bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)
Authors: Liu Yan , Chen Lei , Duan Xing-Zhi , Zhao Dian-Shu , Sun Jing-Tao , Hong Xiao-Yue
Published: May 2019

Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.
The road map of cancer precision medicine with the innovation of advanced cancer detection technology and personalized immunotherapy
Authors: Low Siew-Kee , Nakamura Yusuke
Published: May 2019

The advancement of cancer genomics research due to the development of next generation sequencing technologies is going to bring the promise of cancer precision medicine, in turn revolutionizing cancer detection and treatment. In this review, we will discuss the possible road map for implementation of cancer precision medicine into the clinical practice by mainly focusing on the role of liquid biopsy, particularly circulating tumor DNA, as a potential tool for cancer screening, selection of an appropriate drug(s), surveillance of minimal residual diseases, and early detection of recurrence. We will also review the current status of genome-driven oncology and emerging field of immunotherapies that could be provided to patients to improve their clinical outcome and quality of life. Lastly, we will discuss the usefulness of artificial intelligence that facilitate complex data integration in our health care/medical care system.
Data quality and the comparative method: the case of pregnancy failure in rodents
Authors: Stokes Rachel H , Sandel Aaron A
Published: May 2019

In mammalian species where infanticide by males is likely, females exhibit counterstrategies to prevent or mitigate the costs of infanticide. One putative mitigation strategy is the “Bruce effect,” in which pregnant or inseminated females exposed to an unfamiliar male experience pregnancy block or failure. Females then mate with the new male, thus shifting investment from a “doomed” pregnancy to a more fruitful one. However, the Bruce effect may be an adaptive response to other factors besides infanticide. For example, if paternal care is necessary for offspring survival, and an unfamiliar male replacing the original mate is unlikely to provide such care to offspring of a litter it did not sire, then a female may terminate a pregnancy to initiate a new one. The infanticide and paternal care hypotheses have not been rigorously tested because comparative data on the Bruce effect across mammals are scarce. We compiled data on the Bruce effect, infanticide, and paternal care from one particularly rich source of information, rodents, but found the data set to be less rich than expected. The Bruce effect, infanticide, and paternal care were common among rodent species, but we found no clear relationship among the traits. However, this was likely due to 1) a bias toward positive results, 2) missing data, and 3) a reliance on studies of captive animals. These are common problems in comparative research, and we outline standards that should be implemented to successfully answer questions of importance in the field.
Radio jet structures at ∼100 pc and larger scales of the γ-ray-emitting narrow-line Seyfert 1 galaxy PMN J0948+0022
Authors: Doi Akihiro , Nakahara Satomi , Nakamura Masanori , Kino Motoki , Kawakatu Nozomu , Nagai Hiroshi
Published: May 2019

The narrow-line Seyfert 1 (NLS1) galaxy PMN J0948+0022 is an archetype of γ-ray-emitting NLS1s in active galactic nuclei (AGNs). In this study, we investigate its radio structures using archival data obtained using the Karl G. Jansky Very Large Array (VLA) and the Very Long Baseline Array (VLBA). The new VLA images reveal an outermost radio emission separated by 9.1 arcsec. Its resolved structure and steep spectrum suggest a terminal shock in a radio lobe energized by the jet from the PMN J0948+0022 nucleus. This large-scale radio component is found at almost the same position angle as that of the pc-scale jet, indicating a stable jet direction up to ∼1 Mpc. Its apparent one-sidedness implies a moderate advancing speed (β > 0.27). The kinematic age of <1× 107 yr of the jet activity is consistent with the expected NLS1 phase of ∼107 yr in the AGN lifetime. The VLBA image reveals the jet structure at distances ranging from r = 0.82 milliarcsec to 3.5 milliarcsec, corresponding to approximately 100 pc, where superluminal motions were found. The jet width profile (∝ r1.12) and flux-density profile (∝ r−1.44) depending on the distance r along the jet suggest that the jet kinetic energy is converted to internal energy in this region. The jet is causally connected in a nearly conical streamline, which is supported by ambient pressure at 100 pc scales in the host galaxy of PMN J0948+0022.
Discovery of millihertz quasi-periodic oscillations in the X-ray binary EXO 0748−676
Authors: Mancuso G C , Altamirano D , García F , Lyu M , Méndez M , Combi J A , Díaz-Trigo M , in’t Zand J J M
Published: May 2019

We report the discovery of millihertz quasi-periodic oscillations (mHz QPOs) from the bursting, high-inclination atoll neutron star low-mass X-ray binary (NS LMXB) EXO 0748−676 with the Rossi X-ray Time Explorer (RXTE). This class of QPO, originally discovered in three NS LMXBs, has been interpreted as a consequence of a special mode of nuclear burning on the NS surface. Using all the RXTE archival observations of the source, we detected significant (>3σ) mHz QPOs in 11 observations. The frequency of the oscillations was between ∼5 and ∼13 mHz. We also found a decrease of the QPO frequency with time in two occasions; in one of these the oscillations disappeared with the onset of an X-ray burst, similar to what was reported in other sources. Our analysis of the X-ray colours revealed that EXO 0748−676 was in a soft spectral state when it exhibited the QPOs. This makes EXO 0748−676 the sixth source with mHz oscillations associated with marginally stable burning, and the second one that shows a systematic frequency drift. Our results suggest that the mechanism that produces the drift might always be present if the mHz QPOs are observed in the so-called intermediate state.
Candidates for RR Lyrae in binary systems from the OGLE Galactic bulge survey
Authors: Prudil Z , Skarka M , Liška J , Grebel E K , Lee C-U
Published: May 2019

