Perceptions of the Agency and Responsibility of the NHS COVID-19 App on Twitter: Critical Discourse Analysis

BACKGROUND

Since September 2020, the National Health Service (NHS) COVID-19 contact-tracing app has been used to mitigate the spread of COVID-19 in the United Kingdom. Since its launch, this app has been a part of the discussion regarding the perceived social agency of decision-making algorithms. On the social media website Twitter, a plethora of views about the app have been found but only analyzed for sentiment and topic trajectories thus far, leaving the perceived social agency of the app underexplored.

OBJECTIVE

We aimed to examine the discussion of social agency in social media public discourse regarding algorithm-operated decisions, particularly when the artificial intelligence agency responsible for specific information systems is not openly disclosed in an example such as the COVID-19 contact-tracing app. To do this, we analyzed the presentation of the NHS COVID-19 App on Twitter, focusing on the portrayal of social agency and the impact of its deployment on society. We also aimed to discover what the presentation of social agents communicates about the perceived responsibility of the app.

METHODS

Using corpus linguistics and critical discourse analysis, underpinned by social actor representation, we used the link between grammatical and social agency and analyzed a corpus of 118,316 tweets from September 2020 to July 2021 to see whether the app was portrayed as a social actor.

RESULTS

We found that active presentations of the app-seen mainly through personalization and agency metaphor-dominated the discourse. The app was presented as a social actor in 96% of the cases considered and grew in proportion to passive presentations over time. These active presentations showed the app to be a social actor in 5 main ways: informing, instructing, providing permission, disrupting, and functioning. We found a small number of occasions on which the app was presented passively through backgrounding and exclusion.

CONCLUSIONS

Twitter users presented the NHS COVID-19 App as an active social actor with a clear sense of social agency. The study also revealed that Twitter users perceived the app as responsible for their welfare, particularly when it provided instructions or permission, and this perception remained consistent throughout the discourse, particularly during significant events. Overall, this study contributes to understanding how social agency is discussed in social media discourse related to algorithmic-operated decisions This research offers valuable insights into public perceptions of decision-making digital contact-tracing health care technologies and their perceptions on the web, which, even in a postpandemic world, may shed light on how the public might respond to forthcoming interventions.

Testing Nonmonotonicity in Health Preferences

OBJECTIVE

The main aim of this article is to test monotonicity in life duration. Previous findings suggest that, for poor health states, longer durations are preferred to shorter durations up to some threshold or maximum endurable time (MET), and shorter durations are preferred to longer ones after that threshold.

METHODS

Monotonicity in duration is tested through 2 ordinal tasks: choices and rankings. A convenience sample (n = 90) was recruited in a series of experimental sessions in which participants had to rank-order health episodes and to choose between them, presented in pairs. Health episodes result from the combination of 7 EQ-5D-3L health states and 5 durations. Monotonicity is tested comparing the percentage rate of participants whose preferences were monotonic with the percentage of participants with nonmonotonic preferences for each health state. In addition, to test the existence of preference reversals, we analyze the fraction of people who switch their preference from rankings to choices.

RESULTS

Monotonicity is frequently violated across the 7 EQ-5D health states. Preference patterns for individuals describe violations ranging from almost 49% with choices to about 71% with rankings. Analysis performed by separate states shows that the mean rates of violations with choices and ranking are about 22% and 34%, respectively. We also find new evidence of preference reversals and some evidence-though scarce-of transitivity violations in choices.

CONCLUSIONS

Our results show that there is a medium range of health states for which preferences are nonmonotonic. These findings support previous evidence on MET preferences and introduce a new "choice-ranking" preference reversal. It seems that the use of 2 tasks with a similar response scale may make preference reversals less substantial, although it remains important and systematic.

HIGHLIGHTS

Two procedures based on ordinal comparisons are used to elicit preferences: direct choices and rankings. Our study reports significant rates of nonmonotonic preferences (or maximum endurable time [MET]-type preferences) for different combinations of durations and EQ-5D health states.Analysis for separate health states shows that the mean rates of nonmonotonicity range from 22% (choices) to 34% (rankings), but within-subject analysis shows that nonmonotonicity is even higher, ranging from 49% (choices) to 71% (rankings). These violations challenge the validity of multiplicative QALY models.We find that the MET phenomenon may affect particularly those EQ-5D health states that are in the middle of the severity scale and not so much the extreme health states (i.e., very mild and very severe states).We find new evidence of preference reversals even using 2 procedures of a similar (ordinal) nature. Percentage rates of preference reversals range from 1.5% to 33%. We also find some (although scarce) evidence on violations of transitivity.

Inconsistency identification in network meta-analysis via stochastic search variable selection

The reliability of the results of network meta-analysis (NMA) lies in the plausibility of the key assumption of transitivity. This assumption implies that the effect modifiers' distribution is similar across treatment comparisons. Transitivity is statistically manifested through the consistency assumption which suggests that direct and indirect evidence are in agreement. Several methods have been suggested to evaluate consistency. A popular approach suggests adding inconsistency factors to the NMA model. We follow a different direction by describing each inconsistency factor with a candidate covariate whose choice relies on variable selection techniques. Our proposed method, stochastic search inconsistency factor selection (SSIFS), evaluates the consistency assumption both locally and globally, by applying the stochastic search variable selection method to determine whether the inconsistency factors should be included in the model. The posterior inclusion probability of each inconsistency factor quantifies how likely is a specific comparison to be inconsistent. We use posterior model odds or the median probability model to decide on the importance of inconsistency factors. Differences between direct and indirect evidence can be incorporated into the inconsistency detection process. A key point of our proposed approach is the construction of a reasonable "informative" prior concerning network consistency. The prior is based on the elicitation of information derived historical data from 201 published network meta-analyses. The performance of our proposed method is evaluated in two published network meta-analyses. The proposed methodology is publicly available in an R package called ssifs, published on CRAN and developed and maintained by the authors of this work.

Perceiving the poetic world: A corpus-assisted transitivity analysis of poetry comics

While modern adaptations of Chinese classics have drawn keen scholarly interests lately, the comic adaptation of Chinese traditional poetry remains under-investigated. Extending the previous research on intersemiotic translation and comics, this paper, drawing on the analytical framework of systemic functional semiotics, examines distribution of process types of language in poems in comparison with that in comic images in the exemplary case drawn by Cai Zhizhong, using UAM image as the annotation tool. The comic book formulates a multimodal corpus that consists of 1,097 clauses and 605 images. We have manually analyzed the process type of the poems and their corresponding comic panels. Our quantitative and qualitative results show that there are distinct patterns of process-type distributions between verbal poems and images. Poems have been turned into perceptions, actions, and verbal processes in comic strips, which serve various purposes such as construction of the poet's gaze, relations building, storyline development, dramatization, metaphor visualization, etc. The paper is concluded with discussion on how the intersemiotic translation of poems might produce effects on readers.

