bluuebunny/crossref_metadata_2025 huggingface dataset:
The Dutch verb-spelling paradox in social media
Authors: Schmitz Tijn , Chamalaun Robert , Ernestus Mirjam
Published: November 2018

Although the Dutch verb spelling system seems very straightforward, many spelling errors are made, both by children and adults (e.g., Sandra, Frisson, & Daems 2004). These errors mainly occur with verbs with two or more homophonous forms in their inflectional paradigms. Ample experimental research has been carried out on this topic, but these studies hardly reflect everyday language behavior. In the current corpus study, we reassessed previously found experimental results, but now in a Twitter corpus containing 17,432 tweets with homophonous verb forms. In accordance with previous results, we found a clear preference for the suffix -
compared to both -
and -
, as well as a frequency effect, resulting in fewer errors for more frequent word forms. Furthermore, the results revealed that users with more followers make fewer errors, and that more errors are made during the evening and night.
“Dancing with doxa”
Authors: Finlayson Alan
Published: November 2018

This chapter explains some of the background to political theorists’ and political scientists’ interest in language. It then introduces and explains Rhetorical Political Analysis (RPA), contrasting it with approaches to the study of political language, such as Critical Discourse Studies, found within Linguistics. It then briefly demonstrates the application of RPA through a study of David Cameron’s Bloomberg Speech on Europe. The analysis highlights in particular the way the speech echoes British conservative precedents and the way in which “Britishness” emerges as a key “catachrestical” term.
Off the record
Authors: Shaw Sylvia
Published: November 2018

This chapter examines the benefits and drawbacks of using Official Reports, such as the UK House of Commons “Hansard” for political discourse analysis. Previous studies identifying transformations that occur to the oral version of events in the process of constructing Official Reports (e.g. Slembrouck 1992) show that transcribers and editors make significant changes and omissions, raising questions about their suitability for the analysis of parliamentary discourse. Acknowledging the theoretical, analytical and interpretative elements of all transcriptions, I critically appraise different types of political discourse analysis that use UK Official Report data. I conclude with some suggestions about the categories affected by Official Report transformations, and suggest that using this data for the analysis of parliamentary discourse should always be critical and reflexive.
Making “politics” relevant
Authors: Hofstetter Emily , Stokoe Elizabeth
Published: November 2018

This paper investigates an area of political discourse that has hitherto existed in an analytic “black box”: the constituency office. We focus on the interactions between ordinary British people as they engage directly in “political” discussions with their Member of Parliament. While the majority of surgery talk surrounds complaints about services, we focus on sequences of talk in which either citizens or the MP make “political” topics relevant. Eighty consultations were video-recorded, anonymised and transcribed, and the data analysed using conversation analysis. We found that MP-initiated political comments portray the government as aligned with constituents’ needs, whereas constituents use political comments largely to criticise the government. Constituents privilege the interactional contingencies over other issues. Overall, the paper contributes to our understanding of how constituents navigate interactional and political contingencies in interactions with their representative.
Es-tu Charlie?
Authors: Kopf Susanne , Nichele Elena
Published: November 2018

This chapter examines the representation of the slogan “Je Suis Charlie” (JSC) on Wikipedia. Drawing on corpus tools in addition to purely qualitative analytical tools led to the identification of several themes that recur throughout Wikipedia’s article on JSC as well as on the associated discussion pages. The Wikipedia article represents JSC as a globally-used symbol of freedom of speech and solidarity with victims of specific violent events. On the discussion pages, JSC receives a markedly different treatment, e.g. the debates focus on whether JSC – rather than symbolising freedom of speech – symbolises the freedom to discriminate against groups of people. Furthermore, the discussions focus on JSC as uniting the “West” only and not on JSC as a global phenomenon.
Red lines and rash decisions
Authors: Ferrari Federica , O’Loughlin Ben
Published: November 2018