We present 20 newly discovered candidates for binary systems with an RR Lyrae companion. Using the photometric data from the Optical Gravitational Lensing Experiment (OGLE) and Korea Microlensing Telescope Network (KMTNet) for the Galactic bulge, we searched for binary candidates among non-modulated fundamental-mode RR Lyrae variables. We constructed and investigated over 9000 O − C diagrams for individual pulsators, in order to find signs of the light-travel time effect. We found 20 variables exhibiting cyclic variation in the O − C (time of the observed minus calculated brightness maximum) diagram, which can be associated with a second component in the system, but for confirmation of binarity, a long-term radial velocity study is necessary. The modelling of the O − C diagrams yields orbital parameters, estimates of the semi-amplitude of the radial velocity curve, and the mass function. The orbital periods of our candidates range from 3 to 15 yr. Two of the binary candidates display a minimum mass higher than the assumed mass of the RR Lyrae component, which points towards an evolved companion that can under some circumstances contribute significantly to the total light of the system.
Trehalase Gene as a Molecular Signature of Dietary Diversification in Mammals
Authors: Jiao Hengwu , Zhang Libiao , Xie Huan-Wang , Simmons Nancy B , Liu Hui , Zhao Huabin
Published: May 2019

Diet is a key factor in determining and structuring animal diversity and adaptive radiations. The mammalian fossil record preserves phenotypic evidence of many dietary shifts, whereas genetic changes followed by dietary diversification in mammals remain largely unknown. To test whether living mammals preserve molecular evidence of dietary shifts, we examined the trehalase gene (Treh), which encodes an enzyme capable of digesting trehalose from insect blood, in bats and other mammals with diverse diets. Bats represent the largest dietary radiation among all mammalian orders, with independent origins of frugivory, nectarivory, carnivory, omnivory, and even sanguivory in an otherwise insectivorous clade. We found that Treh has been inactivated in unrelated bat lineages that independently radiated into noninsectivorous niches. Consistently, purifying selection has been markedly relaxed in noninsectivorous bats compared with their insectivorous relatives. Enzymatic assays of intestinal trehalase in bats suggest that trehalase activity tends to be lost or markedly reduced in noninsectivorous bats compared with their insectivorous relatives. Furthermore, our survey of Treh in 119 mammal species, which represent a deeper evolutionary timeframe, additionally identified a number of other independent losses of Treh in noninsectivorous species, recapitulating the evolutionary pattern that we found in bats. These results document a molecular record of dietary diversification in mammals, and suggest that such molecular signatures of dietary shifts would help us understand both historical and modern changes of animal diets.
GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis
Authors: Tang Zefang , Kang Boxi , Li Chenwei , Chen Tianxiang , Zhang Zemin
Published: May 2019

Introduced in 2017, the GEPIA (Gene Expression Profiling Interactive Analysis) web server has been a valuable and highly cited resource for gene expression analysis based on tumor and normal samples from the TCGA and the GTEx databases. Here, we present GEPIA2, an updated and enhanced version to provide insights with higher resolution and more functionalities. Featuring 198 619 isoforms and 84 cancer subtypes, GEPIA2 has extended gene expression quantification from the gene level to the transcript level, and supports analysis of a specific cancer subtype, and comparison between subtypes. In addition, GEPIA2 has adopted new analysis techniques of gene signature quantification inspired by single-cell sequencing studies, and provides customized analysis where users can upload their own RNA-seq data and compare them with TCGA and GTEx samples. We also offer an API for batch process and easy retrieval of the analysis results. The updated web server is publicly accessible at http://gepia2.cancer-pku.cn/.
The structure of human EXD2 reveals a chimeric 3′ to 5′ exonuclease domain that discriminates substrates via metal coordination
Authors: Park Jumi , Lee Song-Yi , Jeong Hanbin , Kang Myeong-Gyun , Van Haute Lindsey , Minczuk Michal , Seo Jeong Kon , Jun Youngsoo , Myung Kyungjae , Rhee Hyun-Woo , Lee Changwook
Published: May 2019