Graphical tools for visualizing the results of network meta-analysis of multicomponent interventions

Network meta-analysis (NMA) is an established method for assessing the comparative efficacy and safety of competing interventions. It is often the case that we deal with interventions that consist of multiple, possibly interacting, components. Examples of interventions' components include characteristics of the intervention, mode (face-to-face, remotely etc.), location (hospital, home etc.), provider (physician, nurse etc.), time of communication (synchronous, asynchronous etc.) and other context related components. Networks of multicomponent interventions are typically sparse and classical NMA inference is not straightforward and prone to confounding. Ideally, we would like to disentangle the effect of each component to find out what works (or does not work). To this aim, we propose novel ways of visualizing the NMA results, describe their use, and illustrate their application in real-life examples. We developed an R package viscomp to produce all the suggested figures.

Reproducing experiential meaning in translation: A systemic functional linguistics analysis on translating ancient Chinese poetry and prose in political texts

Ancient Chinese poetry and prose (ACPP) are the essence of traditional Chinese culture and also literary gems of the world. Despite the long tradition of previous Chinese Presidents using ACPP in their political addresses, the translation work on the three volumes of Xi Jinping: The Governance of China with much ACPP still poses a daunting challenge to the translation of literary texts in non-literary texts. As experiential meaning is inherent in all kinds of texts, literature, and non-literature, this study, drawing on the sights of Halliday's experiential mode of meaning and register theory in Systemic Functional Linguistics (SFL), explored how the ACPP's experiential meaning was rendered in the political texts, and factors motivating transitivity patterns and shift tendencies. Statistics showed that the translations tend to reproduce the experiential meaning such that it involves more representations of the flow of events and the creation of relationships among entities, focusing more on construing the experience of the physical world rather than personal emotions, feelings, or cognition. Besides, the target text is also inclined to simplify the experiential meaning by compressing and omitting unnecessary transitivity processes and the participant and circumstance nominalization. This research found that the factors responsible for such tendencies include the features of political texts, language differences, the distribution of process types, the delicacy of the transitivity system, and register variations of fields of activity. With these findings, the study is expected to contribute to the SFL approach of studying literary translation in non-literary texts through the prism of experiential meaning and offer guidance in the translation of political literature with ACPP.

Systemic silencing of an endogenous plant gene by two classes of mobile 21-nucleotide artificial small RNAs

Artificial small RNAs (art-sRNAs) are 21-nucleotide small RNAs (sRNAs) computationally designed to silence plant genes or pathogenic RNAs with high efficacy and specificity. They are typically produced in transgenic plants to induce silencing at the whole-organism level, although their expression in selected tissues for inactivating genes in distal tissues has not been reported. Here, art-sRNAs designed against the magnesium chelatase subunit CHLI-encoding SULFUR gene (NbSu) were agroinfiltrated in Nicotiana benthamiana leaves, and the induction of local and systemic silencing was analyzed phenotypically by monitoring the appearance of the characteristic bleached phenotype, as well as molecularly by analyzing art-sRNA processing, accumulation and targeting activity and efficacy. We found that the two classes of art-sRNAs, artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs), are able to induce systemic silencing of NbSu, which requires high art-sRNA expression in the vicinity of the leaf petiole but is independent on the production of secondary sRNAs from NbSu mRNAs. Moreover, we revealed that 21-nucleotide amiRNA and syn-tasiRNA duplexes, and not their precursors, are the molecules moving between cells and through the phloem to systemically silence NbSu in upper leaves. In sum, our results indicate that 21-nucleotide art-sRNAs can move throughout the plant to silence plant genes in tissues different from where they are produced. This highlights the biotechnological potential of art-sRNAs, which might be applied locally for triggering whole-plant and highly specific silencing to regulate gene expression or induce resistance against pathogenic RNAs in next-generation crops. The present study demonstrates that artificial small RNAs, such as artificial microRNAs and synthetic trans-acting small interfering RNAs, can move long distances in plants as 21-nucleotide duplexes, specifically silencing endogenous genes in tissues different from where they are applied. This highlights the biotechnological potential of artificial small RNAs, which might be applied locally for triggering whole-plant, highly specific silencing to regulate gene expression or induce resistance against pathogenic RNAs in next-generation crops.

High-pressure sprayed siRNAs influence the efficiency but not the profile of transitive silencing

In plants, small interfering RNAs (siRNAs) are a quintessential class of RNA interference (RNAi)-inducing molecules produced by the endonucleolytic cleavage of double-stranded RNAs (dsRNAs). In order to ensure robust RNAi, siRNAs are amplified through a positive feedback mechanism called transitivity. Transitivity relies on RNA-DIRECTED RNA POLYMERASE 6 (RDR6)-mediated dsRNA synthesis using siRNA-targeted RNA. The newly synthesized dsRNA is subsequently cleaved into secondary siRNAs by DICER-LIKE (DCL) endonucleases. Just like primary siRNAs, secondary siRNAs are also loaded into ARGONAUTE proteins (AGOs) to form an RNA-induced silencing complex reinforcing the cleavage of the target RNA. Although the molecular players underlying transitivity are well established, the mode of action of transitivity remains elusive. In this study, we investigated the influence of primary target sites on transgene silencing and transitivity using the green fluorescent protein (GFP)-expressing Nicotiana benthamiana 16C line, high-pressure spraying protocol, and synthetic 22-nucleotide (nt) long siRNAs. We found that the 22-nt siRNA targeting the 3' of the GFP transgene was less efficient in inducing silencing when compared with the siRNAs targeting the 5' and middle region of the GFP. Moreover, sRNA sequencing of locally silenced leaves showed that the amount but not the profile of secondary RNAs is shaped by the occupancy of the primary siRNA triggers on the target RNA. Our findings suggest that RDR6-mediated dsRNA synthesis is not primed by primary siRNAs and that dsRNA synthesis appears to be generally initiated at the 3'-end of the target RNA.

The dynamics of dominance: open questions, challenges and solutions

Although social hierarchies are recognized as dynamic systems, they are typically treated as static entities for practical reasons. Here, we ask what we can learn from a dynamical view of dominance, and provide a research agenda for the next decades. We identify five broad questions at the individual, dyadic and group levels, exploring the causes and consequences of individual changes in rank, the dynamics underlying dyadic dominance relationships, and the origins and impacts of social instability. Although challenges remain, we propose avenues for overcoming them. We suggest distinguishing between different types of social mobility to provide conceptual clarity about hierarchy dynamics at the individual level, and emphasize the need to explore how these dynamic processes produce dominance trajectories over individual lifespans and impact selection on status-seeking behaviour. At the dyadic level, there is scope for deeper exploration of decision-making processes leading to observed interactions, and how stable but malleable relationships emerge from these interactions. Across scales, model systems where rank is manipulable will be extremely useful for testing hypotheses about dominance dynamics. Long-term individual-based studies will also be critical for understanding the impact of rare events, and for interrogating dynamics that unfold over lifetimes and generations. This article is part of the theme issue 'The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies'.