Obama’s “red lines” metaphor nearly triggered a military intervention in Syria in the summer of 2013. This chapter questions the work that metaphor does in shaping understandings and conduct in international affairs. The term is used by political leaders to express likely behavioural consequences to international rivals and allies and to domestic publics. We explore what difference in diplomatic practice it makes to speak of a line, and a red one, as well as how such metaphors trigger or sustain narratives, and how narratives interact with metaphors. In the context of conflict in Syria we examine the trajectory and remediation of the red lines metaphor, taking as an empirical nexus a series of officials’ speeches in September 2013 by Kerry, Power, Lavrov and other political leaders. We find that the red line initially trapped Obama, leading to rhetorical shifts, before a trajectory shift from the red line to the path forward in mid-September as the US and Russia reach a deal to eliminate the Assad regime’s chemical weapons. The study brings together approaches from International Relations and Cognitive Linguistics to open up theoretical reflection on the function of metaphor and narrative in steering sense-making in diplomatic practice. The political significance of the analysis is to bring into question what alternative metaphors Obama could have used in the first place.
Mental Models across Languages
Authors: Sickinger Pawel
Published: November 2018

This book presents a study that triangulates the meanings of expressions across English, German and Japanese via their perception-based conceptual representations. In an online experiment, native speakers of the three languages were asked to design visual representations of expressions referring to baldness phenomena. These sets of visualizations are used to determine conceptual overlap or distance between expressions in the three languages, resulting in lexical-conceptual 'maps' for MALE BALDNESS. The study is discussed against the background of an embodied, perceptual symbol-based understanding of linguistic meaning. A section of the book further applies this perspective to the issue of translation, developing a process model of translation based on the concept of cognitive equivalence.
The book presents a novel approach to lexical semantics from a cognitive linguistic perspective, tested through a methodologically innovative experiment. It is a compelling read to scholars in cognitive semantics, contrastive semantics, embodied cognition and cognitive translation studies.
Culture, gender, ethnicity, identity in discourse
Authors: Davies Catherine Evans
Published: November 2018

International teaching assistants in charge of undergraduate classes in American universities present the anomalous situation of the non-native speaker in the role of higher authority, but the native-speaker having greater communicative resources and cultural knowledge. This interactional sociolinguistic case study of a facilitated negotiation of discourse style in conversations between a Chinese teaching assistant and an African-American undergraduate explores the situated enactment and interpretation of identity in relation to culture, gender, and ethnicity. A multilayered analysis involves videotaped role-plays based on a prototypical teacher/student interaction with conflicting goals, guided feedback, repeat enactments, playback sessions, and reverse role-plays. It explores the situated presentation of self and the attempt to exercise power, and reveals difficulties in the development of cross-cultural communicative competence when a discourse style is associated with values incompatible with presentation of self and thus emotionally unacceptable (in this case, to the African-American undergraduate).
Discourse management strategies revisited
Authors: Tapper Gordon , Drzazga Grazyna , Mendoza Maria , Grill Jennifer C.
Published: November 2018

This chapter revisits Tyler’s early research on ITA comprehensibility while also considering recent work on instructional discourse. The purpose of the study is to explore Tyler’s early conclusions regarding the sources of listeners’ perception of incoherence in ITA classroom discourse. Following Tyler’s methodology, the data collected consists of videotapes of the same lab session taught by four different TAs, two native speakers and two non-native speakers. The transcripts of the lab sessions are analyzed in terms of the use of discourse management strategies to determine the differences between native speaker and non-native speaker TAs. Finally, we discuss how those differences may affect ITA comprehensibility as well as implications for ITA training.
Senior confessions
Authors: Boxer Diana
Published: November 2018

This study is an ethnographic analysis of narratives of self-disclosure in the context of recurring happy hour events among “the new old” – people in their sixties who are recently retired or who are about to do so. The storytellers herein share recollections that divulge past transgressions, disclosing identities that are sometimes conflicting. In so doing, they reveal identities of foolishness at a younger age that they claim to have “remedied” through maturation. Revealing personal information is, in general, perceived as a risky business. For the conversations observed here, these groups form a ‘temporary’ bond that seeks common ground and accepts a ‘temporary’ understanding of what this personal information means and how it is to be evaluated.
The speech went on (and on) as Kerry dozed off (*and off)
Authors: Strauss Susan , Chang Heesun , Yoon Jungwan
Published: November 2018