EXD2 (3′-5′ exonuclease domain-containing protein 2) is an essential protein with a conserved DEDDy superfamily 3′-5′ exonuclease domain. Recent research suggests that EXD2 has two potential functions: as a component of the DNA double-strand break repair machinery and as a ribonuclease for the regulation of mitochondrial translation. Herein, electron microscope imaging analysis and proximity labeling revealed that EXD2 is anchored to the mitochondrial outer membrane through a conserved N-terminal transmembrane domain, while the C-terminal region is cytosolic. Crystal structures of the exonuclease domain in complex with Mn2+/Mg2+ revealed a domain-swapped dimer in which the central α5−α7 helices are mutually crossed over, resulting in chimeric active sites. Additionally, the C-terminal segments absent in other DnaQ family exonucleases enclose the central chimeric active sites. Combined structural and biochemical analyses demonstrated that the unusual dimeric organization stabilizes the active site, facilitates discrimination between DNA and RNA substrates based on divalent cation coordination and generates a positively charged groove that binds substrates.
Photopenic defects on O-(2-[18F]-fluoroethyl)-L-tyrosine PET: clinical relevance in glioma patients
Authors: Galldiks Norbert , Unterrainer Marcus , Judov Natalie , Stoffels Gabriele , Rapp Marion , Lohmann Philipp , Vettermann Franziska , Dunkl Veronika , Suchorska Bogdana , Tonn Jörg C , Kreth Friedrich-Wilhem , Fink Gereon R , Bartenstein Peter , Langen Karl-Josef , Albert Nathalie L
Published: May 2019

Background

O-(2-[18F]-fluoroethyl)-L-tyrosine (FET) PET has a sensitivity of more than 90% to detect gliomas. In the remaining small fraction of gliomas without increased tracer uptake, some tumors even show photopenic defects whose clinical significance is unclear.

Methods

Glioma patients with a negative FET PET scan prior to neuropathological confirmation were identified retrospectively. Gliomas were rated visually as (i) having indifferent FET uptake or (ii) photopenic, if FET uptake was below background activity. FET uptake in the area of signal hyperintensity on the T2/fluid attenuated inversion recovery–weighted MRI was evaluated by mean standardized uptake value (SUV) and mean tumor-to-brain ratio (TBR). The progression-free survival (PFS) of photopenic gliomas was compared with that of gliomas with indifferent FET uptake.

Results

Of 100 FET-negative gliomas, 40 cases with photopenic defects were identified. Fifteen of these 40 cases (38%) had World Health Organization (WHO) grades III and IV gliomas. FET uptake in photopenic gliomas was significantly decreased compared with both the healthy-appearing brain tissue (SUV, 0.89 ± 0.26 vs 1.08 ± 0.23; P < 0.001) and gliomas with indifferent FET uptake (TBR, 0.82 ± 0.09 vs 0.96 ± 0.13; P < 0.001). Irrespective of the applied treatment, isocitrate dehydrogenase (IDH)–mutated WHO grade II diffuse astrocytoma patients with indifferent FET uptake (n = 25) had a significantly longer PFS than patients with IDH-mutated diffuse astrocytomas (WHO grade II) with photopenic defects (n = 11) (51 vs 24 mo; P = 0.027). The multivariate survival analysis indicated that photopenic defects predict an unfavorable PFS (P = 0.009).

Conclusion

Photopenic gliomas in negative FET PET scans should be managed more actively, as they seem to have a higher risk of harboring a higher-grade glioma and an unfavorable outcome.
A Retrospective Cohort Study of Longitudinal Audiologic Assessment in Single and Fractionated Stereotactic Radiosurgery for Vestibular Schwannoma
Authors: Khattab Mohamed H , Sherry Alexander D , Whitaker Ryan , Wharton David M , Weaver Kyle D , Chambless Lola B , Cmelak Anthony J , Attia Albert
Published: May 2019

BACKGROUND

Fractionated stereotactic radiosurgery (SRS) for vestibular schwannomas (VS) has been theorized to allow for tumor control with higher rates of hearing preservation in selected patients with useful hearing. However, there is a paucity of literature with formal audiologic measures of hearing preservation to support the standard use of fractionated SRS in VS. We hypothesized that fractionation would diminish the amount of hearing damage.

OBJECTIVE

To evaluate the relationship between audiologic performance and SRS fractionation scheme.

METHODS

We performed an IRB-approved retrospective review of patients treated with 1, 3, or 5 fraction SRS for VS at our institution from 1998 to 2016. Pre- and post-SRS audiograms with speech awareness threshold (SAT) in treated and contralateral ears were obtained. Contralateral ear measurements were used for hearing normalization to account for presbycusis.

RESULTS

Fifty-six patients with median audiologic follow-up 2.0 yr (mean 2.66 yr, min-max 0.50-9.45 yr) were included. Patients treated with single fractionation had a significantly worsened SAT (dB) compared to patients treated with 5 fractions (P = .008) and compared to all multifraction patients (P = .009) at 12 to 24 mo follow-up.