Transitivity Violations Undermine Rating Scales in Motivation Research

Measures of psychological attributes, such as motivation, typically involve rating scales, assuming that an attribute can be ordered. If an attribute has an ordinal structure, its levels stand in ordinal relations to one another, and these must be transitive. We tested if transitivity is preserved when people compare different motives in terms of their importance to learning. We found transitivity violations in both strict (Study 1) and non-strict (Study 2) orderings in about half of the participants. Nevertheless, based on the distribution of such violations, we conclude that an ordinal structure of motivation can be found, but only when levels of motives differ noticeably. As the levels become subjectively similar, transitivity is not preserved, and the ordinal structure cannot be justified even in non-strict ordering. The findings question the mainstream practice of measuring psychological attributes before their structure is properly explored.

Reporting of Cochrane systematic review protocols with network meta-analyses-A scoping review

Publishing systematic review protocols is a fundamental part of systematic reviews to ensure transparency and reproducibility. In this scoping review, we aimed to evaluate reporting of Cochrane systematic review protocols with network meta-analyses (NMA). We searched all Cochrane NMA protocols published in 2018 and 2019, and assessed the characteristics and reporting of methodologies relevant to NMA. We reported frequencies for each reporting item. Forty-five protocols were assessed, including two for overviews and 43 for intervention reviews. Thirty-three (73%) were labelled as NMA protocols in the title. Forty-two (95%) justified the need of an NMA and 40 (89%) used appropriate search strategies to identify potential eligible studies. About half (24, 53%) considered the transitivity assumption when reporting inclusion criteria and 35 (78%) specified potential effect modifiers. Forty-three (96%) reported statistical software for NMA, 25 (56%) reported NMA model choice, 32 (71%) reported framework choice and 32 (71%) reported assumption about heterogeneity variances. Protocols varied in whether they reported methods for relative ranking (35, 78%), statistical inconsistency (40, 89%), reporting bias (44, 98%) and sources of heterogeneity (39, 87%). In conclusion, Cochrane NMA protocols reported multiple NMA-specific items well, but could be further improved, especially regarding transitivity assumptions. Our recommendations for NMA protocol reporting based on this scoping review could assist authors, reviewers, and editors to improve NMA protocols.

The key role of terminators on the expression and post-transcriptional gene silencing of transgenes

Transgenes have become essential to modern biology, being an important tool in functional genomic studies and also in the development of biotechnological products. One of the major challenges in the generation of transgenic lines concerns the expression of transgenes, which, compared to endogenes, are particularly susceptible to silencing mediated by small RNAs (sRNAs). Several reasons have been put forward to explain why transgenes often trigger the production of sRNAs, such as the high level of expression induced by commonly used strong constitutive promoters, the lack of introns, and features resembling viral and other exogenous sequences. However, the relative contributions of the different genomic elements with respect to protecting genes from the silencing machinery and their molecular mechanisms remain unclear. Here, we present the results of a mutagenesis screen conceived to identify features involved in the protection of endogenes against becoming a template for the production of sRNAs. Interestingly, all of the recovered mutants had alterations in genes with proposed function in transcription termination, suggesting a central role of terminators in this process. Indeed, using a GFP reporter system, we show that, among different genetic elements tested, the terminator sequence had the greatest effect on transgene-derived sRNA accumulation and that a well-defined poly(A) site might be especially important. Finally, we describe an unexpected mechanism, where transgenes containing certain intron/terminator combinations lead to an increase in the production of sRNAs, which appears to interfere with splicing.

Network meta-analyses in reproductive medicine: challenges and opportunities

Network meta-analysis allows researchers to synthesise both direct and indirect evidence, thus enabling simultaneous comparisons of multiple treatments. A relatively recent addition to evidence synthesis in reproductive medicine, this approach has become increasingly popular. Yet, the underlying assumptions of network meta-analyses, which drive the validity of their findings, have been frequently ignored. In this article, we discuss the strengths and limitations of network meta-analyses. In addition, we present an overview of published network meta-analyses in reproductive medicine, summarize their challenges and provide insights into future research opportunities.

From the Kinetic Theory of Gases to the Kinetics of Rate Processes: On the Verge of the Thermodynamic and Kinetic Limits

A variety of current experiments and molecular dynamics computations are expanding our understanding of rate processes occurring in extreme environments, especially at low temperatures, where deviations from linearity of Arrhenius plots are revealed. The thermodynamic behavior of molecular systems is determined at a specific temperature within conditions on large volume and number of particles at a given density (the thermodynamic limit): on the other side, kinetic features are intuitively perceived as defined in a range between the extreme temperatures, which limit the existence of each specific phase. In this paper, extending the statistical mechanics approach due to Fowler and collaborators, ensembles and partition functions are defined to evaluate initial state averages and activation energies involved in the kinetics of rate processes. A key step is delayed access to the thermodynamic limit when conditions on a large volume and number of particles are not fulfilled: the involved mathematical analysis requires consideration of the role of the succession for the exponential function due to Euler, precursor to the Poisson and Boltzmann classical distributions, recently discussed. Arguments are presented to demonstrate that a universal feature emerges: Convex Arrhenius plots (super-Arrhenius behavior) as temperature decreases are amply documented in progressively wider contexts, such as viscosity and glass transitions, biological processes, enzymatic catalysis, plasma catalysis, geochemical fluidity, and chemical reactions involving collective phenomena. The treatment expands the classical Tolman’s theorem formulated quantally by Fowler and Guggenheim: the activation energy of processes is related to the averages of microscopic energies. We previously introduced the concept of “transitivity”, a function that compactly accounts for the development of heuristic formulas and suggests the search for universal behavior. The velocity distribution function far from the thermodynamic limit is illustrated; the fraction of molecules with energy in excess of a certain threshold for the description of the kinetics of low-temperature transitions and of non-equilibrium reaction rates is derived. Uniform extension beyond the classical case to include quantum tunneling (leading to the concavity of plots, sub-Arrhenius behavior) and to Fermi and Bose statistics has been considered elsewhere. A companion paper presents a computational code permitting applications to a variety of phenomena and provides further examples.

The Whys and Wherefores of Transitivity in Plants

Transitivity in plants is a mechanism that produces secondary small interfering RNAs (siRNAs) from a transcript targeted by primary small RNAs (sRNAs). It expands the silencing signal to additional sequences of the transcript. The process requires RNA-dependent RNA polymerases (RDRs), which convert single-stranded RNA targets into a double-stranded (ds) RNA, the precursor of siRNAs and is critical for effective and amplified responses to virus infection. It is also important for the production of endogenous secondary siRNAs, such as phased siRNAs (phasiRNAs), which regulate several genes involved in development and adaptation. Transitivity on endogenous transcripts is very specific, utilizing special primary sRNAs, such as miRNAs with unique features, and particular ARGONAUTEs. In contrast, transitivity on transgene and virus (exogenous) transcripts is more generic. This dichotomy of responses implies the existence of a mechanism that differentiates self from non-self targets. In this work, we examine the possible mechanistic process behind the dichotomy and the intriguing counter-intuitive directionality of transitive sequence-spread in plants.