This chapter provides an encapsulated segment of a larger, on-going study centering on a complex set of prepositions and their corresponding phrasal verb particles and adverbs viewed from the methodological and analytic perspective of Conceptual Grammar. Conceptual Grammar is an approach to the analysis and teaching of grammar that combines three paradigms: corpus, discourse analysis, and cognitive linguistics to reveal systematically patterned grammatical meanings. The visual conceptual system is intended to dually represent various gradations of spatial/temporal/metaphorical/abstract meanings in graphic terms, using simple shapes as a mnemonic to aid in the apprehension of conceptual meaning. The system is intended to be generalizable across all uses and meanings of the target lexemes and thus to facilitate productivity of use, serving as a new type of “grammatical rule”.
The role of embodiment in the semantic analysis of phrasal verbs
Authors: Mahpeykar Narges
Published: November 2018

Many of the meanings of prepositions are derived from our bodily experience and conceptualization of the spatial-physical world. This study examines the relationship between frequency and embodied meaning in spatial particles. Tyler and Evans’ Principled Polysemy Model was used to analyze high and low frequency particles. The analysis shows that particles including up, out, off and over appear frequently in phrasal verbs due to a larger set of embodied experiences and a more complex semantic network associated with these particles. In contrast, low frequency particles such as through, under, into and for appear less frequently in phrasal verbs due to the nature of the embodied meanings motivating these uses. Implausible constructions such as hold under and drop up were found to be explainable by examining the basic embodied meanings of the verb and the particle.
Formulaicity and context in second language pragmatics
Authors: Bardovi-Harlig Kathleen
Published: November 2018

Pragmatic routines are realized by a range of expressions at different points on the formulaicity scale, meaning that some expressions are more set than others. This chapter draws on acquisition research to highlight the types of pragmatic knowledge that underpin successful use and emerging use of formulaic language in pragmatics, exploring the alignment of speech act, pragmatic strategy, content, meaning, and form in the acquisition and use of conventional expressions and routines, and the role of context. Examples are drawn primarily from two studies on pragmatics, a large cross-sectional study (N = 179; 5,504 responses to a conversation simulation, Bardovi-Harlig 2009), and an instructional effects study (responses to simulated group work, Bardovi-Harlig, Mossman, and Vellenga, 2015a).
What is happened? Your amazon.com order has shipped
Authors: Ortega Lourdes , Lee Sang-Ki , Miyata Munehiko
Published: November 2018

It is well known that many L2 users overpassivize unaccusatives. The same L2 users may also be reluctant to accept constructions with unaccusative meanings. We examined the responses from 56 L2 users of English on a scaled grammaticality judgment task. We predicted that performance would be negatively affected in the presence of a conceptualizable agent in the discourse scene that biases an external causation construal and with low-frequency verbs and alternating verbs. We found clear effects for frequency and alternation in the hypothesized direction. However, there was no evidence for an independent contribution of the conceptualization bias condition. Our study supports the claim that learners build their L2 grammars by abstracting not only the statistical properties but also the complex, polysemous meanings of the constructions they experience in usage.
Effects of L2 exposure on the use of discourse devices in L2 storytelling
Authors: Nakahama Yuko
Published: November 2018

This study builds on Nakahama, Tyler and van Lier (2001), which showed that conversation provides a plethora of learning opportunities as opposed to decontextualized, mechanical types of activities. The study investigates second language (L2) storytelling by Japanese learners of English as a second language (ESL) and English as a foreign language (EFL) while talking with native speaker interlocutors. Major differences were found between the two groups. ESL learners produced more words and discourse markers (DMs) than their EFL counterparts. Furthermore, while the EFL learners’ narratives were monologic, the ESL learners’ narratives were dialogic and involved NS collaborations. Negotiation of meaning was found in both groups when non-understanding occurred during the storytelling. However, while the EFL learners’ errors received recasts from the NS, the ESL learners’ errors went uncorrected by their interlocutor.
Microstructure and heat treatment effect on transformation strain in steels: Part1 experiment
Authors: Otsuka Takayuki , Satani Daisuke , Yamamoto Kenji , Okamura Kazuo , Brenner Renald , Bacroix Brigitte
Published: November 2018