CONCLUSION

This retrospective analysis supports the use of fractionated SRS to preserve hearing in patients with VS. SAT can be used as an objective metric of hearing response to radiosurgery.
Potential role of neglected and underutilized plant species in improving women’s empowerment and nutrition in areas of sub-Saharan Africa
Authors: Conti Maria Vittoria , Campanaro Ausilia , Coccetti Paola , De Giuseppe Rachele , Galimberti Andrea , Labra Massimo , Cena Hellas
Published: May 2019

In the context of the nutrition transition, women in sub-Sahara Africa are a critical target group from a nutrition standpoint, and they experience significant discrimination in food production. Food-based, women-centered strategies are recommended to address nutrient gaps, and to educate and empower women. In this context, local natural resources, such as neglected and underutilized plant species (NUS), may contribute to adding nutritional value, enriching diet diversity, and ensuring nutrition security. The aim of the current narrative review is to investigate the nutritional status of the sub-Saharan African population and the potential role of local agriculture strategies in improving food production and diet diversity and in expanding income-generating activities for women. The nutritional properties of the most important regional NUS are also discussed.
A Critical Encyclopedia of Heterosex
Authors: Farvid Panteá , Braun Virginia
Published: May 2019

Building on theoretical discussions regarding the institution of heterosexuality and heteronormativity, this chapter demonstrates how language and heterosexual sex (that is, heterosex) are intimately intertwined. The chapter teases out the ways in which the norms of heterosexuality have changed over time yet also remained the same in several fundamental ways. The first section maps the broad discursive conditions that shape dominant norms of contemporary heterosexuality in Anglo-Western contexts. The second section demonstrates the cultural imperatives that govern the desires, norms, and acts of heterosex, outlining how they create specific modes of being and doing in everyday practice. Finally, the conclusion considers the possibility that recent global activism may lead to a revamping of gendered norms and their tired rigidity.
Critical Discourse Studies of Language and Sexuality
Authors: Koller Veronika
Published: May 2019

This chapter looks at how sexuality, including sexual identity, has been addressed in critical discourse studies. It will first review previous work (e.g., Marko 2008; Morrish and Sauntson 2011) and point out the relative lack of relevant studies in this area, given that research into language and sexuality is mostly indebted to anthropology, sociolinguistics, and conversation analysis. Building on queer discourse studies (Motschenbacher and Stegu 2013), the chapter suggests a way of critically analyzing discourses on sexuality, where discourse is defined as textually mediated social action, with text producers utilizing linguistic resources and sociocognitive representations to establish, maintain, or challenge power relations. Critical discourse studies combine the description of linguistic features with their interpretation and explanation in context and ultimately make transparent the way in which language and discourse either construct and reinforce, or challenge and subvert, normativity. The chapter closes with an illustrative example of the discursive construction of lesbian identities.
Fiduciary Principles in Health Care
Authors: Hall Mark A.
Published: May 2019

This chapter examines fiduciary principles in health care law. There is no unanimous agreement when it comes to the precise doctrinal consequences of labeling health care actors as fiduciaries in various contexts, such as personal injury, decisional authority, financial influence, and procedural rules. In the case of patients and physicians, certain attributes are said to constitute an archetypal fiduciary relationship, including agency, dependency, trust, and information asymmetry. Thus, many legal decisions and commentators argue that physicians have fiduciary responsibilities to patients. For courts, however, hospitals are not fiduciaries. They regard private hospitals as ordinary commercial enterprises. This chapter first provides an overview of arguments over whether physicians and non-physicians (for example, hospitals and health insurers) are “fiduciaries” before discussing health care fiduciaries’ duty of loyalty and duty of care, along with their other obligations such as duties of confidentiality and full disclosure. It also explores the ability of health care fiduciaries and patients to waive fiduciary duties, as well as how courts have addressed distinct causes of action for physicians’ breach of fiduciary duty. It shows that courts often invoke fiduciary concepts and terminology in discussing physicians’ obligations to patients, and that physician-patient (and other medical treatment) relationships have classic attributes of fiduciary status.
Innovation in Work Teams
Authors: Stollberger Jakob , West Michael A. , Sacramento Claudia A.
Published: May 2019

Researchers and practitioners have recognized the importance of team innovation for organizational effectiveness. This chapter provides an overview of the factors that influence team innovation using an input–process–output structure. It identifies factors relating to the team and organizational context as inputs for various team processes that translate into innovative outputs. It further suggests that leadership acts as a contingency factor that facilitates the transition of input factors into team processes. Highlighting the often-overlooked difference between idea generation and idea implementation as part of team innovation, it discusses which input factors and processes are more likely to exert more influence over idea generation and/or idea implementation. It concludes by emphasizing the importance of implementing creative ideas for achieving innovation success.
Contrasting Scientific Discourses of Skin Lightening in Domestic and Global Contexts
Authors: Curington Celeste Vaughan , Kang Miliann
Published: May 2019

This chapter examines how racial and gender ideologies shape and are shaped by scientific understandings of beauty practices via a critical examination of the scholarly discourses on skin lightening. Based on qualitative content analysis of thirty domestic and international scholarly articles on skin lightening and whitening published between 2000 and 2017, the authors found that products in Europe and the United States marketed to white customers were likely to be framed as benign beauty products, with health risks attributed to imported products. In contrast, the use of similar products overseas, particularly in Asia, the Middle East, and Africa, were depicted as higher risk and locally sourced. Further, by mapping certain skin-related pathologies onto distinct human bodies, these studies reinforce discredited biological understandings of race. Overall, scientific studies of skin whitening and lightening practices enforce the scientific validation of white/western beauty practices alongside the problematization of similar practices/products when used by non-white or non-western subjects. These studies often recognize the dominance of a white cultural ideal but, rather than tracing its structural and historical determinants, instead pathologize those who aspire to it, often neglecting the dynamics of global white supremacy, marketing, production, and distribution in the global beauty economy that fuel the desire and consumption for these products.
Ways out of the Globalization Trilemma
Authors: Herrmann-Pillath Carsten
Published: May 2019

Based on Rodrik’s diagnosis of a “globalization trilemma” in designing the institutions of international economic exchange, this chapter suggests a solution that applies Sen’s argument favoring realization-focused comparisons over transcendental institutionalism in evaluating institutions. In the paradigm of deliberative trade policy, this contribution approaches the World Trade Organization (WTO) as a regime of deliberation, reaching beyond the scope of interactions with civil society. This prepares the ground for normative principles of WTO reform that shift the emphasis from efficiency to justice, mainly in the procedural sense. The central operational criterion is the inclusiveness of international trade and trade policy. This is applied on the issues of multilateralism versus regionalism and the design of the dispute settlement process. A WTO renewed under the auspices of deliberative trade policy can meet the challenges of new trade policy issues such as coordination of regulatory regimes under the conditions of rapid and unpredictable technological change, and can resolve the tension between democracy and globalization as laid out in the globalization trilemma.
Corporate Liabilities
Authors: Priemel Kim Christian
Published: May 2019

The debate on how to rein in transnational corporate power has greatly intensified over the past decades. Following a series of scandals, conflicts, and crises, civil rights activists, lawyers, and heterodox economists have been promoting efforts to hold private business accountable for the social, economic, ecological, and political costs of its actions. National legal cultures, however, differ widely on that issue, in particular with an eye to corporate personhood and extraterritoriality. After centuries of not prosecuting corporations on grounds of their lack of mens rea, the pattern changed in the twentieth century as developments in different legal spheres intertwined. When competition law coalesced with tightened national corruption standards as well as the emergence of international war crimes prosecution, a path toward international corporate liability opened up. By now a patchwork set of approaches has emerged in which soft and hard law, statutory and treaty law, and national and international regulation converge on corporate liability.
Animals in Graphic Narrative
Authors: Alaniz José
Published: May 2019

Animal representation in graphic narrative has figured in many of the medium’s important developments and anchored one of its most popular genres, funny-animal comics. Since the modern emergence of the form sometime around the end of the nineteenth century, major figures such a Richard Outcault, Winsor McCay, George Herriman, Edwina Dumm, Carl Barks, Robert Crumb, and Jim Woodring have made extensive use of the animal figure, in both highly and minimally anthropomorphized forms. As argued by John Berger, David Herman, and other scholars, the animal’s lack of human speech renders it vulnerable to a brand of representational colonialism whereby its in-itself existence is emptied in favor of other symbolic, metaphorical, or ideological functions. Many works since the 1980s by Grant Morrison, Steven Murphy and Michael Zulli, and Nicole Georges have striven for less anthropomorphized depictions, in a bid to address the ethics involved in representing the animal subject.
Distributivity
Authors: Syrett Kristen
Published: May 2019

This chapter introduces the related topics of distributivity, collectivity, and cumulativity. Evidence is reviewed for the availability of multiple readings of ambiguous sentences that support distributive and collective interpretations, and the constrained interpretation of sentences arising from the lexical semantics of a universal quantifier, a predicate (adjective), an adverbial modifier, a determiner, or quantification scope. Off-line tasks with child and adult participants reveal a developmental comparison in the availability of these readings and the predication of individuals and groups of individuals, while on-line processing tasks with adults provide fine-grained behavioural evidence for the role of lexical and structural factors in facilitating or suppressing such readings.
Ironic Utterances
Authors: Spotorno Nicola , Noveck Ira
Published: May 2019

Irony is a compelling pragmatic phenomenon to investigate experimentally because a) it clearly exposes how an utterance’s meaning can change as a function of context; b) it invites investigations of the cognitive functions that go beyond mere linguistic decoding and, specifically; c) it allows one to have a clearer understanding of the role played by attitude ascription, which we show is central. This chapter will review how attitude ascription became a central topic in the theoretical debate on irony in the 1980s, how it almost disappeared from the experimental literature for about twenty years and how it deserves a place both as a hallmark of irony processing and as a hallway that connects various subfields of cognitive science, including neuroscience.
Word Senses
Authors: Rabagliati Hugh , Srinivasan Mahesh
Published: May 2019

