Transdisciplinary working to shape systematic reviews and interpret the findings: Commentary

This is the final version. Available from BMC via the DOI in this record. Important policy questions tend to span a range of academic disciplines, and the relevant research is often carried out in a variety of social, economic and geographic contexts. In efforts to synthesise research to help inform decisions arising from the policy questions, systematic reviews need conceptual frameworks and ways of thinking that combine knowledge drawn from different academic traditions and contexts; in other words, transdisciplinary research. This paper considers how transdisciplinary working can be achieved with: conceptual frameworks that span traditional academic boundaries; methods for shaping review questions and conceptual frameworks; and methods for interpreting the relevance of findings to different contexts. It also discusses the practical challenges and ultimate benefits of transdisciplinary working for systematic reviews.World Health OrganizationUK Department for International DevelopmentUK aidNational Institute for Health Research (NIHR

Geometric Logic in Computer Science

We present an introduction to geometric logic and the mathematical structures associated with it, such as categorical logic and toposes. We also describe some of its applications in computer science including its potential as a logic for spec-i cation languages.

Continuous Truth II: Reflections

Abstract. In the late 1960s, Dana Scott first showed how the Stone-Tarski topological interpretation of Heyting’s calculus could be extended to model intuitionistic analysis; in particular Brouwer’s continuity prin-ciple. In the early ’80s we and others outlined a general treatment of non-constructive objects, using sheaf models—constructions from topos theory—to model not only Brouwer’s non-classical conclusions, but also his creation of “new mathematical entities”. These categorical models are intimately related to, but more general than Scott’s topological model. The primary goal of this paper is to consider the question of iterated extensions. Can we derive new insights by repeating the second act? In Continuous Truth I, presented at Logic Colloquium ’82 in Florence, we showed that general principles of continuity, local choice and local com-pactness hold in the gros topos of sheaves over the category of separable locales equipped with the open cover topology. We touched on the question of iteration. Here we develop a more gen-eral analysis of iterated categorical extensions, that leads to a reflection schema for statements of predicative analysis. We also take the opportunity to revisit some aspects of both Continuous Truth I and Formal Spaces (Fourman & Grayson 1982), and correct two long-standing errors therein

A Proposed Categorial Semantics for Pure ML

SIGLEAvailable from British Library Document Supply Centre- DSC:5186.0913(ECS-LFCS--92-213) / BLDSC - British Library Document Supply CentreGBUnited Kingdo

A topos for algebraic quantum theory

The aim of this paper is to relate algebraic quantum mechanics to topos theory, so as to construct new foundations for quantum logic and quantum spaces. Motivated by Bohr's idea that the empirical content of quantum physics is accessible only through classical physics, we show how a C*-algebra of observables A induces a topos T(A) in which the amalgamation of all of its commutative subalgebras comprises a single commutative C*-algebra. According to the constructive Gelfand duality theorem of Banaschewski and Mulvey, the latter has an internal spectrum S(A) in T(A), which in our approach plays the role of a quantum phase space of the system. Thus we associate a locale (which is the topos-theoretical notion of a space and which intrinsically carries the intuitionistic logical structure of a Heyting algebra) to a C*-algebra (which is the noncommutative notion of a space). In this setting, states on A become probability measures (more precisely, valuations) on S(A), and self-adjoint elements of A define continuous functions (more precisely, locale maps) from S(A) to Scott's interval domain. Noting that open subsets of S(A) correspond to propositions about the system, the pairing map that assigns a (generalized) truth value to a state and a proposition assumes an extremely simple categorical form. Formulated in this way, the quantum theory defined by A is essentially turned into a classical theory, internal to the topos T(A).Comment: 52 pages, final version, to appear in Communications in Mathematical Physic

An overview of population-based algorithms for multi-objective optimisation

In this work we present an overview of the most prominent population-based algorithms and the methodologies used to extend them to multiple objective problems. Although not exact in the mathematical sense, it has long been recognised that population-based multi-objective optimisation techniques for real-world applications are immensely valuable and versatile. These techniques are usually employed when exact optimisation methods are not easily applicable or simply when, due to sheer complexity, such techniques could potentially be very costly. Another advantage is that since a population of decision vectors is considered in each generation these algorithms are implicitly parallelisable and can generate an approximation of the entire Pareto front at each iteration. A critique of their capabilities is also provided

ParadisEO-MOEO: A Software Framework for Evolutionary Multi-Objective Optimization

This chapter presents ParadisEO-MOEO, a white-box object-oriented software framework dedicated to the flexible design of metaheuristics for multi-objective optimization. This paradigm-free software proposes a unified view for major evolutionary multi-objective metaheuristics. It embeds some features and techniques for multi-objective resolution and aims to provide a set of classes allowing to ease and speed up the development of computationally efficient programs. It is based on a clear conceptual distinction between the solution methods and the problems they are intended to solve. This separation confers a maximum design and code reuse. This general-purpose framework provides a broad range of fitness assignment strategies, the most common diversity preservation mechanisms, some elitistrelated features as well as statistical tools. Furthermore, a number of state-of-the-art search methods, including NSGA-II, SPEA2 and IBEA, have been implemented in a user-friendly way, based on the fine-grained ParadisEO-MOEO components

Impaired distal nephron acidification in chronically phosphate depleted rats

Renal tubular bicarbonate reabsorption and acidification were evaluated in phosphate depleted rats (PD) and controls. After 33 days of phosphate depletion, urine pH of PD rats ( N =5, 6.36±0.15) was significantly higher than control ( N =5, 5.64±0.09, P <0.005) following an NH 4 Cl load. Urinary titratable acid of PD rats (9.6±1.8) was significantly reduced compared to control (117.2±19.7 μEq/3 h, P <0.001), whereas NH 4 + excretion was not different. The plasma HCO 3 − thresholds at which bicarbonaturia occurred (approximately 25 mEq/l) were identical in controls and phosphate depleted rats during isotonic bicarbonate infusion. The higher urine pH of phosphate depleted rats following NH 4 Cl administration was not due to low urinary phosphate as 3-day phosphate depleted rats could normally acidify urine after NH 4 Cl (pH=5.86±0.09, N =6 vs. control 5.87±0.08, N =6, P =N.S.) despite urinary phosphate excretion as low as in 33-day PD rats. These data indicate the presence of impaired distal tubular acidification in chronically phosphate depleted rats.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47445/1/424_2004_Article_BF00584277.pd

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease