bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction
Authors: Predelli Stefano 
Published: March 2020

Abstract
This introduction presents a concise plan for the book, and it provides a sketch of the sense of ‘fictionalism’ relevant for what will follow. It also anticipates the relationships between Radical Fictionalism and so-called non-realist views of fictional discourse, it sketches the consequences of Radical Fictionalism for the distinction between storyworld and periphery, and it introduces the reverberations of Radical Fictionalism on some central themes in the study of narrative. Three homages serve as an indirect preliminary description of the background for Radical Fictionalism, namely Kendall Walton’s Mimesis as Make-Believe, David Lewis’ ‘Truth in Fiction’, and John Searle’s ‘The Logical Status of Fictional Discourse’.
An Occurrence at Owl Creek Bridge
Authors: Predelli Stefano 
Published: March 2020

Abstract
This chapter presents a Radical Fictionalist analysis of talk about fiction, as in my utterances of ‘Fahrquhar was a well to do planter’ or of ‘according to Bierce’s Occurrence, Fahrquhar was a well to do planter’. According to this chapter’s favourite approach, namely the Way of Retelling, the former sentence does not encode a proposition, and the latter does not involve a sentential operator. The central sections of this chapter justify the sense in which these sentences are not in the business of truth, and are rather to be assessed according to the normative dimension of faithfulness. The final sections of this chapter present an alternative to the Way of Retelling, namely the Way of Truth. This hypothesis remains consistent with the premises of Radical Fictionalism, but it satisfies those who insist that fiction talk is to be analysed as elliptical talk concerned with actual truth.
Reflex and Bone Structure
Authors: Predelli Stefano 
Published: March 2020

Abstract
This chapter covers some central topics related to narrative fiction, taking as its starting point the Radical Fictionalist focus on peripheral discourse and fictional telling. In particular, the chapter discusses certain features of allegedly inconsistent fictions and of storyworld importation, with particular attention to the theory in David Lewis’ ‘Truth in Fiction’ and to the case of postmodernist literature. The chapter also discusses some aspects of unreliable narratives, and it puts forth an analysis of alleged cases of importation by appealing to the closure of peripheral discourse. Finally, this chapter defends a Radical Fictionalist take on the distinction between nested and framed narratives.
The Turn of the Screw
Authors: Predelli Stefano 
Published: March 2020

Abstract
This chapter proposes a Radical Fictionalist analysis of critical discourse. In particular, it contrasts actuality-concerned modes of criticism directed towards educated naturalization with two different, non-propositional enterprises. One is a form of critical retelling aimed at bringing to the foreground certain allegedly important but not obvious features of the storyworld. Accordingly, this chapter discusses the idea of underreading and the critics’ commitment to faithfulness, paying particular attention to examples from the critical literature on Henry James’ The Turn of the Screw. The other type of critical retelling is a form of biased retelling which abandons faithfulness in favour of canonicity, that is, in favour of retellings consonant with the critical canon.
History and overview of ‘IFF’
Authors: Cobham Alex , Janský Petr 
Published: March 2020

Abstract
This chapter provides a history of the rise of the term ‘illicit financial flows’ (IFF), and the emergence since 2000 of a global tax justice movement. As a broad umbrella term, the phrase was useful in ensuring the political consensus behind the establishment of a target to curtail IFF in the UN Sustainable Development Goals. But that consensus has hidden, to some extent, disagreements over the relative priorities—from the old view of corruption as a problem predominantly of lower-income countries, to the more recent recognition of the central role of typically high-income financial secrecy jurisdictions. Disagreements over political priority have played out as disputes over the definition of IFF, and over the quality of estimates of scale. This chapter provides a comprehensive typology of IFF, and summarises the evidence on the importance of the phenomenon for human development.
Capital and Wealth Estimates
Authors: Cobham Alex , Janský Petr 
Published: March 2020

Abstract
Capital account-based estimates form an important part of the literature on the scale of illicit financial flows (IFF), along with related approaches to estimate the scale of wealth held offshore and undeclared for tax purposes. This chapter provides a critical survey of the leading estimates. It is clear that offshore wealth is both a significant element in IFF, and offers a valuable avenue to construct indicators of scale. At the same time, however, current estimates of this deliberately hidden quantum are characterised by a high degree of uncertainty, or are based on necessarily partial data sources. But the importance of the area and the relatively high quality of estimates, combined with reasons to expect improving data availability, suggest that offshore wealth should form a core element of IFF scale indicators.
Beyond Scale
Authors: Cobham Alex , Janský Petr 
Published: March 2020