Across languages, most frequent words are also highly ambiguous, and carry multiple distinct but related senses of meaning. This chapter aims to explain why words have the particular senses that they do, discussing to what degree word senses are arbitrary cultural conventions or reflections of how speakers conceptualize the world around them. The chapter reviews theoretical proposals about the nature of word senses drawn from linguistics and psychology, and evaluates these proposals against a large recent body of experimental work on the topic. Finally, the chapter suggests that word senses reflect a balance between two communicative pressures: a pressure toward facilitating fast and efficient conversational exchanges, and one toward making languages easier for children to learn.
Theory of Mind
Authors: Rubio-Fernández Paula
Published: May 2019

Current accounts of Theory of Mind development have tried to explain the results of false-belief tasks with infants and children, but failed to account for the evidence of early belief reasoning reported in the experimental pragmatics literature. This chapter reviews a number of studies on the acquisition of the mental state verb know; toddlers’ understanding of factivity (or the difference between knowing and thinking); early referential communication and toddlers’ reliance on others’ engagement as a proxy for their knowledge, and the emergence of preschoolers’ understanding of the seeing-knowing relation. The results of these studies reveal a more nuanced picture than those of false-belief tasks, with some Theory of Mind abilities emerging earlier in conversation than in laboratory tasks, while children’s epistemic theories continue to develop beyond their passing of standard Theory of Mind tasks.
Negation
Authors: Tian Ye , Breheny Richard
Published: May 2019

Negation has long been of interest to logicians and philosophers, and relatively recently to psycholinguists and pragmatists. In terms of the processing of negation, psycholinguistics studies have shown two effects that call for an explanation: the first is the asymmetry between its frequent use in natural language and its apparent processing costs, often reported in psycholinguistics studies; the second is the finding that, in early stages of processing, negation seems to be ignored and attention seems to be focused on its positive argument. In terms of pragmatic functions, it has been shown that despite its simple semantic meaning, negation interacts with context to produce rich pragmatic effects. Both negation processing and its pragmatic functions present puzzles that cannot be explained by its semantic function.
Quantification
Authors: Brasoveanu Adrian , Dotlačil Jakub
Published: May 2019

Quantification is abundant in natural language and is one of the most studied topics in generative grammar. Sentences with multiple quantifiers are famously ambiguous with respect to their quantifier scope, representing a type of ambiguity related to, but not necessary the same as, structural ambiguity. Two key questions in the psycholinguistic study of quantification are: (i) how does the human processor assign quantifier scope? and (ii) how and under what circumstances is this scope assignment reanalysed? The investigation of these questions lies at the intersection of psycholinguistics and theoretical linguistics. The chapter summarizes both strands of research, and discusses experimental data that played an essential role in the (psycho)linguistic theorizing about the topic of processing quantification and quantifier scope.
Negative Polarity Items
Authors: Xiang Ming
Published: May 2019

This chapter presents an overview of the experimental investigations on Negative Polarity Items (NPIs). NPIs are grammatically licensed under a set of complex semantic, syntactic and pragmatic conditions. The linguistic complexity of NPI licensing makes it a rich empirical domain for investigating the cognitive architecture of language processing and acquisition. This chapter brings together a rich set of empirical findings to address two issues: first, during language comprehension, how information from different sources, syntactic, semantic, and pragmatic, are incrementally combined, stored, accessed, and continuously consolidated over time to form an appropriate licensing context for NPIs; and second, what learning mechanisms are necessary for children to acquire the complex set of NPI licensing conditions from their linguistic input.
Counterfactuals
Authors: Ferguson Heather
Published: May 2019

This chapter explores counterfactual language understanding (e.g. If money grew on trees…), which requires false information to be accepted as temporarily true (and vice versa). First, counterfactual constructions are defined, then counterfactual reasoning strategies are reviewed, and understanding is linked to existing theories of language comprehension. The key focus of this chapter is to evaluate recent empirical work that has sought to understand how counterfactuals are represented and accessed on-line during language comprehension. Thus, temporally sensitive cognitive neuroscientific methodologies are discussed alongside a variety of language comprehension tasks. Overall, it is concluded that healthy adult readers can make appropriate inferences following a counterfactual context, showing rapid (possibly simultaneous) access to both the counterfactual and factual interpretations of events, which parallels the processes involved in mental state attributions.
V723 Persei: A short-period Algol-like near-contact binary
Authors: Tian Xiao-Man , Zhu Li-Ying
Published: May 2019

