A capture–recapture approach for screening using two diagnostic tests with availability of disease status for the test positives only

The article considers screening human populations with two screening tests. If any of the two tests is positive, then full evaluation of the disease status is undertaken; however, if both diagnostic tests are negative, then disease status remains unknown. This procedure leads to a data constellation in which, for each disease status, the 2 × 2 table associated with the two diagnostic tests used in screening has exactly one empty, unknown cell. To estimate the unobserved cell counts, previous approaches assume independence of the two diagnostic tests and use specific models, including the special mixture model of Walter or unconstrained capture–recapture estimates. Often, as is also demonstrated in this article by means of a simple test, the independence of the two screening tests is not supported by the data. Two new estimators are suggested that allow associations of the screening test, although the form of association must be assumed to be homogeneous over disease status. These estimators are modifications of the simple capture–recapture estimator and easy to construct. The estimators are investigated for several screening studies with fully evaluated disease status in which the superior behavior of the new estimators compared to the previous conventional ones can be shown. Finally, the performance of the new estimators is compared with maximum likelihood estimators, which are more difficult to obtain in these models. The results indicate the loss of efficiency as minor.

A capture-recapture approach for screening using two diagnostic tests with availability of disease status for the test positives only

The article considers screening human populations with two screening tests. If any of the two tests is positive, then full evaluation of the disease status is undertaken; however, if both diagnostic tests are negative, then disease status remains unknown. This procedure leads to a data constellation in which, for each disease status, the 2 x 2 table associated with the two diagnostic tests used in screening has exactly one empty, unknown cell. To estimate the unobserved cell counts, previous approaches assume independence of the two diagnostic tests and use specific models, including the special mixture model of Walter or unconstrained capture-recapture estimates. Often, as is also demonstrated in this article by means of a simple test, the independence of the two screening tests is not supported by the data. Two new estimators are suggested that allow associations of the screening test, although the form of association must be assumed to be homogeneous over disease status. These estimators are modifications of the simple capture-recapture estimator and easy to construct. The estimators are investigated for several screening studies with fully evaluated disease status in which the superior behavior of the new estimators compared to the previous conventional ones can be shown. Finally, the performance of the new estimators is compared with maximum likelihood estimators, which are more difficult to obtain in these models. The results indicate the loss of efficiency as minor.

Mechanisms of femtosecond laser-induced refractive index modification of poly(methyl methacrylate)

The mechanisms of refractive index change in poly(methyl methacrylate) by frequency doubled femtosecond laser pulses are investigated. It is demonstrated that positive refractive index modificaton can be caused by a combination of depolymerization and crosslinking.

Comparing a discrete and continuum model of the intestinal crypt

The integration of processes at different scales is a key problem in the modelling of cell populations. Owing to increased computational resources and the accumulation of data at the cellular and subcellular scales, the use of discrete, cell-level models, which are typically solved using numerical simulations, has become prominent. One of the merits of this approach is that important biological factors, such as cell heterogeneity and noise, can be easily incorporated. However, it can be difficult to efficiently draw generalizations from the simulation results, as, often, many simulation runs are required to investigate model behaviour in typically large parameter spaces. In some cases, discrete cell-level models can be coarse-grained, yielding continuum models whose analysis can lead to the development of insight into the underlying simulations. In this paper we apply such an approach to the case of a discrete model of cell dynamics in the intestinal crypt. An analysis of the resulting continuum model demonstrates that there is a limited region of parameter space within which steady-state (and hence biologically realistic) solutions exist. Continuum model predictions show good agreement with corresponding results from the underlying simulations and experimental data taken from murine intestinal crypts.