A criterion-based approach to systematic and transparent comparative effectiveness: a case study in psoriatic arthritis

Aim: Indirect treatment comparisons are used when no direct comparison is available. Comparison networks should satisfy the transitivity assumption, that is, equal likelihood of treatment assignment for a given patient based on comparability of studies. Materials & methods: Seven criteria were evaluated across 18 randomized controlled trials in psoriatic arthritis: inclusion/exclusion criteria, clinical trial design and follow-up, patient-level baseline characteristics, disease severity, prior therapies, concomitant and extended-trial treatment and placebo response differences. Results: Across studies, placebo was a common comparator, and key efficacy end points were reported. Collectively, several potential sources of insufficient transitivity were identified, most often related to trial design and population differences. Conclusion: Potential challenges in satisfying transitivity occur frequently and should be evaluated thoroughly.

Transfer of baseline reject control to transitivity trials and its effect on equivalence class formation

This study explored the role of baseline reject control on transitivity responding. In Experiment 1, participants learned to respond to a baseline of arbitrary AB and AC conditional relations, and then they were exposed to transitivity-like BC and CB trials in which the correct comparison stimulus was replaced by a novel stimulus (D). Five of 10 participants selected stimulus D, but only 1 showed expansion of the baseline stimulus classes to include the D stimuli. In Experiment 2, the emergence of symmetry and transitivity from baseline relations was assessed before participants were exposed to the transitivity-like trials. Six of 8 participants who showed emergence of equivalence relations selected the D stimuli on transitivity-like trials and provided evidence that baseline classes expanded to include these stimuli. In Experiment 3, these 6 participants selected novel stimuli (E) in additional transitivity-like trials, and all showed that the E stimuli had become members of the previously established classes, which now comprised 5 members. A route for the emergence of transitivity by way of the transfer of baseline between-classes reject control is discussed.

Network Structure Predicts Changes in Perception Accuracy of Social Relationships

The goal of this study was to test how changes in perception accuracy of affiliative networks (i.e., the ability to accurately identify who affiliates with whom) are related to an important structural feature of peer groups- the likelihood of children to affiliate with mutual partners (transitivity). Data from three longitudinal samples (two from elementary school children and one from young adolescents; N = 257, 618 observations) show that children and adolescents in classrooms with a higher proportion of transitive relationships are better at perceiving who affiliates with whom, and that increases in transitivity associate with increases in perception accuracy. This is the first study to show that structural features of peer groups relate with individual perceptions of affiliative relationships, providing further evidence that these features have an important role in promoting individual adaptation and supporting previous suggestions that classroom-variables play a role in fostering accurate perceptions of social relationships.

The influence of episodic memory decline on value-based choice

Recent studies suggest the involvement of episodic memory in value-based decisions as a source of information about subjective values of choice options. We therefore tested the link between age-related memory decline and inconsistencies in value-based decisions in 30 cognitively healthy older adults. Within the pre-registered experiment, the inconsistencies were measured in two ways: i) the consistency between stated preferences and revealed choices; ii) the amount of intransitivities in choice triplets, revealed in a forced paired choice task including all possible pairings of 20 food products. Although no significant association of memory functions to number of intransitive triplets was observed, participants with lower memory scores were more likely to choose the item for which they stated a lower preference. The results suggest a higher noise in the underlying preference signal in participants with lower memory. We discuss the results in the context of the unique needs of elderly consumers.

Diversity of Grammars and Their Diverging Evolutionary and Processing Paths: Evidence From Functional MRI Study of Serbian

We address the puzzle of "unity in diversity" in human languages by advocating the (minimal) common denominator for the diverse expressions of transitivity across human languages, consistent with the view that early in language evolution there was a modest beginning for syntax and that this beginning provided the foundation for the further elaboration of syntactic complexity. This study reports the results of a functional MRI experiment investigating differential patterns of brain activation during processing of sentences with minimal versus fuller syntactic structures. These structural layers have been postulated to represent different stages in the evolution of syntax, potentially engaging different brain networks. We focused on the Serbian "middles," analyzed as lacking the transitivity (vP) layer, contrasted with matched transitives, containing the transitivity layer. Our main hypothesis was that transitives will produce more activation in the syntactic (Broca's-Basal Ganglia) brain network, in comparison to more rudimentary middles. The participants (n = 14) were healthy adults (Mean age = 33.36; SD = 12.23), native speakers of Serbo-Croatian. The task consisted of reading a series of sentences (middles and transitives; n = 64) presented in blocks of 8, while being engaged in a detection of repetition task. We found that the processing of transitives, compared to middles, was associated with an increase in activation in the basal ganglia bilaterally. Although we did not find an effect in Broca's area, transitives, compared to middles, evoked greater activation in the precentral gyrus (BA 6), proposed to be part of the "Broca's complex." Our results add to the previous findings that Broca's area is not the sole center for syntactic processing, but rather is part of a larger circuit that involves subcortical structures. We discuss our results in the context of the recent findings concerning the gene-brain-language pathway involving mutations in FOXP2 that likely contributed to the enhancement of the frontal-striatal brain network, facilitating human capacity for complex syntax.

Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation

Genes or alleles can interact by small RNAs in a homology dependent manner meaning that short interfering (siRNAs) can act in trans at the chromatin level producing stable and heritable silencing phenotypes. Because of the puzzling data on endogenous paramutations, their impact contributing to adaptive evolution in a Lamarckian manner remains unknown. An increasing number of studies characterizes the underlying siRNA accumulation pathways using transgene experiments. Also in the ciliate Paramecium tetraurelia, we induce trans silencing on the chromatin level by injection of truncated transgenes. Here, we characterize the efficiency of this mechanism at different temperatures showing that silencing of the endogenous genes is temperature dependent. Analyzing different transgene constructs at different copy numbers, we dissected whether silencing efficiency is due to varying precursor RNAs or siRNA accumulation. Our data shows that silencing efficiency correlates with more efficient accumulation of primary siRNAs at higher temperatures rather than higher expression of precursor RNAs. Due to higher primary levels, secondary siRNAs also show temperature dependency and interestingly increase their relative proportion to primary siRNAs. Our data shows that efficient trans silencing on the chromatin level in P. tetraurelia depends on environmental parameters, thus being an important epigenetic factor limiting regulatory effects of siRNAs.

Syntactic Priming As a Test of Argument Structure: A Self-paced Reading Experiment

Using data from a behavioral structural priming experiment, we test two competing theoretical approaches to argument structure, which attribute different configurations to (in)transitive structures. These approaches make different claims about the relationship between unergatives and transitive structures selecting either a DP complement or a small clause complement in structurally unambiguous sentences, thus making different predictions about priming relations between them. Using statistical tools that combine a factorial 6 × 6 within subjects ANOVA, a mixed effects ANCOVA and a linear mixed effects regression model, we report syntactic priming effects in comprehension, which suggest a stronger predictive contribution of a model that supports an interpretive semantics view of syntax, whereby syntactic structures do not necessarily reflect argument/event structure in semantically unambiguous configurations. They also contribute novel experimental evidence that correlate representational complexity with language processing in the mind and brain. Our study further upholds the validity of combining quantitative methods and theoretical approaches to linguistics for advancing our knowledge of syntactic phenomena.