Abstract
This chapter lays out the alternatives to measures of the scale of illicit financial flows (IFF). These include policy-based indicators offering the scope to track global process on transparency measures that are key to curtailing illicit financial flows, and also offer the jurisdiction-level disaggregation to support accountability for policies that maintain opacity; and two related sets of IFF risk measure, which extend the logic of evaluating IFF-facilitating secrecy jurisdictions, to evaluate the exposure of each country to the IFF risks of secrecy elsewhere. While these measures do not offer the single, dollar measure of IFF that the UN target requires, they have the potential to support national, regional and international policymakers in prioritising their responses and ensuring appropriate accountability.
Concerts and Inadvertent Secularization: Religious Music in the Entertainment Market of Eighteenth-Century Paris*
Authors: Pesic Andrei 
Published: March 2020

Abstract
Public concerts offer a new perspective on the controversial subject of secularization and the Enlightenment. From 1725–90, the Concert spirituel in Paris, one of the earliest and most famous concert series in Europe, presented a mixture of sacred and secular music when other entertainments were forbidden during religious holidays. Over the course of the century, the proportion of religious works in its repertoire declined significantly. Whereas previous interpretations tended to describe secularization as resulting either from battles between philosophes and the Church or from broader declines in belief, this article casts doubt on these explanations by showing the heterogeneous composition of the Concert’s audience. Instead, it depicts a process of ‘inadvertent secularization’ stemming from market pressure, in this case due to the multiplication of new concert series and other entertainments in Paris during the second half of the eighteenth century. This framework accounts for secularization at the institutional level without assuming that the society as a whole was marked by declining Christian belief. Bringing together the study of markets and religion reveals how multiple logics increased the autonomy of artistic fields formerly subject to religious constraints.
Near-Infrared Light Increases Functional Connectivity with a Non-thermal Mechanism
Authors: Dmochowski Grzegorz M , Shereen Ahmed Duke , Berisha Destiny , Dmochowski Jacek P 
Published: March 2020

Abstract
Although techniques for noninvasive brain stimulation are under intense investigation, an approach that has received limited attention is transcranial photobiomodulation (tPBM), the delivery of near-infrared light to the brain with a laser or light-emitting diode directed at the scalp. Here we employed functional magnetic resonance imaging to measure the blood-oxygenation-level–dependent signal in n = 20 healthy human participants while concurrently stimulating their right frontal pole with a near-infrared laser. Functional connectivity with the illuminated region increased by up to 15% during stimulation, with a quarter of all connections experiencing a significant increase. The time course of connectivity exhibited a sharp rise approximately 1 min after illumination onset. Brain-wide connectivity increases were also observed, with connections involving the stimulated hemisphere showing a significantly larger increase than those in the contralateral hemisphere. We subsequently employed magnetic resonance thermometry to measure brain temperature during tPBM (separate cohort, n = 20) and found no significant temperature differences between active and sham stimulation. Our findings suggest that near-infrared light synchronizes brain activity with a nonthermal mechanism, underscoring the promise of tPBM as a new technique for stimulating brain function.
Sensitivity of the lateral flow urine lipoarabinomannan assay in ambulant adults with advanced HIV disease: data from the TB Fast Track study
Authors: Tlali Mpho , Fielding Katherine L , Karat Aaron S , Hoffmann Christopher J , Muravha Tshifhiwa , Grant Alison D , Charalambous Salome 
Published: March 2020

Abstract

Background
WHO guidelines recommend the lateral flow urine lipoarabinomannan assay (LF-LAM) for TB diagnosis in hospitalised HIV-positive individuals. The role of LF-LAM among ambulant patients remains less well defined. We investigated the sensitivity of LF-LAM among ambulant HIV-positive adults in primary health clinics in South Africa.

Methods
We enrolled adults (aged ≥18 y) with CD4 counts of ≤150 cells/mm3 who had not received TB treatment or antiretroviral therapy in the preceding 3 or 6 mo, respectively. Research nurses performed the LF-LAM test on freshly voided urine. Results were compared with a reference standard of positive mycobacterial culture (sputum or urine).

Results
Of 1505 (54.5% female; median age 37 y; median CD4 count 73 cells/mm3) participants, 973 (64.7%) had a mycobacterial culture result; 105/973 (10.8%) were positive for Mycobacterium tuberculosis. LF-LAM sensitivity was 41.9% (95% CI 32.3 to 51.9%) and 19.0% (95% CI 12.0 to 27.9%) using grade 1+ and grade 2+ cut-off points, respectively. Sensitivity increased with severe immunosuppression and in the presence of poor prognostic indicators (low haemoglobin, body mass index).