Beyond the American century: Walter Lippmann and American grand strategy, 1943-1950

As the United States became a world Power, journalist and intellectual Walter Lippmann feared that it would become its own worst enemy. During and after the Second World War, he tried to steer the country towards coherent statecraft, to define the national interest and the limits of power, and give geopolitical expression to the role of the United States as the core of an Atlantic strategic system. But in response to world war, the Truman Doctrine, and the Korean War, he became pessimistic about the country's ability to conduct strategy effectively. In the prophetic tradition, he believed that a fatal symbiosis between America's growing strength and domestic politics led it towards crisis. Though at times ahistorical, Lippmann's concept of strategy deserves attention for its dialogue between power and identity, for its questioning of “ends” as well as means, and for its focus on the danger of self-defeating behaviour.

Back to the margins in search of the core: "Foreign Land"'s geography of exclusion

The crisis of the national project in the early 1990s, caused by a short-lived but disastrous government, led Brazilian art cinema, for the first time, to look at itself as periphery and re-approach the old colonial center, Portugal. Terra estrangeira/Foreign Land (Walter Salles & Daniela Thomas, Brazil/Portugal, 1995), a film about Brazilian exiles in Portugal, is the best illustration of this perspective shift which provides a new sense of Brazil’s scale and position within a global context. Shot mainly on location in São Paulo, Lisbon and Cape Verde, it promotes the encounter of Lusophone peoples who find a common ground in their marginal situation. Rather than as a former empire, Portugal is defined by its situation at the edge of Europe and by beliefs such as Sebastianism, whose origins go back to the time when the country was dominated by Spain. As a result, notions of “core” or “center” are devolved to the realm of myth. The film’s carefully crafted dialogue combines Brazilian, Portuguese and Creole linguistic peculiarities into a common dialect of exclusion, while language puns trigger visual rhymes which refer back to the Cinema Novo (the Brazilian New Wave) repertoire and restage the imaginary of the discovery turned into unfulfilled utopia. The main characters also acquire historical resonances, as they are depicted as descendants of Iberian conquistadors turned into smugglers of precious stones in the present. Their activities define a circuit of international exchange which resonates with that of globalized cinema, a realm in which Foreign Land, made up of citations and homage to other cinemas, tries to retrieve a sense of belonging.

The zero, the centre and the empty utopia: from Rossellini to Walter Salles

This article examines utopian gestures and inaugural desires in two films which became symbolic of the Brazilian Film Revival in the late 1990s: Central Station (1998) and Midnight (1999). Both evolve around the idea of an overcrowded or empty centre in a country trapped between past and future, in which the motif of the zero stands for both the announcement and the negation of utopia. The analysis draws parallels between them and new wave films which also elaborate on the idea of the zero, with examples picked from Italian neo-realism, the Brazilian Cinema Novo and the New German Cinema. In Central Station, the ‘point zero’, or the core of the homeland, is retrieved in the archaic backlands, where political issues are resolved in the private sphere and the social drama turns into family melodrama. Midnight, in its turn, recycles Glauber Rocha’s utopian prophecies in the new millennium’s hour zero, when the earthly paradise represented by the sea is re-encountered by the middle-class character, but not by the poor migrant. In both cases, public injustice is compensated by the heroes’ personal achievements, but those do not refer to the real nation, its history or society. Their utopian breadth, based on nostalgia, citation and genre techniques, is of a virtual kind, attune to cinema only.

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.