NEW SURVEY QUESTIONS AND ESTIMATORS FOR NETWORK CLUSTERING WITH RESPONDENT-DRIVEN SAMPLING DATA

Respondent-driven sampling (RDS) is a popular method for sampling hard-to-survey populations that leverages social network connections through peer recruitment. While RDS is most frequently applied to estimate the prevalence of infections and risk behaviors of interest to public health, such as HIV/AIDS or condom use, it is rarely used to draw inferences about the structural properties of social networks among such populations because it does not typically collect the necessary data. Drawing on recent advances in computer science, we introduce a set of data collection instruments and RDS estimators for network clustering, an important topological property that has been linked to a network's potential for diffusion of information, disease, and health behaviors. We use simulations to explore how these estimators, originally developed for random walk samples of computer networks, perform when applied to RDS samples with characteristics encountered in realistic field settings that depart from random walks. In particular, we explore the effects of multiple seeds, without replacement versus with replacement, branching chains, imperfect response rates, preferential recruitment, and misreporting of ties. We find that clustering coefficient estimators retain desirable properties in RDS samples. This paper takes an important step toward calculating network characteristics using nontraditional sampling methods, and it expands the potential of RDS to tell researchers more about hidden populations and the social factors driving disease prevalence.

Who or what has agency in the discussion of antimicrobial resistance in UK news media (2010-2015)? A transitivity analysis

The increase in infections resistant to the existing antimicrobial medicines has become a topic of concern for health professionals, policy makers and publics across the globe; however, among the public there is a sense that this is an issue beyond their control. Research has shown that the news media can have a significant role to play in the public's understanding of science and medicine. In this article, we respond to a call by research councils in the United Kingdom to study antibiotic or antimicrobial resistance as a social phenomenon by providing a linguistic analysis of reporting on this issue in the UK press. We combine transitivity analysis with a social representations framework to determine who and what the social actors are in discussions of antimicrobial resistance in the UK press (2010-2015), as well as which of those social actors are characterised as having agency in the processes around antimicrobial resistance. Findings show that antibiotics and the infections they are designed to treat are instilled with agency, that there is a tension between allocating responsibility to either doctors-as-prescribers or patients-as-users and collectivisation of the general public as an unspecified 'we': marginalising livestock farming and pharmaceutical industry responsibilities.

Monkeys choose as if maximizing utility compatible with basic principles of revealed preference theory

Revealed preference theory provides axiomatic tools for assessing whether individuals make observable choices "as if" they are maximizing an underlying utility function. The theory evokes a tradeoff between goods whereby individuals improve themselves by trading one good for another good to obtain the best combination. Preferences revealed in these choices are modeled as curves of equal choice (indifference curves) and reflect an underlying process of optimization. These notions have far-reaching applications in consumer choice theory and impact the welfare of human and animal populations. However, they lack the empirical implementation in animals that would be required to establish a common biological basis. In a design using basic features of revealed preference theory, we measured in rhesus monkeys the frequency of repeated choices between bundles of two liquids. For various liquids, the animals' choices were compatible with the notion of giving up a quantity of one good to gain one unit of another good while maintaining choice indifference, thereby implementing the concept of marginal rate of substitution. The indifference maps consisted of nonoverlapping, linear, convex, and occasionally concave curves with typically negative, but also sometimes positive, slopes depending on bundle composition. Out-of-sample predictions using homothetic polynomials validated the indifference curves. The animals' preferences were internally consistent in satisfying transitivity. Change of option set size demonstrated choice optimality and satisfied the Weak Axiom of Revealed Preference (WARP). These data are consistent with a version of revealed preference theory in which preferences are stochastic; the monkeys behaved "as if" they had well-structured preferences and maximized utility.

Corpus-Based Transitivity Biases in Individuals with Aphasia

BACKGROUND

This study investigated whether individuals with aphasia (IWA) retain verb biases in expressive language. Verb biases refer to the likelihood that a given verb will occur in different sentence structures. We focused on the likelihood of verbs occurring in transitive and intransitive structures.

AIMS

The main goal of this study was to determine whether IWA and controls show similar verb biases or whether IWA show a preference for transitive or intransitive structures that supersedes individual verb biases. We also investigated whether IWA show a preference for intransitively or transitively biased verbs, whether verb biases differ as a function of aphasia type, and how verb bias affects errors in IWA's speech production.

METHODS

The current study analyzed 236 transcribed interviews of IWA from AphasiaBank. All uses of 54 verbs were coded based on the sentence structure and the presence of errors. We report data from 11 transitively biased and 11 intransitively biased verbs.

OUTCOMES AND RESULTS

IWA's transitivity biases were indistinguishable from controls' biases. In addition, IWA produced more intransitively biased verbs than transitively biased verbs overall. In ungrammatical productions, IWA's error rates were higher in sentence structures that conflicted with verb bias and highest when an intransitively biased verb was attempted in a transitive structure.

MAIN CONCLUSIONS

These findings indicate that IWA are sensitive to verb bias and verb complexity within expressive language. The effects are consistent with previous literature concerning IWA's sensitivity to verb bias in receptive language tasks and to verb complexity in verb retrieval tasks.

Impaired inference in a case of developmental amnesia

Amnesia is associated with impairments in relational memory, which is critically supported by the hippocampus. By adapting the transitivity paradigm, we previously showed that age-related impairments in inference were mitigated when judgments could be predicated on known pairwise relations, however, such advantages were not observed in the adult-onset amnesic case D.A. Here, we replicate and extend this finding in a developmental amnesic case (N.C.), who also shows impaired relational learning and transitive expression. Unlike D.A., N.C.'s damage affected the extended hippocampal system and diencephalic structures, and does not extend to neocortical areas that are affected in D.A. Critically, despite their differences in etiology and affected structures, N.C. and D.A. perform similarly on the task. N.C. showed intact pairwise knowledge, suggesting that he is able to use existing semantic information, but this semantic knowledge was insufficient to support transitive expression. The present results suggest a critical role for regions connected to the hippocampus and/or medial prefrontal cortex in inference beyond learning of pairwise relations. © 2016 The Authors Hippocampus Published by Wiley Periodicals, Inc.

Disrupted Network Topology in Patients with Stable and Progressive Mild Cognitive Impairment and Alzheimer's Disease

Recent findings suggest that Alzheimer's disease (AD) is a disconnection syndrome characterized by abnormalities in large-scale networks. However, the alterations that occur in network topology during the prodromal stages of AD, particularly in patients with stable mild cognitive impairment (MCI) and those that show a slow or faster progression to dementia, are still poorly understood. In this study, we used graph theory to assess the organization of structural MRI networks in stable MCI (sMCI) subjects, late MCI converters (lMCIc), early MCI converters (eMCIc), and AD patients from 2 large multicenter cohorts: ADNI and AddNeuroMed. Our findings showed an abnormal global network organization in all patient groups, as reflected by an increased path length, reduced transitivity, and increased modularity compared with controls. In addition, lMCIc, eMCIc, and AD patients showed a decreased path length and mean clustering compared with the sMCI group. At the local level, there were nodal clustering decreases mostly in AD patients, while the nodal closeness centrality detected abnormalities across all patient groups, showing overlapping changes in the hippocampi and amygdala and nonoverlapping changes in parietal, entorhinal, and orbitofrontal regions. These findings suggest that the prodromal and clinical stages of AD are associated with an abnormal network topology.