Conclusions
When used as the only TB diagnostic test, LF-LAM sensitivity is suboptimal, particularly using the grade 2+ cut-off. More sensitive tests for TB are needed that can be used in primary care settings.
Predicting of COVID-19 Confirmed Cases in Different Countries with ARIMA Models in 2020
Authors: Dehesh Tania , Mardani-Fard Heydar Ali , Dehesh Paria 
Published: March 2020

AbstractThe epidemic of a novel coronavirus illness (COVID-19) becomes as a global threat. The aim of this study is first to find the best prediction models for daily confirmed cases in countries with high number of confirmed cases in the world and second to predict confirmed cases with these models in order to have more readiness in healthcare systems. This study was conducted based on daily confirmed cases of COVID-19 that were collected from the official website of Johns Hopkins University from January 22th, 2020 to March 1th, 2020. Auto Regressive Integrated Moving Average (ARIMA) model was used to predict the trend of confirmed cases. Stata version 12 and R version 3.6.2 were used. Parameters used for ARIMA were (2,1,0) for Mainland China, ARIMA(1,0,0) for South Korea, and ARIMA(3,1,0) for Thailand. Mainland China and Thailand were successful in haltering COVID-19 epidemic. Investigating their protocol in this control like quarantine should be in the first line of other countries’ program
One experiment to rule them all? Testing multiple drivers of the temperature-size rule with nonlinear temperature increase
Authors: Tabi Andrea , Garnier Aurelie , Pennekamp Frank 
Published: March 2020

AbstractThe temperature-size rule (TSR) describes the inverse relationship between organism size and environmental temperature in uni- and multicellular species. Despite the TSR being widespread, the mechanisms for shrinking body size with warming remain elusive. Here, we experimentally test three hypotheses (differential development and growth [DDG], maintain aerobic scope and regulate oxygen supply [MASROS] and the supply-demand hypothesis [SD]) potentially explaining the TSR using the aquatic protistColpidium striatumin three gradually changing and one constant temperature environment crossed with three different nutrient levels. We find that the constant and slowly warming environments show similar responses in terms of population dynamics, whereas populations with linear and fast warming quickly decline and show a stronger temperature-size response. Our analyses suggest that acclimation may have played a role in observing these differences among treatments. The SD hypothesis is most parsimonious with the data, however, neither the DDG nor the MASROS hypothesis can be firmly dismissed. We conclude that the TSR is driven by multiple ecological and acclimatory responses and hence multicausal.Author statementA.T. designed and led the experiment, and A.T. and A.G. performed the sampling. A.T. and F.P. analyzed and interpreted the data. All authors contributed to the writing of the manuscript.
Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms
Authors: Guiglielmoni Nadège , Houtain Antoine , Derzelle Alessandro , van Doninck Karine , Flot Jean-François 
Published: March 2020

ABSTRACTBackgroundThird-generation sequencing, also called long-read sequencing, is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are also error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Although failure to properly collapse haplotypes results in fragmented and/or structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, this serious issue is rarely acknowledged and dealt with in genomic projects, and an independent, comparative benchmark of the capacity of assemblers and post-processing tools to properly collapse or purge haplotypes is still lacking.ResultsTo fill this gap, we tested different assembly strategies on the genome of the rotiferAdineta vaga, a non-model organism for which high coverages of both PacBio and Nanopore reads were available. The assemblers we tested (Canu, Flye, NextDenovo, Ra, Raven, Shasta and wtdbg2) exhibited strikingly different behaviors when dealing with highly heterozygous regions, resulting in variable amounts of uncollapsed haplotypes. Filtering out shorter reads generally improved haploid assemblies, and we also benchmarked three post-processing tools aimed at detecting and purging uncollapsed haplotypes in long-read assemblies: HaploMerger2, purge_haplotigs and purge_dups.ConclusionsTesting these strategies separately and in combination revealed several approaches able to generate haploid assemblies with genome sizes, coverage distributions, and completeness close to expectations.
‘Macrobot’–an automated segmentation-based system for powdery mildew disease quantification
Authors: Lück Stefanie , Strickert Marc , Lorbeer Maximilian , Melchert Friedrich , Backhaus Andreas , Kilias David , Seiffert Udo , Schweizer Patrick , Djamei Armin , Douchkov Dimitar 
Published: March 2020

AbstractPlant diseases, as one of the perpetual problems in agriculture, is increasingly difficult to manage due to intensifying of the field production, global trafficking, reduction of genetic variability of crops, climatic changes-driven expansion of pests, redraw and loss of effectiveness of pesticides and rapid breakdown of the disease resistance in the field. The substantial progress in genomics of both plants and pathogens, achieved in the last decades has the potential to counteract this negative trend, however, only when the genomic data is supported by relevant phenotypic data that allows linking the genomic information to specific traits. In this respect, phenotyping is and will remain an essential element of any comprehensive functional genomics study.We have developed a set of methods and equipment and combined them into a “Macrophenomics pipeline”. The pipeline has been optimized for the quantification of powdery mildew infection symptoms on wheat and barley but it can be adapted to other diseases and host plants. The Macrophenomics pipeline scores the visible disease symptoms, typically 5-7 days after inoculation (dai) in a highly automated manner. The system can precisely and reproducibly quantify the percentage of the infected leaf area with a throughput of the image acquisition module of up to 10 000 individual samples per day, making it appropriate for phenotyping of large germplasms collections and crossing populations.
On the problems of not accounting for measurement- and sampling uncertainty in ecological and environmental models
Authors: Damgaard Christian 
Published: March 2020