Back to the margins in search of the core: foreign land's geography of exclusion

The crisis of the national project in the early 1990s, caused by a short-lived but disastrous government, led Brazilian art cinema, for the first time, to look at itself as periphery and re-approach the old colonial centre, Portugal. Terra estrangeira/Foreign Land (Walter Salles & Daniela Thomas, Brazil/Portugal, 1995), a film about Brazilian exiles in Portugal, is the best illustration of this perspective shift aimed at providing a new sense of Brazil’s scale and position within a global context. Shot mainly on location in São Paulo, Lisbon and Cape Verde, it promotes the encounter of Lusophone peoples who find a common ground in their marginal situation. Even Portugal is defined by its location at the edge of Europe and by beliefs such as Sebastianism, whose origins go back to the time when the country was dominated by Spain. As a result, notions of ‘core’ or ‘centre’ are devolved to the realm of myth. The film’s carefully crafted dialogues combine Brazilian, Portuguese and Creole linguistic peculiarities into a common dialect of exclusion, while language puns trigger visual rhymes which refer back to the Cinema Novo (the Brazilian New Wave) repertoire and restage the imaginary of the discovery turned into unfulfilled utopia. The main characters also acquire historical resonances, as they are depicted as descendants of Iberian conquistadors turned into smugglers of precious stones in the present. Their activities define a circuit of international exchange which resonates with that of globalized cinema, a realm in which Foreign Land, made up of citations and homage to other cinemas, tries to retrieve a sense of belonging.

Reflexive stasis, scale reversal and the myth of modern cinema

This chapter looks at three films whose Portuguese urban settings offer a privileged ground for the re-evaluation of the classical-modern-postmodern categorisation with regard to cinema. They are The State of Things (Wim Wenders, 1982), Foreign Land (Walter Salles and Daniela Thomas, 1995) and Mysteries of Lisbon (Raúl Ruiz, 2010). In them, the city is the place where characters lose their bearings, names, identities, and where vicious circles, mirrors, replicas and mise-en-abyme bring the vertiginous movement that had characterised the modernist city of 1920s cinema to a halt. Curiously, too, it is the place where so-called postmodern aesthetics finally finds an ideal home in self-ironical tales that expose the film medium’s narrative shortcomings. Intermedial devices, whether Polaroid stills or a cardboard cut-out theatre, are then resorted to in order to turn a larger-than-life reality into framed, manageable narrative miniatures. The scaled-down real, however, turns out to be a disappointing simulacrum, a memory ersatz that unveils the illusory character of cosmopolitan teleology. In my approach, I start by examining the intertwined and transnational genesis of these films that resulted in three correlated visions of the end of history and of storytelling, typical of postmodern aesthetics. I move on to consider intermedia miniaturism as an attempt to stop time within movement, an equation that inevitably brings to mind the Deleuzian movement-time binary, which I revisit in an attempt to disentangle it from the classical-modern opposition. I conclude by proposing reflexive stasis and scale reversal as the common denominator across all modern projects, hence, perhaps, a more advantageous model than modernity to signify artistic and political values.

A comparative review of skill assessment: performance, prediction and profiling

The assessment of chess players is an increasingly attractive opportunity and an unfortunate necessity. The chess community needs to limit potential reputational damage by inhibiting cheating and unjustified accusations of cheating: there has been a recent rise in both. A number of counter-intuitive discoveries have been made by benchmarking the intrinsic merit of players’ moves: these call for further investigation. Is Capablanca actually, objectively the most accurate World Champion? Has ELO rating inflation not taken place? Stimulated by FIDE/ACP, we revisit the fundamentals of the subject to advance a framework suitable for improved standards of computational experiment and more precise results. Other domains look to chess as the demonstrator of good practice, including the rating of professionals making high-value decisions under pressure, personnel evaluation by Multichoice Assessment and the organization of crowd-sourcing in citizen science projects. The ‘3P’ themes of performance, prediction and profiling pervade all these domains.

Transreal proof of the existence of universal possible worlds

Transreal arithmetic is total, in the sense that the fundamental operations of addition, subtraction, multiplication and division can be applied to any transreal numbers with the result being a transreal number [1]. In particular division by zero is allowed. It is proved, in [3], that transreal arithmetic is consistent and contains real arithmetic. The entire set of transreal numbers is a total semantics that models all of the semantic values, that is truth values, commonly used in logics, such as the classical, dialetheaic, fuzzy and gap values [2]. By virtue of the totality of transreal arithmetic, these logics can be implemented using total, arithmetical functions, specifically operators, whose domain and counterdomain is the entire set of transreal numbers