A Winding Road: Alzheimer's Disease Increases Circuitous Functional Connectivity Pathways

Neuroimaging has been successful in characterizing the pattern of cerebral atrophy that accompanies the progression of Alzheimer’s disease (AD). Examination of functional connectivity, the strength of signal synchronicity between brain regions, has gathered pace as another way of understanding changes to the brain that are associated with AD. It appears to have good sensitivity and detect effects that precede cognitive decline, and thus offers the possibility to understand the neurobiology of the disease in its earliest phases. However, functional connectivity analyzes to date generally consider only the strongest connections, with weaker links ignored. This proof-of-concept study compared patients with mild-to-moderate AD (N = 11) and matched control individuals (N = 12) based on functional connectivities derived from blood-oxygenation level dependent (BOLD) sensitive functional MRI acquired during resting wakefulness. All positive connectivities irrespective of their strength were included. Transitive closures of the resulting connectome were calculated that classified connections as either direct or indirect. Between-group differences in the proportion of indirect paths were observed. In AD, there was broadly increased indirect connectivity across greater spatial distances. Furthermore, the indirect pathways in AD had greater between-subject topological variance than controls. The prevailing characterization of AD as being a disconnection syndrome is refined by the observation that direct links between regions that are impaired are perhaps replaced by an increase in indirect functional pathways that is only detectable through inclusion of connections across the entire range of connection strengths.

The network motif architecture of dominance hierarchies

The widespread existence of dominance hierarchies has been a central puzzle in social evolution, yet we lack a framework for synthesizing the vast empirical data on hierarchy structure in animal groups. We applied network motif analysis to compare the structures of dominance networks from data published over the past 80 years. Overall patterns of dominance relations, including some aspects of non-interactions, were strikingly similar across disparate group types. For example, nearly all groups exhibited high frequencies of transitive triads, whereas cycles were very rare. Moreover, pass-along triads were rare, and double-dominant triads were common in most groups. These patterns did not vary in any systematic way across taxa, study settings (captive or wild) or group size. Two factors significantly affected network motif structure: the proportion of dyads that were observed to interact and the interaction rates of the top-ranked individuals. Thus, study design (i.e. how many interactions were observed) and the behaviour of key individuals in the group could explain much of the variations we see in social hierarchies across animals. Our findings confirm the ubiquity of dominance hierarchies across all animal systems, and demonstrate that network analysis provides new avenues for comparative analyses of social hierarchies.

Relational learning and transitive expression in aging and amnesia

Aging has been associated with a decline in relational memory, which is critically supported by the hippocampus. By adapting the transitivity paradigm (Bunsey and Eichenbaum (1996) Nature 379:255‐257), which traditionally has been used in nonhuman animal research, this work examined the extent to which aging is accompanied by deficits in relational learning and flexible expression of relational information. Older adults' performance was additionally contrasted with that of amnesic case DA to understand the critical contributions of the medial temporal lobe, and specifically, the hippocampus, which endures structural and functional changes in healthy aging. Participants were required to select the correct choice item (B versus Y) based on the presented sample item (e.g., A). Pairwise relations must be learned (A‐>B, B‐>C, C‐>D) so that ultimately, the correct relations can be inferred when presented with a novel probe item (A‐>C?Z?). Participants completed four conditions of transitivity that varied in terms of the degree to which the stimuli and the relations among them were known pre‐experimentally. Younger adults, older adults, and DA performed similarly when the condition employed all pre‐experimentally known, semantic, relations. Older adults and DA were less accurate than younger adults when all to‐be‐learned relations were arbitrary. However, accuracy improved for older adults when they could use pre‐experimentally known pairwise relations to express understanding of arbitrary relations as indexed through inference judgments. DA could not learn arbitrary relations nor use existing knowledge to support novel inferences. These results suggest that while aging has often been associated with an emerging decline in hippocampal function, prior knowledge can be used to support novel inferences. However, in case DA, significant damage to the hippocampus likely impaired his ability to learn novel relations, while additional damage to ventromedial prefrontal and anterior temporal regions may have resulted in an inability to use prior knowledge to flexibly express indirect relational knowledge. © 2015 The Authors Hippocampus Published by Wiley Periodicals, Inc.

Determinants of judgment and decision making quality: the interplay between information processing style and situational factors

A framework is presented to better characterize the role of individual differences in information processing style and their interplay with contextual factors in determining decision making quality. In Experiment 1, we show that individual differences in information processing style are flexible and can be modified by situational factors. Specifically, a situational manipulation that induced an analytical mode of thought improved decision quality. In Experiment 2, we show that this improvement in decision quality is highly contingent on the compatibility between the dominant thinking mode and the nature of the task. That is, encouraging an intuitive mode of thought led to better performance on an intuitive task but hampered performance on an analytical task. The reverse pattern was obtained when an analytical mode of thought was encouraged. We discuss the implications of these results for the assessment of decision making competence, and suggest practical directions to help individuals better adjust their information processing style to the situation at hand and make optimal decisions.

A successful search for symmetry (and other derived relations) in the conditional discriminations of pigeons. CONDUCTUAL : REVISTA INTERNACIONAL DE INTERCONDUCTISMO Y ANALISIS DE CONDUCTA 2015;3:4-25. [PMID: 28386579 PMCID: PMC5380386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Symmetry is one of three derived relations (along with transitivity and reflexivity) that indicate that explicitly trained conditional relations are equivalence relations and that the elements of those trained relations are members of a stimulus class. Although BA symmetry is typically observed after AB conditional discrimination training in humans, it has been an elusive phenomenon in other animals until just recently. This paper describes past unsuccessful attempts to observe symmetry in non-human animals and the likely reasons for that lack of success. I then describe how methodological changes made in response to the earlier findings have now yielded robust evidence for symmetry in pigeons, and what these changes indicate about the functional matching stimuli. Finally, I describe a theory of stimulus-class formation (Urcuioli, 2008) which specifies how and why symmetry and other derived relations arise from different sets of trained relations. These derived relations are noteworthy because they demonstrate an impressive repertoire of non-similarity-based categorization effects in animals and the generative effects of reinforcement and stimulus control processes on behavior.

Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis

The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE Synthase (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.

Tetracycline modifies competitive interactions in experimental microcosms containing bacteria isolated from freshwater

Interspecific microbial interactions are important for community structure, function and evolution, but it is not fully understood how interactions among bacterial species are influenced by some types of abiotic environmental variation, such as exposure to antibiotics. We tested for the effect of an antibiotic, tetracycline, on interspecific interactions in vitro among four species of aquatic bacteria isolated from European water bodies. Interactions among species in experimental microcosms containing artificial lake water (ALW) supplemented with glucose were largely competitive, as detected by comparing mixed cultures to pure cultures of their constituent species. Sublethal concentrations of tetracycline changed the relative competitive abilities of different species and revealed considerable variation in antibiotic sensitivity, but did not reduce the average strength of competition. Interspecific interactions at a given concentration were largely predictable from growth in pure cultures and indirect interactions with other species. These results suggest that antibiotics such as tetracycline may have important consequences for interactions among bacterial species, but in our experiments this was because species varied in their capacities for growth in the presence of tetracycline, rather than reduced competition at increasing tetracycline concentrations.

