in various ways. According to the view I will be concerned with, it is a fundamental difference in the personal-level structure of both states. Against this version of disjunctivism, I will raise a new challenge. It is a variant of what can be seen as the (...) standard challenge against disjunctivism: how to do justice to the indistinguishability of veridical perceptions and hallucinations. It differs, however, from common versions of this challenge in where it locates the potential incompatibility of disjunctivism with the relevant fact of indistinguishability. Commonly, it is the disjunctivist assumption of a fundamental difference between both kinds of states which is regarded as incompatible with the indistinguishability of these states. In contrast, I will suggest that if hallucinations and veridical perceptions differed in the way proposed by structural disjunctivism, this difference would induce a corresponding difference in the psychological processes of their introspection and that the assumption of such a difference in the manner of introspection is most likely incompatible with a properly formulated indistinguishability claim. (shrink)

In this paper we prove that three of the main propositional logics of dependence, none of which is structural, are structurally complete with respect to a class of substitutions under which the logics are closed. We obtain an analogous result with respect to stable substitutions, for the negative variants of some well-known intermediate logics, which are intermediate theories that are closely related to inquisitive logic.

The SARS‐CoV‐2 virus is responsible for the COVID‐19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein at (...) the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants. (shrink)

In this dissertation I develop a structural model of phenomenal consciousness that integrates contemporary experimental and theoretical work in philosophy and cognitive science. I argue that phenomenology must be “naturalized” and that it should be acknowledged as a major component of empirical research. I use this model to describe important phenomenal structures, and I then employ it to provide a detailed explication of tip-of-tongue phenomena. The primary aim of “structural phenomenology” is the creation of a general framework within (...) which descriptions of experiences may be organized. The work of Husserl, Gurwitsch, the Gestalt psychologists, and many contemporary philosophers and cognitive scientists reveals several basic parameters underlying subjectivity. Chapter I argues that Husserlian methodology possesses problems both of praxis and of internal logic, and that its phenomenological descriptions cannot have the certainty he claimed. Consequently, an adequate phenomenology must incorporate empirical studies. This conclusion enables explicit transitions between empirical investigations and phenomenological insights. Chapter II introduces the theoretical framework underlying my model. I identify four parameters applicable to all experiences: 1) the degree of volitional emphasis with which something is experienced, i.e., the intensity of our focus on it, 2) the degree of non-volitional emphasis, i.e., the degree to which it is salient, 3) a variant of intentionality I term “directionality”, and 4) the property of recursion. Experiences are embedded within a complex set of relationships that unify and direct a layered phenomenal structure. I support these claims with evidence discovered over the past two centuries of research. Chapter III applies my model to the tip-of-tongue (TOT) state, in which difficulty remembering is accompanied by a sense of active searching. I show that a phenomenological description of the TOT experience is dependent on cognitive data, and that a phenomenological analysis is necessary to properly interpret these data. By showing how structural phenomenology offers a perspective from which to elucidate the results of experimental studies, I hope to clarify and establish the explicit role of introspection in empiricism, and of empiricism in phenomenology. (shrink)

Some Anglophone legal theorists look to analytic philosophy for core presuppositions. For example, the epistemological theories of Ludwig Wittgenstein and Willard Quine shape the theories of Dennis Patterson and Brian Leiter, respectively. These epistemologies are anti-foundational since they reject the kind of certain grounding that is exemplified in Cartesian philosophy. And, they are coherentist in that they seek to legitimate truth-claims by reference to entire linguistic systems. While these theories are insightful, the current context of information and communication technologies (ICT) (...) has created new informational concepts and issues. As a result, the analytic epistemologies are increasingly challenged by alternative perspectives. One such alternative is Structural Realism (SR), which is influential among the natural sciences, and especially physics. “Informational Structural Realism,” (ISR) is a variant of SR that was introduced by Luciano Floridi. Unlike the coherentist theories, ISR promotes examination of the connections among types of information and informational structures. It is an important shift for legal theory today, since the challenges that the ICT presents have to do with pattern recognition across vast domains of diverse data. An informational jurisprudence is now required to understand the issues emerging from the ICT. (shrink)