Anisotropic strain is observed during phase transformation even though no external stress is applied when band structure is formed. The anisotropic strain can result in a change in shape and dimension or residual stress after heat treatment process and thus it achieved much attention. In this paper, three steel grades with different carbon content were prepared to explore the effect of carbon amount and resulting pearlite band thickness as well as heat treatment condition on anisotropic dilatation behaviour during phase transformation. Steel grades containing 0.05 and 0.15 wt-% carbon exhibit a pronounced anisotropy during reverse transformation, whereas 0.44 wt-% carbon shows more isotropic transformation strain. During cooling, transformation strain is anisotropic but less pronounced than that during heating.
Cochlear implantation in patients afflicted with inner ear malformations – the Pécs experience
Authors: Bako Peter , Nemeth Adrienn , Molnar Krisztian , Toth Tamas , Harmat Kinga , Rath Gabor , Gerlinger Imre
Published: November 2018

Purpose:

To successfully analyze the surgical and audiological results of cochlear implantation in patients afflicted with inner ear malformations. This study briefly presents our surgical strategies, the selected implants and the audiological results.

Method:

Objective hearing threshold was measured using an auditory brainstem response and middle latency response audiometry. Structural imaging of high resolution temporal bone computer tomography and inner ear MR scan was performed in support of all patients. Images revealed bilateral cochlear malformation in seven patients. Three ears with common cavity deformity, two ears with incomplete partition type I and three ears suffering from cochlear hypoplasia were all rehabilitated using cochlear implantation. The type of the electrode and the surgical technique were individually determined reflective of the type of malformation. The success of the surgery and potential postoperative complications were duly noted and fully registered. Postoperative audiological measurements were performed and the results were analyzed.

Results:

The average audiological follow-up was 40.3 months. The average free field, pure-tone threshold of speech frequencies (0.5–3 kHz) gained postoperatively were within the range of 32.5–41.6 dB. In two of the procedures, a cerebrospinal fluid gusher did occur and was successfully managed intraoperatively, all without any postoperative complications.

Conclusion:

Temporal bone high resolution CT and inner ear MRI imaging are mandatory to detect and characterize the inner ear malformation. Early implantation of malformed cochlea is crucial towards achieving ideal postoperative audiological results. Notably, an intraoperative gusher is not regarded as a contraindication of the cochlear implantation.
Citizenship as a Communicative Effect
Authors: Jonnalagadda Indivar
Published: November 2018

Using ethnographic field notes on the media circulation and uptake of two specific government orders in Hyderabad, India, I propose a semiotic approach to looking at how emblems of citizenship are not simply products of state ideologies, but rather products of a dialogic relationship (sometimes contentious, often ordinary) between “state” and “citizens,” and always with reference to a history of communicative events between the two. I argue that citizenship should be understood as a communicative effect that is mediated not solely by sovereign power and strident collective movements, but more often through everyday processes by which emblems of citizenship are entextualized and the discursive interactions through which substantive claims are mobilized, negotiated, and contested. Such an approach can add both epistemological and methodological specificity to political anthropology and push it beyond the limitations of an anthropology of the state.
Multilayered regulation of TORC1-body formation in budding yeast
Authors: Sullivan Arron , Wallace Ryan L. , Wellington Rachel , Luo Xiangxia , Capaldi Andrew P.
Published: November 2018

The target of rapamycin kinase complex 1 (TORC1) regulates cell growth and metabolism in eukaryotes. In Saccharomyces cerevisiae, TORC1 activity is known to be controlled by the conserved GTPases, Gtr1/2, and movement into and out of an inactive agglomerate/body. However, it is unclear whether/how these regulatory steps are coupled. Here we show that active Gtr1/2 is a potent inhibitor of TORC1-body formation, but cells missing Gtr1/2 still form TORC1-bodies in a glucose/nitrogen starvation-dependent manner. We also identify 13 new activators of TORC1-body formation and show that seven of these proteins regulate the Gtr1/2-dependent repression of TORC1-body formation, while the remaining proteins drive the subsequent steps in TORC1 agglomeration. Finally, we show that the conserved phosphatidylinositol-3-phosphate (PI(3)P) binding protein, Pib2, forms a complex with TORC1 and overrides the Gtr1/2-dependent repression of TORC1-body formation during starvation. These data provide a unified, systems-level model of TORC1 regulation in yeast.
Modeling the functional link between movement, feeding activity, and condition in a marine predator
Authors: Pirotta Enrico , Schwarz Lisa K , Costa Daniel P , Robinson Patrick W , New Leslie
Published: November 2018

The ability to quantify animals’ feeding activity and the resulting changes in their body condition as they move in the environment is fundamental to our understanding of a population’s ecology. We use satellite tracking data from northern elephant seals (Mirounga angustirostris), paired with simultaneous diving information, to develop a Bayesian state-space model that concurrently estimates an individual’s location, feeding activity, and changes in condition. The model identifies important foraging areas and times, the relative amount of feeding occurring therein, and thus the different behavioral strategies in which the seals engage. The fitness implications of these strategies can be assessed by looking at the resulting variation in individuals’ condition, which in turn affects the condition and survival of their offspring. Therefore, our results shed light on the processes affecting an individual’s decision-making as it moves and feeds in the environment. In addition, we demonstrate how the model can be used to simulate realistic patterns of disturbance at different stages of the trip, and how the predicted accumulation of lipid reserves varies as a consequence. Particularly, disturbing an animal in periods of high feeding activity or shortly after leaving the colony was predicted to have the potential to lead to starvation. In contrast, an individual could compensate even for very severe disturbance if such disturbance occurred outside the main foraging grounds. Our modeling approach is applicable to marine mammal species that perform drift dives and can be extended to other species where an individual’s buoyancy can be inferred from its diving behavior.
Genome-wide search of nucleosome patterns using visual analytics
Authors: Santamaría Rodrigo , Therón Roberto , Durán Laura , García Alicia , González Sara , Sánchez Mar , Antequera Francisco
Published: November 2018

Motivation

The Burrows-Wheeler transform (BWT) is widely used for the fast alignment of high-throughput sequence data. This method also has potential applications in other areas of bioinformatics, and it can be specially useful for the fast searching of patterns on coverage data from different sources.

Results

We present a nucleosome pattern search method that converts levels of nucleosomal occupancy to a sequence-like format to which BWT searches can be applied. The method is embedded in a nucleosome map browser, ‘Nucleosee‘, an interactive visual tool specifically designed to enhance BWT searches, giving them context and making them suitable for visual discourse analysis of the results. The proposed method is fast, flexible and sufficiently generic for the exploration of data in a broad and interactive way.

Availability and implementation

The proposed algorithm and visual browser are available for testing at http://cpg3.der.usal.es/nucleosee. The source code and installation packages are also available at https://github.com/rodrigoSantamaria/nucleosee.

Supplementary information

Supplementary data are available at Bioinformatics online.
Detection of rare disease variants in extended pedigrees using RVS
Authors: Sherman Thomas , Fu Jack , Scharpf Robert B , Bureau Alexandre , Ruczinski Ingo
Published: November 2018

Family-based sequencing studies enable researchers to identify highly penetrant genetic variants too rare to be tested in conventional case-control studies, by studying co-segregation of variant and disease phenotypes. When multiple affected subjects in a family are sequenced, the probability that a variant or a set of variants is shared identical-by-descent by some or all affected relatives provides evidence against the null hypothesis of complete absence of linkage and association. The Rare Variant Sharing software package RVS implements a suite of tools to assess association and linkage between rare genetic variants and a dichotomous disease indicator in family pedigrees.