Complete multi-color photometric observations in the BVRCIC bands and low-resolution spectra of the short-period binary V723 Per are presented for the first time. The stellar atmospheric parameters of effective temperature, gravitational acceleration, and metallicity are determined as Teff = 7407 ± 53 K, log g = 3.98 ± 0.10 cm s−2, and [Fe/H] = −0.25 ± 0.10 dex, respectively. Photometric solutions are obtained by analyzing the phased light curves with the Wilson–Devinney method. We found that V723 Per is an Algol-like semi-detached-type near-contact binary with a mass ratio of q = 0.3168 ± 0.0011. The secondary component is filling the critical Roche lobe, while the primary is nearly filling its Roche lobe (the filling degree is about 80.93%). The primary component contributes about 96% of the luminosity of the total system, and the temperature difference between the two component stars is about 3000 K. All available times of light minimum, including three new observed eclipse times, were used to construct the O − C curve. The period shows a continuous increase at a rate of dP/dt = +7.63(±0.75) × 10−6 d yr−1 superposed with a periodic oscillation of amplitude of 0.0392 d and period 17.4 yr. The period increase could be explained by mass transfer from the secondary component to the primary one on the thermal timescale, which is in agreement with the semi-detached configuration. The cyclic change may be caused by the light-time effect due to a massive ($M_3=3.03\, M_\odot$) but quite faint (L3/Ltotal ≃ 3%) tertiary companion orbiting the central binary. Such a third body might be a black hole or a binary with two nearly identical stars. More observations are required in the future to confirm our conclusion about the cycle variation and tertiary companion.
Regulation by FurC in Anabaena Links the Oxidative Stress Response to Photosynthetic Metabolism
Authors: Sevilla Emma , Sarasa-Buisan Cristina , Gonz�lez Andr�s , Cases Rafael , Kufryk Galyna , Peleato M Luisa , Fillat Mar�a F
Published: May 2019

The FUR (Ferric Uptake Regulator) family in Anabaena sp. PCC 7120 consists of three paralogs named FurA (Fur), FurB (Zur) and FurC (PerR). furC seems to be an essential gene in the filamentous nitrogen-fixing strain Anabaena sp. PCC 7120, suggesting that it plays a fundamental role in this organism. In order to better understand the functions of FurC in Anabaena, the phenotype of a derivative strain that overexpresses this regulator (EB2770FurC) has been characterized. The furC-overexpressing variant presented alterations in growth rate, morphology and ultrastructure, as well as higher sensitivity to peroxide than Anabaena sp. PCC 7120. Interestingly, the overexpression of furC led to reduced photosynthetic O2 evolution, increased respiratory activity, and had a significant influence in the composition and efficiency of both photosystems. Comparative transcriptional analyses, together with electrophoretic mobility shift assays allowed the identification of different genes directly controlled by FurC, and involved in processes not previously related to PerR proteins, such as the cell division gene ftsZ and the major thylakoid membrane protease ftsH. The rise in the transcription of ftsH in EB2770FurC cells correlated with reduced levels of the D1 protein, which is involved in the PSII repair cycle. Deregulation of the oxidative stress response in EB2770FurC cells led to the identification of novel FurC targets involved in the response to H2O2 through different mechanisms. These results, together with the effect of furC overexpression on the composition, stability and efficiency of the photosynthetic machinery of Anabaena, disclose novel links between PerR proteins, cell division and photosynthesis in filamentous cyanobacteria.
Automatized, Standardized, and Patient-Tailored Progressive Walking-Adaptability Training: A Proof-of-Concept Study
Authors: Timmermans Celine , Roerdink Melvyn , Janssen Thomas W J , Beek Peter J , Meskers Carel G M
Published: May 2019

Background

Treadmill training augmented with visual images projected on the belt's surface can help improve walking adaptability. Moreover, patient-tailored automatization and standardization can increase the feasibility of walking-adaptability therapy. We developed C-Gait, a treadmill protocol consisting of a baseline walking-adaptability assessment involving 7 putatively distinct walking-adaptability tasks and a decision algorithm, to automatically update training content and execution parameters to a patients’ performance and perceived challenge.

Objectives

The main objective was to examine the feasibility, acceptability, and clinical potential of C-Gait training. The secondary objective was to evaluate the validity of the baseline assessment.

Design

This was a longitudinal proof-of-concept study with pretraining, posttraining, and retention tests encompassing baseline assessment and walking-related clinical measures.

Methods

Twenty-four healthy adults, 12 healthy older persons, and 28 patients with gait and/or balance deficits performed the baseline assessment; the gait deficit group received 10 C-Gait training sessions over a 5-week period. Baseline assessment scores and walking-related clinical measures served as outcome measures.

Results

C-Gait training exhibited significant progression in training content and execution, with considerable between-patient variation and minimal overruling by therapists. C-Gait training was well accepted and led to improvements in walking adaptability and general walking ability, which persisted after training cessation. Baseline assessment scores differed over groups and difficulty levels, had no-to-moderate correlations with walking-related clinical measures, and had limited correlations among walking-adaptability tasks.

Limitations

C-Gait was evaluated in a small yet diverse cohort. More encompassing studies are required to further establish its apparent merits. The validity of treadmill-based walking-adaptability assessment against an overground standard remains to be established.