This paper aims to develop the implications of logical expressivism for a theory of dialogue coherence. I proceed in three steps. Firstly, certain structural properties of cooperative dialogue are identified. Secondly, I describe a variant of the multi-agent natural deduction calculus that I introduced in Piwek (J Logic Lang Inf 16(4):403–421, 2007 ) and demonstrate how it accounts for the aforementioned structures. Thirdly, I examine how the aforementioned system can be used to formalise an expressivist account of logical (...) vocabulary that is inspired by Brandom (Making it explicit: reasoning, representing, and discursive commitment, 1994 ; Articulating reasons: an introduction to inferentialism, 2000 ). This account conceives of the logical vocabulary as a tool which allows speakers to describe the inferential practices which underlie their language use, i.e., it allows them to make those practices explicit. The rewards of this exercise are twofold: (1) We obtain a more precise account of logical expressivism which can be defended more effectively against the critique that such accounts lead to cultural relativism. (2) The formalised distinction between engaging in a practice and expressing it, opens the way for a revision of the theory of dialogue coherence. This revision eliminates the need for logically complex formulae to account for certain structural properties of cooperative dialogue. (shrink)

Physical theories are complex and necessary tools for gaining new knowledge about their areas of application. A distinction is made between abstract and practical theories. The last are constantly being improved in the cognitive activity of professional physicists and studied by future physicists. A variant of the philosophy of physics based on a modified structural-nominative reconstruction of practical theories is proposed. Readers should decide whether this option is useful for their understanding of the philosophy of physics, as well (...) as other philosophies of particular sciences. (shrink)

A wave of recent philosophical work on practical rationality is organized by the following implicit argument: Practical reasoning is figuring out what to do; to do is to act; so the forms of practical inference can be derived from the structure or features of action. Now it is not as though earlier work, in analytic philosophy, had failed to register the connection between action and practical rationality; in fact, practical reasoning was usually picked out as, roughly, reasoning directed toward action. (...) But for much of the twentieth century, attention moved quickly away from this initial delineation of the subject area, to the interplay of beliefs and desires within the mind (Humean theories, including their Davidsonian and Williamsian variants), or to procedures for checking that a plan of action was supported by sufficient yet consistent reasons (Kantian theories), or to the ultrarefined sensibilities of the practically intelligent reasoner (Aristotelian theories). The hallmark of the emerging family of treatments to be surveyed here is, first, the sustained attention paid to answering the question, "What does it take to be an action (at all)?", and second, the use made of a distinction between full-fledged action and its lesser relatives. (Characterizations and terminology vary, but often the less robust alternative is called "mere activity" or "mere behavior".) Very schematically, these arguments for a theory of practical reasoning try to show that reasons brought to bear on choice must have some particular logical form, if action is not to lapse into something less than that. (shrink)

In 1982, Wolniewicz proposed a formal ontology of situations based on the lattice of elementary situations (cf. [7, 8]). In [3], I constructed some types of formal structure Porphyrian Tree Structures (PTS), Concepts Structures (CS) and the Structures of Individuals (U) that formally represent ontologically fundamental categories: species and genera (PTS), concepts (CS) and individual beings (U) (cf. [3, 4]). From an ontological perspective, situations and concepts belong to different categories. But, unexpectedly, as I shall show, some variants of CS (...) and Wolniewicz’s lattice are similar. The main theorem states that a subset of a modified concepts structure (called CS+) based on CS fulfils the axioms of Wolniewicz’ lattice. Finally, I shall draw some philosophical conclusions and state some formal facts. (shrink)

A novel algebraic structure of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient spaces of the genetic code vector space over the Galois field of the four DNA bases. The new algebraic structure shows strong connections among algebraic relationships, codon assignment and physicochemical properties of amino acids. Moreover, a distance function defined between the codon binary representations in the vector space was demonstrated to have a linear behavior (...) respect to physical variables such as the mean of amino acids interaction energies in proteins. It was also noticed that the distance between wild type and mutant codons approach to smaller values in mutational variants of four genes, i.e., human phenylalanine hydroxylase, human β-globin, HIV-1 protease and HIV-1 reverse transcriptase. These results strongly suggest that deterministic rules must be involved in the genetic code origin. (shrink)