AbstractIn many applied cases of ecological and environmental modelling, there is a sizeable variation among the measured variables due to measurement- and sampling error. Such measurement- and sampling error among the independent variables may lead to regression dilution and biased prediction intervals in traditional empirical modelling. It is possible to avoid these shortcomings by subsampling and hierarchical modelling, but this is still not a common practice. Here, it is recommended to model the measurement- and sampling errors by integrating the stochastic modelling of the errors into hierarchical ecological and environmental models.
Explainable Transformer Models for Functional Genomics in Prokaryotes
Authors: Clauwaert Jim , Menschaert Gerben , Waegeman Willem 
Published: March 2020

AbstractThe effectiveness of deep learning methods can be largely attributed to the automated extraction of relevant features from raw data. In the field of functional genomics, this generally comprises the automatic selection of relevant nucleotide motifs from DNA sequences. To benefit from automated learning methods, new strategies are required that unveil the decision-making process of trained models. In this paper, we present several methods that can be used to gather insights on biological processes that drive any genome annotation task. This work builds upon a transformer-based neural network framework designed for prokaryotic genome annotation purposes. We find that the majority of sub-units (attention heads) of the model are specialized towards identifying DNA binding sites. Working with a neural network trained to detect transcription start sites in E. coli, we successfully characterize both locations and consensus sequences of transcription factor binding sites, including both well-known and potentially novel elements involved in the initiation of the transcription process.
gauseR: Simple methods for fitting Lotka-Volterra models describing Gause’s “Struggle for Existence”
Authors: Mühlbauer Lina K. , Schulze Maximilienne , Harpole W. Stanley , Clark Adam T. 
Published: March 2020

AbstractThe ecological models of Alfred J. Lotka and Vito Volterra have had an enormous impact on ecology over the past century. Some of the earliest – and clearest – experimental tests of these models were famously conducted by Georgy Gause in the 1930’s. Although well known, the data from these experiments are not widely available, and are often difficult to analyze using standard statistical and computational tools. Here, we introduce thegauseRpackage, a collection of tools for fitting Lotka-Volterra models to time series data of one or more species. The package includes several methods for parameter estimation and optimization, and includes 42 datasets from Gause’s species interaction experiments and related work. Additionally, we include with this paper a short blog post discussing the historical importance of these data and models, and an R vignette with a walk-through introducing the package methods. The package is available for download at github.com/adamtclark/gauseR. To demonstrate the package, we apply it to several classic experimental studies from Gause, as well as two other well-known datasets on multi-trophic dynamics on Isle Royale, and in spatially structured mite populations. In almost all cases, models fit observations closely, and fitted parameter values make ecological sense. Taken together, we hope that the methods, data, and analyses that we present here provide a simple and user-friendly way to interact with complex ecological data. We are optimistic that these methods will be especially useful to students and educators who are studying ecological dynamics, as well as researchers who would like a fast tool for basic analyses.
An osmolality/ salinity-responsive enhancer 1 (OSRE1) in intron 1 promotes salinity induction of tilapia glutamine synthetase
Authors: Kim Chanhee , Kültz Dietmar 
Published: March 2020

ABSTRACTEuryhaline tilapia (Oreochromis mossambicus) are fish that tolerate a wide salinity range from fresh water to >3x seawater. Even though the physiological effector mechanisms of osmoregulation that maintain plasma homeostasis in fresh water and seawater fish are well known, the corresponding molecular mechanisms that control switching between hyper- (fresh water) and hypo-osmoregulation (seawater) remain mostly elusive. In this study we show that hyperosmotic induction ofglutamine synthetaserepresents a prominent part of this switch. Proteomics analysis of theO. mossambicusOmB cell line revealed that glutamine synthetase is transcriptionally regulated by hyperosmolality. Therefore, the 5’ regulatory sequence ofO. mossambicus glutamine synthetasewas investigated. Using an enhancer trapping assay, we discovered a novel osmosensitive mechanism by which intron 1 positively mediatesglutamine synthetasetranscription. Intron 1 includes a single, functional copy of an osmoresponsive element, osmolality/salinity-responsive enhancer 1 (OSRE1). Unlike for conventional enhancers, the hyperosmotic induction ofglutamine synthetaseby intron 1 is position dependent. But irrespective of intron 1 position, OSRE1 deletion from intron 1 abolishes hyperosmotic enhancer activity. These findings indicate that proper intron 1 positioning and the presence of an OSRE1 in intron 1 are required for precise enhancement of hyperosmoticglutamine synthetaseexpression.