Availability and Implementation

RVS is available as open source software from the Bioconductor webpage at https://bioconductor.org/packages/release/bioc/html/RVS.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Differential Representations of Perceived and Retrieved Visual Information in Hippocampus and Cortex
Authors: Lee Sue-Hyun , Kravitz Dwight J , Baker Chris I
Published: November 2018

Memory retrieval is thought to depend on interactions between hippocampus and cortex, but the nature of representation in these regions and their relationship remains unclear. Here, we performed an ultra-high field fMRI (7T) experiment, comprising perception, learning and retrieval sessions. We observed a fundamental difference between representations in hippocampus and high-level visual cortex during perception and retrieval. First, while object-selective posterior fusiform cortex showed consistent responses that allowed us to decode object identity across both perception and retrieval one day after learning, object decoding in hippocampus was much stronger during retrieval than perception. Second, in visual cortex but not hippocampus, there was consistency in response patterns between perception and retrieval, suggesting that substantial neural populations are shared for both perception and retrieval. Finally, the decoding in hippocampus during retrieval was not observed when retrieval was tested on the same day as learning suggesting that the retrieval process itself is not sufficient to elicit decodable object representations. Collectively, these findings suggest that while cortical representations are stable between perception and retrieval, hippocampal representations are much stronger during retrieval, implying some form of reorganization of the representations between perception and retrieval.
Acquisition of Spatial Search Strategies and Reversal Learning in the Morris Water Maze Depend on Disparate Brain Functional Connectivity in Mice
Authors: Shah Disha , Verhoye Marleen , Van der Linden Annemie , D’Hooge Rudi
Published: November 2018

Learning has been proposed to coincide with changes in connections between brain regions. In the present study, we used resting-state fMRI (rsfMRI) to map brain-wide functional connectivity (FC) in mice that were trained in the hidden-platform version of the Morris water maze. C57BL6 mice were investigated in a small animal MRI scanner following 2, 10, or 15 days of acquisition learning, or 5 days of reversal learning. Spatial learning coincided with progressive and changing FC between telencephalic regions that have been implemented in spatial learning (such as hippocampus, cingulate, visual, and motor cortex). Search strategy assessment demonstrated that the use of cognitively advanced spatial strategies correlated positively with extensive telencephalic connectivity, whereas non-spatial strategies correlated negatively with connectivity. FC patterns were different and more extensive after reversal learning compared with after extended acquisition learning, which could explain why reversal learning has been shown to be more sensitive to subtle functional defects.
Targeting cervical cancer campaigns on teenage high schoolers in resource-limited economies: lessons from an intervention study of Nigerian senior secondary school girls
Authors: Ifediora Chris O , Azuike Emmanuel C
Published: November 2018

Background

Given the dearth of government-sponsored programmes, preventive lifestyles and practices are the realistic hopes for millions of women in developing countries against cervical cancer. Early interventions for teenage high school girls have been advocated recently, but evidence-base for sustainable activities at this demographic is lacking. This article reduces this gap by determining the impact of two cervical cancer education techniques.

Method

This is a 6-month interventional cohort study of 432 female high school students in South-eastern Nigeria.

Results

A total of 317 (73.4%) and 301 (69.7%) valid responses were received from the pre-intervention (16.8 ± 1.5 years) and post-intervention (17.2 ± 1.6 years) surveys, respectively. About 213 (70.8%) were fully engaged with the interventions. Logistic regression revealed that participants who were ‘engaged’ with the interventions, either through symposium attendance or by reading of the printed handouts, showed significant improvements across multiple cervical cancer parameters regarding knowledge on ‘pap smears’ (analysed with four items), ‘HPV vaccine’ (two items) and ‘risk factors’ (two items). Improvements in Knowledge of ‘early symptoms’ were not improved, with ‘post-coital bleeding’ [odds ratio (OR) = 0.95; P = 0.87] and ‘being asymptomatic’ (OR = 0.69; P = 0.32) remaining statistically similar between the engaged and the unengaged. If ‘engagement’ with either intervention was disregarded, a chi-square analysis identified no significant improvement in knowledge on any parameter.