Loss of insight is a prominent clinical manifestation of behavioral variant frontotemporal dementia , but its characteristics are poorly understood. Twelve bvFTD patients were compared with 12 Alzheimer’s disease patients on a structured insight interview of cognitive insight and emotional insight . Compared to the AD patients, the bvFTD patients were less aware and less concerned about their disorder, and they had less appreciation of its effects on themselves and on others. After corrective feedback , the bvFTD patients were (...) just as aware of their disorder as the AD patients but remained unconcerned and unappreciative of its effects. These findings suggest that lack of insight in bvFTD is not due to “anosognosia,” or impaired cognitive and executive awareness of disease, but to “frontal anosodiaphoria,” or lack of emotional concern over having bvFTD and its impact on themselves and others. (shrink)

We introduce the notion of a Minkowskian Branching Structure ("MBS" for short). Then we prove some results concerning the phenomenon of funny business in its finitary and infinitary variants.

This paper is an investigation in the use of truthmaker theory for exploring the relation of logic to world, and as a tool for metaphysics. A variant of truthmaker theory, which we call the simple theory, is defined and defended against objections. It is characterized formally, and its central features are derived. As part of this project, we give a formal metaphysics based on nondeterministic necessitation relations among possible entities. In what is called the fundamental theorem of truthmaking, it (...) is shown that, as long as a logic is sound and complete, its inferential structure will be isomorphic to the necessitation structure of our metaphysics. We thus arrive at a purely structural logic–world relationship which can be used for metaphysical investigations. Other products of our investigation are a sound and complete semantics for first-order logic with identity and a solution to a result of Restall which has threatened to make truthmaker theory trivial. (shrink)

In this paper, bi-intuitionistic multilattice logic, which is a combination of multilattice logic and the bi-intuitionistic logic also known as Heyting–Brouwer logic, is introduced as a Gentzen-type sequent calculus. A Kripke semantics is developed for this logic, and the completeness theorem with respect to this semantics is proved via theorems for embedding this logic into bi-intuitionistic logic. The logic proposed is an extension of first-degree entailment logic and can be regarded as a bi-intuitionistic variant of the original classical multilattice (...) logic determined by the algebraic structure of multilattices. Similar completeness and embedding results are also shown for another logic called bi-intuitionistic connexive multilattice logic, obtained by replacing the connectives of intuitionistic implication and co-implication with their connexive variants. (shrink)

Fibronectin (FN) is a multi‐functional extracellular matrix protein required for cell adhesion and migration, blood clotting, wound healing, and oncogenic transformation. The functional complexity is paralleled by structural diversity in that multiple forms of FN are generated by cell type‐specific alternative splicing. In the rat, up to 12 different combinations of the three alternatively spliced segments (EIIIA, EIIIB, and the V region) are produced. What effects do these segments have on FN function? Recently, progress has been made in the (...) identification of specific activities for the three Variants of the V region, V120, V95, and V0. FN‐mediated cell adhesion, FN synthesis and secretion, and incorporation into blood clots are differentially affected by these isoforms. These results suggest that cellular behavior is modulated by environmental cues provided by different types and proportions of alternatively spliced FN variants. (shrink)

We present and study the category of formal topologies and some of its variants. Two main results are proven. The first is that, for any inductively generated formal cover, there exists a formal topology whose cover extends in the minimal way the given one. This result is obtained by enhancing the method for the inductive generation of the cover relation by adding a coinductive generation of the positivity predicate. Categorically, this result can be rephrased by saying that inductively generated formal (...) topologies are coreflective into inductively generated formal covers. The second result is that unary formal covers are exponentiable in the category of inductively generated formal covers and hence, thanks to the coreflection, unary formal topologies are exponentiable in the category of inductively generated formal topologies. From a localic point of view the exponentiability of unary formal topologies means that algebraic dcpos are exponentiable in the category of open locales. But, the coreflection theorem states that open locales are coreflective in locales and hence, as a consequence of well-known impredicative results on exponentiable locales, it allows to prove that locally compact open locales are exponentiable in the category of open locales. (shrink)

We introduce several highness notions on degrees related to the problem of computing isomorphisms between structures, provided that isomorphisms exist. We consider variants along axes of uniformity, inclusion of negative information, and several other problems related to computing isomorphisms. These other problems include Scott analysis (in the form of back-and-forth relations), jump hierarchies, and computing descending sequences in linear orders.