Natural selection can favour 'irrational' behaviour

Understanding decisions is the fundamental aim of the behavioural sciences. The theory of rational choice is based on axiomatic principles such as transitivity and independence of irrelevant alternatives (IIA). Empirical studies have demonstrated that the behaviour of humans and other animals often seems irrational; there can be a lack of transitivity in choice and seemingly irrelevant alternatives can alter decisions. These violations of transitivity and IIA undermine rational choice theory. However, we show that an individual that is maximizing its rate of food gain can exhibit failure of transitivity and IIA. We show that such violations can be caused because a current option may disappear in the near future or a better option may reappear soon. Current food options can be indicative of food availability in the near future, and this key feature can result in apparently irrational behaviour.

Patient-related constraints on get- and be-passive uses in English: evidence from paraphrasing

In English, transitive events can be described in various ways. The main possibilities are active-voice and passive-voice, which are assumed to have distinct semantic and pragmatic functions. Within the passive, there are two further options, namely be-passive or get-passive. While these two forms are generally understood to differ, there is little agreement on precisely how and why. The passive Patient is frequently cited as playing a role, though again agreement on the specifics is rare. Here we present three paraphrasing experiments investigating Patient-related constraints on the selection of active vs. passive voice, and be- vs. get-passive, respectively. Participants either had to re-tell short stories in their own words (Experiments 1 and 2) or had to answer specific questions about the Patient in those short stories (Experiment 3). We found that a given Agent in a story promotes the use of active-voice, while a given Patient promotes be-passives specifically. Meanwhile, get-passive use increases when the Patient is marked as important. We argue that the three forms of transitive description are functionally and semantically distinct, and can be arranged along two dimensions: Patient Prominence and Patient Importance. We claim that active-voice has a near-complementary relationship with the be-passive, driven by which protagonist is given. Since both get and be are passive, they share the features of a Patient-subject and an optional Agent by-phrase; however, get specifically responds to a Patient being marked as important. Each of these descriptions has its own set of features that differentiate it from the others.

Optimal behaviour can violate the principle of regularity

Understanding decisions is a fundamental aim of behavioural ecology, psychology and economics. The regularity axiom of utility theory holds that a preference between options should be maintained when other options are made available. Empirical studies have shown that animals violate regularity but this has not been understood from a theoretical perspective, such decisions have therefore been labelled as irrational. Here, I use models of state-dependent behaviour to demonstrate that choices can violate regularity even when behavioural strategies are optimal. I also show that the range of conditions over which regularity should be violated can be larger when options do not always persist into the future. Consequently, utility theory--based on axioms, including transitivity, regularity and the independence of irrelevant alternatives--is undermined, because even alternatives that are never chosen by an animal (in its current state) can be relevant to a decision.

Starlings uphold principles of economic rationality for delay and probability of reward

Rationality principles are the bedrock of normative theories of decision-making in biology and microeconomics, but whereas in microeconomics, consistent choice underlies the notion of utility; in biology, the assumption of consistent selective pressures justifies modelling decision mechanisms as if they were designed to maximize fitness. In either case, violations of consistency contradict expectations and attract theoretical interest. Reported violations of rationality in non-humans include intransitivity (i.e. circular preferences) and lack of independence of irrelevant alternatives (changes in relative preference between options when embedded in different choice sets), but the extent to which these observations truly represent breaches of rationality is debatable. We tested both principles with starlings (Sturnus vulgaris), training subjects either with five options differing in food delay (exp. 1) or with six options differing in reward probability (exp. 2), before letting them choose repeatedly one option out of several binary and trinary sets of options. The starlings conformed to economic rationality on both tests, showing strong stochastic transitivity and no violation of the independence principle. These results endorse the rational choice and optimality approaches used in behavioural ecology, and highlight the need for functional and mechanistic enquiring when apparent violations of such principles are observed.

Symmetric diffeomorphic modeling of longitudinal structural MRI

This technology report describes the longitudinal registration approach that we intend to incorporate into SPM12. It essentially describes a group-wise intra-subject modeling framework, which combines diffeomorphic and rigid-body registration, incorporating a correction for the intensity inhomogeneity artifact usually seen in MRI data. Emphasis is placed on achieving internal consistency and accounting for many of the mathematical subtleties that most implementations overlook. The implementation was evaluated using examples from the OASIS Longitudinal MRI Data in Non-demented and Demented Older Adults.

An in planta, Agrobacterium-mediated transient gene expression method for inducing gene silencing in rice (Oryza sativa L.) leaves

BACKGROUND

Localized introduction and transient expression of T-DNA constructs mediated by agro-infiltration of leaf tissues has been largely used in dicot plants for analyzing the transitivity and the cell-to cell movement of the RNAi signal. In cereals, however, the morphology of the leaf and particularly the structure of the leaf epidermis, prevent infiltration of a bacterial suspension in cells by simple pressure, a method otherwise successful in dicots leaves. This study aimed at establishing a rapid method for the functional analysis of rice genes based on the triggering of RNA interference (RNAi) following Agrobacterium-mediated transient transformation of leaves.

RESULTS

Using an agro-infection protocol combining a wound treatment and a surfactant, we were able to obtain in a reliable manner transient expression of a T-DNA-borne uidA gene in leaf cells of japonica and indica rice cultivars. Using this protocol to transiently inhibit gene expression in leaf cells, we introduced hairpin RNA (hpRNA) T-DNA constructs containing gene specific tags of the phytoene desaturase (OsPDS) and of the SLENDER 1 (OsSLR1) genes previously proven to trigger RNAi of target genes in stable transformants. SiRNA accumulation was observed in the agro-infected leaf area for both constructs indicating successful triggering of the silencing signal. Accumulation of secondary siRNA was observed in both stably and transiently transformed leaf tissues expressing the HpRNA OsSLR1 construct. Gene silencing signalling was investigated in monitoring the parallel time course of OsPDS-derived mRNA and siRNA accumulation in the agro-infiltrated leaf area and adjacent systemic sectors. The sensitive RT-Q-PCR method evidenced a consistent, parallel decrease of OsPDS transcripts in both the agroinfiltred and adjacent tissues, with a time lag for the latter.

CONCLUSIONS

These results indicate that the method is efficient at inducing gene silencing in the agro-infected leaf area. The transfer of low amounts of siRNA, probably occurring passively through the symplastic pathway from the agro-infected area, seemed sufficient to trigger degradation of target transcripts in the adjacent tissues. This method is therefore well suited to study the cell-to-cell movement of the silencing signal in a monocot plant and further test the functionality of natural and artificial miRNA expression constructs.