Conclusion

Ensuring ‘engagement’ with intervention campaigns is vital to achieving effective and sustainable cervical cancer knowledge. Engagement may be achieved by repeating the education activities across all the years/classes that make up high school in each developing country, along with formal examinations at each level.
Strong approximation of monotone stochastic partial differential equations driven by white noise
Authors: Liu Zhihui , Qiao Zhonghua
Published: November 2018

We establish an optimal strong convergence rate of a fully discrete numerical scheme for second-order parabolic stochastic partial differential equations with monotone drifts, including the stochastic Allen–Cahn equation, driven by an additive space-time white noise. Our first step is to transform the original stochastic equation into an equivalent random equation whose solution possesses more regularity than the original one. Then we use the backward Euler in time and spectral Galerkin in space to fully discretise this random equation. By the monotonicity assumption, in combination with the factorisation method and stochastic calculus in martingale-type 2 Banach spaces, we derive a uniform maximum norm estimation and a Hölder-type regularity for both stochastic and random equations. Finally, the strong convergence rate of the proposed fully discrete scheme is obtained. Several numerical experiments are carried out to verify the theoretical result.
Standard work-up of the low-risk kidney transplant candidate: a European expert survey of the ERA-EDTA Developing Education Science and Care for Renal Transplantation in European States Working Group
Authors: Maggiore Umberto , Abramowicz Daniel , Budde Klemens , Crespo Marta , Mariat Christophe , Oberbauer Rainer , Pascual Julio , Peruzzi Licia , Schwartz Sorensen Soren , Viklicky Ondrej , Watschinger Bruno , Oniscu Gabriel C , Heemann Uwe , Hilbrands Luuk B ,   ERA-EDTA DESCARTES Working Group
Published: November 2018

Background

Existing guidelines on the evaluation and preparation of recipients for kidney transplantation target the entire spectrum of patients with end-stage renal disease. Within the ERA-EDTA Developing Education Science and Care for Renal Transplantation in European States (DESCARTES) Working Group, it was proposed that in a subset of relatively young patients (<40 years) without significant comorbidities (such as diabetes or cardiovascular disease), the work-up for transplantation could be restricted to a small set of tests.

Methods

Aiming for agreement between transplant centres across Europe, we surveyed the opinion of 80 transplant professionals from 11 European states on the composition of a minimal work-up.

Results

We show that there is a wide agreement among European experts that the work-up for kidney transplantation of the low-risk candidate, as opposed to the standard risk candidate, could include a limited number of investigations. However, there is some disagreement regarding the small number of diagnostic procedures, which is related to geographical location within Europe and the professional background of respondents.

Conclusions

Based on the results of the survey, published guidelines and expert meetings by the DESCARTES Working Group, we have formulated a proposal for the work-up of low-risk kidney transplant candidates.
Recent advances in structural studies of the CRISPR-Cas-mediated genome editing tools
Authors: Zhu Yuwei , Huang Zhiwei
Published: November 2018

Clustered regularly interspaced short palindromic repeats (CRISPR) and accompanying CRISPR-associated (Cas) proteins provide RNA-guided adaptive immunity for prokaryotes to defend themselves against viruses. The CRISPR-Cas systems have attracted much attention in recent years for their power in aiding the development of genome editing tools. Based on the composition of the CRISPR RNA-effector complex, the CRISPR-Cas systems can be divided into two classes and six types. In this review, we summarize recent advances in the structural biology of the CRISPR-Cas-mediated genome editing tools, which helps us to understand the mechanism of how the guide RNAs assemble with diverse Cas proteins to cleave target nucleic acids.
Star formation and polycyclic aromatic hydrocarbons in ELAIS N1 galaxies as seen by AKARI
Authors: Kovács Tímea O , Burgarella Denis , Kaneda Hidehiro , Molnár Dániel Cs , Oyabu Shinki , Pinter Sandor , Toth L Viktor
Published: November 2018