The focus of the paper is a discussion around one of the versions of scientific realism – ontic structural realism, which has gained popularity due to the development of quantum field theory. According to OSR, individual objects do not exist as ontological primitives. The ontology of objects and their properties is replaced by the ontology of structures and relations. The paper discusses the arguments of the proponents of OSR, describing it as the only way to preserve scientific realism in (...) general relativity and in quantum physics, which are reduced to mathematical structures with different symmetries. Five possible variants of the ontological relationship between structures and objects are analyzed in detail. Particular attention is paid to the eliminative and non-eliminative versions of OSR. If the former in principle excludes any existence of objects, then in the latter, objects receive their secondary existence due to relations, and their identity is reduced to nodes in the structures of relations. The main objections to OSR and the answers of its proponents are analyzed. It is shown that references to quantum physics are both its strengths and weaknesses of OSR, since they often superficially refer to the formalism of the theory, not accepting one or another of its interpretation. The paper argues the thesis that the extreme eliminative OSR, despite all its advantages, has several serious limitations. The best way out of the situation may be the development of the non-eliminative versions of OSR. In conclusion, it provides a critical analysis of one of these versions – moderate OSR of M. Esfeld and V. Lam, who believe that structures should have causal properties, something resembling a disposition. (shrink)

We achieve several results. First, we develop a variant of the theory of absolute Galois groups in the context of many sorted structures. Second, we provide a method for coding absolute Galois groups of structures, so they can be interpreted in some monster model with an additional predicate. Third, we prove the “Weak Independence Theorem” for pseudo-algebraically closed (PAC) substructures of an ambient structure with no finite cover property (nfcp) and the property [Formula: see text]. Fourth, we describe Kim-dividing (...) in these PAC substructures and show several results related to the SOPnhierarchy. Fifth, we characterize the algebraic closure in PAC structures. (shrink)

Path dependency is a most valuable tool for understanding Russian history since 1480, which coincides with the ending of the “Mongol yoke,” Moscow’s annexation of northwest Russia, formerly controlled by Novgorod, and the introduction of a new method for financing the cavalry—the core of a new service class. The cavalry had to hold off formidable adversaries for Muscovy to retain its independence. Russia in 1480 was a poor country lacking subsurface mineral resources and with a very poor climate and soil (...) for the support of agriculture. These basic problems inspired autocratic power and by 1515 an ideology was in place justifying it. Religion, literature, and law were employed to support the autocracy. A variant of a caste society was created to support the army. This made up the substance of the first service-class revolution in which all resources were mobilized to support a garrison state. After 1667 the external threats to Muscovy diminished, but the service class kept its privileges, especially the land fund and the peasant-serfs. Russia faced major foreign threats again in 1700 and in the 1920s and 1930s. Those threats precipitated the second and third service-class revolutions. The second and third service-class revolutions broadly paralleled the first. Reinvigorated service classes were created with state institutions to support them. As society became more complex, so did the service classes and their privileges. Ideologies were converted into devices to support the infallible autocratic ruler and his elites. Almost the entire population was bound to state service, either directly, working to support the service state, or paying taxes. The church and clergy were harnessed first by Peter’s Holy Synod and then Stalin’s Department 5 of the Secret Police after he revived the church during World War II. Writers and artists were also put into uniform, until they finally rebelled—but the arts retained their civic functions, first supporting the regime, and then criticizing it. Finally, law retained its traditional programmatic functions in regimes themselves beholden to no law. As the foreign threats diminished, the service classes lost their function, but the elite servicemen kept their privileges as the service states disintegrated and the service classes lost their collective élan. Both the Russian Empire and then the Soviet Empire collapsed almost without a whimper. (shrink)

We generalize the model theory of small profinite structures developed by Newelski to the case of compact metric spaces considered together with compact groups of homeomorphisms and satisfying the existence of m-independent extensions (we call them compact e-structures). We analyze the relationships between smallness and different versions of the assumption of the existence of m-independent extensions and we obtain some topological consequences of these assumptions. Using them, we adopt Newelski's proofs of various results about small profinite structures to compact e-structures. (...) In particular, we notice that a variant of the group configuration theorem holds in this context. A general construction of compact structures is described. Using it, a class of examples of compact e-structures which are not small is constructed. It is also noticed that in an m-stable compact e-structure every orbit is equidominant with a product of m-regular orbits. (shrink)