Conclusions

C-Gait offers automatized, standardized, and patient-tailored walking-adaptability training that is feasible and well accepted, with good potential for improving task-specific and generic measures of walking.
Diversity of Pestalotiopsis-Like Species Causing Gray Blight Disease of Tea Plants (Camellia sinensis) in China, Including two Novel Pestalotiopsis Species, and Analysis of Their Pathogenicity
Authors: Wang Yuchun , Xiong Fei , Lu Qinhua , Hao Xinyuan , Zheng Mengxia , Wang Lu , Li Nana , Ding Changqing , Wang Xinchao , Yang Yajun
Published: May 2019

Several Pestalotiopsis-like species cause gray blight disease in tea plants, resulting in severe tea production losses. However, systematic and comprehensive research on the diversity, geographical distribution, and pathogenicity of pathogenic species associated with tea plants in China is limited. In this study, 168 Pestalotiopsis-like isolates were obtained from diseased tea plant leaves from 13 primary tea-producing provinces and cities in China. Based on a multilocus (internal transcribed spacer, translation elongation factor 1-α, and β-tubulin gene region) phylogenetic analysis coupled with an assessment of conidial characteristics, 20 Neopestalotiopsis unclassified isolates, seven Pestalotiopsis species, including two novel (Pestalotiopsis menhaiensis and Pestalotiopsis sichuanensis), four known (Pestalotiopsis camelliae, Pestalotiopsis chamaeropis, Pestalotiopsis kenyana, and Pestalotiopsis rhodomyrtus) and one indistinguishable species, and three Pseudopestalotiopsis species, including two known (Pseudopestalotiopsis camelliae-sinensis and Pseudopestalotiopsis chinensis) and one indistinguishable species, were identified. This study is the first to evaluate Pestalotiopsis chamaeropis on tea plants in China. The geographical distribution and pathogenicity tests showed Pseudopestalotiopsis camelliae-sinensis to be the dominant cause of gray blight of tea plants in China. In vitro antifungal assays demonstrated that theobromine not only derepressed mycelial growth of the 29 representative isolates but also increased their growth. Correlation analysis revealed a linear positive relationship between the mycelial growth rate and pathogenicity (P = 0.0148).
An Alternative Bioassay forSynchytrium endobioticumDemonstrates the Expression of Potato Wart Resistance in Aboveground Plant Parts
Authors: van de Vossenberg B. T. L. H. , van Gent-Pelzer M. P. E. , Boerma M. , van der Gouw L. P. , van der Lee T. A. J. , Vossen J. H.
Published: May 2019

The obligate biotrophic chytrid species Synchytrium endobioticum is the causal agent of potato wart disease. Currently, 39 pathotypes have been described based on their interaction with a differential set of potato varieties. Wart resistance and pathotyping is performed using bioassays in which etiolated tuber sprouts are inoculated. Here, we describe an alternative method in which aboveground plant parts are inoculated. Susceptible plants produced typical wart symptoms in developing but not in fully expanded aboveground organs. Colonization of the host by S. endobioticum was verified by screening for resting spores by microscopy and by molecular techniques using TaqMan polymerase chain reaction and RNAseq analysis. When applied to resistant plants, none of these symptoms were detectable. Recognition of S. endobioticum pathotypes by differentially resistant potato varieties was identical in axillary buds and the tuber-based bioassays. This suggests that S. endobioticum resistance genes are expressed in both etiolated “belowground” sprouts and green aboveground organs. RNAseq analysis demonstrated that the symptomatic aboveground materials contain less contaminants compared with resting spores extracted from tuber-based assays. This reduced microbial contamination in the aboveground bioassay could be an important advantage to study this obligate biotrophic plant–pathogen interaction. Because wart resistance is active in both below- and aboveground organs, the aboveground bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs because it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding.

[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Using Dynamic Changes of Chlorophyll Fluorescence in Arabidopsis thaliana to Evaluate Plant Immunity-Intensifying Bacillus spp. Strains
Authors: Wang Yi-Hsin , Lai I-Ling , Zheng Jing-Lin , Lin Yi-Hsien
Published: May 2019

The integral defense responses of plants triggered by the small molecules of plant pathogens are regarded as plant immunity. The pathogen-associated molecular pattern-triggered immunity (PTI) occurs on the recognition of a pathogen by receptors on plant cell surfaces as an infection begins. During the activation of PTI, the effectiveness of a plant’s photosynthetic system may be altered. In this study, chlorophyll fluorescence was used to assay the dynamic changes of PTI. When we used flg22Pst as an elicitor, we found that the photosynthetic electron transport rate (ETR) of Arabidopsis thaliana Col-0 was significantly decreased at 2, 4, and 24 h on treatment with a PTI-intensifying protein, plant ferredoxin-like protein (PFLP). In addition, this reduction in the photosynthetic ETR was also carried out with a PTI-intensifying Bacillus amyloliquefaciens strain, PMB05, on the induction of flg22Pst. The disease resistance against bacterial soft rot caused by Pectobacterium carotovorum subsp. carotovorum (Pcc) was still enhanced by PMB05. Interestingly, among the eight tested Bacillus species strains, the PTI triggered by HrpNPcc from P. carotovorum subsp. carotovorum exhibited an ETR that was significantly decreased by PMB05. Furthermore, this decrease was consistent with rapid H2O2 generation and callose deposition triggered by HrpNPcc and the disease resistance against bacterial soft rot. Taken together, such results led us to conclude that the assay based on the ETR established in this study can be used as a model for evaluating the effectiveness of plant immunity-intensifying microbes for controlling plant diseases.