Indirect and mixed-treatment comparison, network, or multiple-treatments meta-analysis: many names, many benefits, many concerns for the next generation evidence synthesis tool

The ever increasing number of alternative treatment options and the plethora of clinical trials have put systematic reviews and meta-analysis under a new perspective by emphasizing the need to make inferences about competing treatments for the same condition. The statistical component in reviews that compare multiple interventions, network meta-analysis, is the next generation evidence synthesis toolkit which, when properly applied, can serve decision-making better than the established pairwise meta-analysis. The criticism and enthusiasm for network meta-analysis echo those that greeted the advent of simple meta-analysis. The main criticism is associated with the difficulty in evaluating the assumption underlying the statistical synthesis of direct and indirect evidence. In the present article, the assumption of the network meta-analysis are presented using various formulations, the statistical and nonstatistical methodological considerations are elucidated, and the progress achieved in this field is summarized. Throughout, focus is put on highlighting the analogy between the concerns and difficulties that the scientific community had some time ago when advancing from individual trials to their quantitative synthesis via meta-analysis and those currently expressed about the transition from head-to-head meta-analyses to network meta-analysis. Copyright © 2012 John Wiley & Sons, Ltd.

Emergent identity matching after successive matching training. II: Reflexivity or transitivity

Three experiments evaluated whether the apparent reflexivity effect reported by Sweeney and Urcuioli (2010) for pigeons might, in fact, be transitivity. In Experiment 1, pigeons learned symmetrically reinforced hue-form (A-B) and form-hue (B-A) successive matching. Those also trained on form-form (B-B) matching responded more to hue comparisons that matched their preceding samples on subsequent hue-hue (A-A) probe trials. By contrast, most pigeons trained on just A-B and B-A matching did not show this effect; but some did--a finding consistent with transitivity. Experiment 2 showed that the latter pigeons also responded more to form comparisons that matched their preceding samples on form-form (B-B) probe trials. Experiment 3 tested the prediction that hue-hue matching versus hue-hue oddity, respectively, should emerge after symmetrically versus asymmetrically reinforced arbitrary matching relations if those relations are truly transitive. For the few pigeons showing an emergent effect, comparison response rates were higher when a probe-trial comparison matched its preceding sample independently of the baseline contingencies. These results indicate neither a reflexivity nor a transitivity effect but, rather, a possible identity bias.

Exponential-family random graph models for valued networks

Exponential-family random graph models (ERGMs) provide a principled and flexible way to model and simulate features common in social networks, such as propensities for homophily, mutuality, and friend-of-a-friend triad closure, through choice of model terms (sufficient statistics). However, those ERGMs modeling the more complex features have, to date, been limited to binary data: presence or absence of ties. Thus, analysis of valued networks, such as those where counts, measurements, or ranks are observed, has necessitated dichotomizing them, losing information and introducing biases. In this work, we generalize ERGMs to valued networks. Focusing on modeling counts, we formulate an ERGM for networks whose ties are counts and discuss issues that arise when moving beyond the binary case. We introduce model terms that generalize and model common social network features for such data and apply these methods to a network dataset whose values are counts of interactions.

Transitivity in health utility measurement: An experimental analysis

Several experimental studies have observed substantial violations of transitivity for decisions between risky lotteries over monetary outcomes. The goal of our experiment is to test whether these violations also affect the evaluation of health states. A particular feature of our experimental design is that it takes into account the possible role of decision errors for generating violations of transitivity. Since we find neither substantial nor systematic deviations from transitive choice behaviour, we can conclude that previously reported violations do not seem to bias health utility measurement.

Testing transitivity of preferences on two-alternative forced choice data

As Duncan Luce and other prominent scholars have pointed out on several occasions, testing algebraic models against empirical data raises difficult conceptual, mathematical, and statistical challenges. Empirical data often result from statistical sampling processes, whereas algebraic theories are nonprobabilistic. Many probabilistic specifications lead to statistical boundary problems and are subject to nontrivial order constrained statistical inference. The present paper discusses Luce's challenge for a particularly prominent axiom: Transitivity. The axiom of transitivity is a central component in many algebraic theories of preference and choice. We offer the currently most complete solution to the challenge in the case of transitivity of binary preference on the theory side and two-alternative forced choice on the empirical side, explicitly for up to five, and implicitly for up to seven, choice alternatives. We also discuss the relationship between our proposed solution and weak stochastic transitivity. We recommend to abandon the latter as a model of transitive individual preferences.

Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins

In plants, worms, and fungi, RNA-dependent RNA polymerases (RDRs) amplify the production of short-interfering RNAs (siRNAs) that mediate RNA silencing. In Arabidopsis, RDR6 is thought to copy endogenous and exogenous RNA templates into double-stranded RNAs (dsRNAs), which are subsequently processed into siRNAs by one or several of the four Dicer-like enzymes (DCL1-->4). This reaction produces secondary siRNAs corresponding to sequences outside the primary targeted regions of a transcript, a phenomenon called transitivity. One recognized role of RDR6 is to strengthen the RNA silencing response mounted by plants against viruses. Accordingly, suppressor proteins deployed by viruses inhibit this defense. However, interactions between silencing suppressors and RDR6 have not yet been documented. Additionally, the mechanism underlying transitivity remains poorly understood. Here, we report how several viral silencing suppressors inhibit the RDR6-dependent amplification of virus-induced and transgene-induced gene silencing. Viral suppression of primary siRNA accumulation shows that transitivity can be initiated with minute amounts of DCL4-dependent 21-nucleotide (nt)-long siRNAs, whereas DCL3-dependent 24-nt siRNAs appear dispensable for this process. We further show that unidirectional (3-->5') transitivity requires the hierarchical and redundant functions of DCL4 and DCL2 acting downstream from RDR6 to produce 21- and 22-nt-long siRNAs, respectively. The 3-->5' transitive reaction is likely to be processive over >750 nt, with secondary siRNA production progressively decreasing as the reaction proceeds toward the 5'-proximal region of target transcripts. Finally, we show that target cleavage by a primary small RNA and 3-->5' transitivity can be genetically uncoupled, and we provide in vivo evidence supporting a key role for priming in this specific reaction.

Down-regulation of endogenes mediated by a transitive silencing signal

Some RNA silencing systems in plants, nematodes, and fungi show spreading of silencing along target sequences, termed transitive silencing. Here, we address the question of whether endogenous targets can be silenced by a transitive silencing signal in plants. In transgenic Arabidopsis thaliana plants that harbored a silencing-inducing locus and a transgenic chimeric primary target, silencing of a secondary transgenic target occurred and the expression of the endogenous catalase genes was down-regulated, coinciding with a knock-down phenotype. Strikingly, the efficiency of the catalase silencing appeared to be correlated with the zygosity of the primary target locus and, to a lesser extent, with that of the silencing-inducing locus. These data suggest that silencing of an endogene induced by transgenic secondary small interfering RNAs (siRNAs) might depend on the amount of primary target transcripts that can act as template for the production of an efficient transitive silencing signal.