The semantic approach to scientific representation is now long established as a favourite amongst philosophers of science. One of the foremost strains of this approach—the model-theoretic approach —is to represent scientific theories as families of models, all of which satisfy or ‘make true’ a given set of constraints. However some authors have criticised the approach on the grounds that certain scientific theories are logically inconsistent, and there can be no models of an inconsistent set of constraints. Thus it would seem (...) that the MTA fails to represent inconsistent scientific theories at all, and this raises concerns about the way it represents in general. In a series of papers and a recent book da Costa and French have developed a variant of the MTA approach which they call ‘partial structures’, and which they claim can accommodate inconsistent theories. I assess this claim, looking to two theories which have been called ‘inconsistent’: Bohr’s theory of the atom and classical electrodynamics. (shrink)

When I began to think about normative questions of rationality and morality, I soon became a consequentialist. This is the natural result of questioning socially established institutional and moral rules and their metaphysical underpinnings. A critical mind cannot accept a duty to do this or that just because it is told that this duty is implied by some general principle. The immediate question is: Where does this principle come from and how is it justified? And if this question cannot be (...) answered satisfactorily, some critical minds become normative sceptics and others search for rational grounds. Those who search for rational grounds easily end up with one form or other of consequentialism. A rational person does not act by established convention or acquired habit but chooses her action as a means to cause the preferred effects. Thus it seems that the rational person tries to optimize, and this seems to imply that moral action as a variant of rational action should optimize results from a universal point of view, e. g. by maximizing the sum of individual utilities. (shrink)

C-minimality is a variant of o-minimality in which structures carry, instead of a linear ordering, a ternary relation interpretable in a natural way on set of maximal chains of a tree. This notion is discussed, a cell-decomposition theorem for C-minimal structures is proved, and a notion of dimension is introduced. It is shown that C-minimal fields are precisely valued algebraically closed fields. It is also shown that, if certain specific ‘bad’ functions are not definable, then algebraic closure has the (...) exchange property, and for definable sets dimension coincides with the rank obtained from algebraic closure. (shrink)

This article examines the thematic structure and progression of an extract of a spontaneous conversation using the inference-boundary model and the thematic progression framework of Daneš. This article argues that equal attention should be paid to both thematic and rhematic progression. Insofar as rheme carries the body of the message, it would be tremendously helpful for us to gain an understanding of the patterned behaviour of the rhematic element and how theme and rheme together shape the message in the unfolding (...) discourse. The article also examines the different patterns of theme–rheme development in the extract. The boxed, gapped, holistic, and multiple developments, including their variant forms, are presented and discussed. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Continuing the paper [7], in which the Blum-Shub-Smale approach to computability over the reals has been generalized to arbitrary algebraic structures, this paper deals with computability and recognizability over structures of infinite signature. It begins with discussing related properties of the linear and scalar real structures and of their discrete counterparts over the natural numbers. Then the existence of universal functions is shown to be equivalent to the effective encodability of the underlying structure. Such structures even have universal functions satisfying (...) the s-m-n theorem and related features. The real and discrete examples are discussed with respect to effective encodability. Megiddo structures and computational extensions of effectively encodable structures are encodable, too. As further variants of universality, universal functions with enumerable sets of program codes and such ones with constructible codes are investigated. Finally, the existence of m-complete sets is shown to be independent of the effective encodability of structures, and the linear and scalar structures are discussed once more, under this aspect. (shrink)

We present and study the category of formal topologies and some of its variants. Two main results are proven. The first is that, for any inductively generated formal cover, there exists a formal topology whose cover extends in the minimal way the given one. This result is obtained by enhancing the method for the inductive generation of the cover relation by adding a coinductive generation of the positivity predicate. Categorically, this result can be rephrased by saying that inductively generated formal (...) topologies are coreflective into inductively generated formal covers. The second result is that unary formal covers are exponentiable in the category of inductively generated formal covers and hence, thanks to the coreflection, unary formal topologies are exponentiable in the category of inductively generated formal topologies. From a localic point of view the exponentiability of unary formal topologies means that algebraic dcpos are exponentiable in the category of open locales. But, the coreflection theorem states that open locales are coreflective in locales and hence, as a consequence of well-known impredicative results on exponentiable locales, it allows to prove that locally compact open locales are exponentiable in the category of open locales. (shrink)