We have examined the relationship between star formation and polycyclic aromatic hydrocarbons (PAHs) in a variety of galaxies. PAHs are excited by the ultraviolet photons of young stars, but they are disassociated by strong UV radiation in starbursts. Therefore their emission (which is in the wavelength range covered by AKARI) can be used as a star formation tracer in main sequence galaxies. We selected our targets in the ELAIS N1 field with AKARI detections, matched them with the Herschel Point Source Catalog, and collected other publicly available photometric data. Their spectral energy distributions (SEDs) were fitted, and several parameters of the galaxies were estimated, e.g., star formation rate (SFR), stellar mass, and the fraction of PAHs compared to dust mass (qPAH), and we examined the relationships between these parameters. The final sample consisted of 48 galaxies, with redshifts from 0.04 to 2.36. The estimated qPAH values were lower on average than typical values in the literature. This could be due to various reasons, such as low metallicity, or ongoing active galactic nucleus or starburst activity. Of our sample, 83% of the objects fell in the star-forming main sequence of galaxies, while only 8% could be considered as starbursts. We found a decreasing qPAH trend with increasing AV and consequently LIR, suggesting the possible presence of compact star-forming regions. We compared the qPAH values with the known relations of the PAH luminosities, but they did not always follow the same trends (SFR, LIR), and showed only slight correlation with the PAH luminosities.
A state-of-the-art perspective on microgliopathic pain
Authors: Inoue Kazuhide
Published: November 2018

Acute nociceptive pain is an undesirable feeling but has a physiological significance as a warning system for living organisms. Conversely, chronic pain is lacking physiological significance, but rather represents a confusion of nerve functions. The neuropathic pain that occurs after peripheral nerve injury (PNI) is perhaps the most important type of chronic pain because it is refractory to available medications and thus remains a heavy clinical burden. In recent decades, studies have shown that spinal microglia play a principal role in the alterations in synaptic functions evoking this pain. It is also clear that the P2X4 receptor (P2X4R), a subtype of ionotropic ATP receptors, is upregulated exclusively in spinal microglia after PNI and plays a key role in evoking neuropathic pain. Neuropathic pain is caused by several conditions associated with activated microglia without nerve damage. ‘Microgliopathic pain’ is a new concept indicating such abnormal pain related to activated microglia.
Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences
Authors: Lozano Gloria , Francisco-Velilla Rosario , Martinez-Salas Encarnacion
Published: November 2018

Beyond the general cap-dependent translation initiation, eukaryotic organisms use alternative mechanisms to initiate protein synthesis. Internal ribosome entry site (IRES) elements are
cis
-acting RNA regions that promote internal initiation of translation using a cap-independent mechanism. However, their lack of primary sequence and secondary RNA structure conservation, as well as the diversity of host factor requirement to recruit the ribosomal subunits, suggest distinct types of IRES elements. In spite of this heterogeneity, conserved motifs preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES-driven translation. This conservation brings the question of whether IRES elements could consist of basic building blocks, which upon evolutionary selection result in functional elements with different properties. Although RNA-binding proteins (RBPs) perform a crucial role in the assembly of ribonucleoprotein complexes, the versatility and plasticity of RNA molecules, together with their high flexibility and dynamism, determines formation of macromolecular complexes in response to different signals. These properties rely on the presence of short RNA motifs, which operate as modular entities, and suggest that decomposition of IRES elements in short modules could help to understand the different mechanisms driven by these regulatory elements. Here we will review evidence suggesting that model IRES elements consist of the combination of short modules, providing sites of interaction for ribosome subunits, eIFs and RBPs, with implications for definition of criteria to identify novel IRES-like elements genome wide.
α-Amylase immobilization on amidoximated acrylic microfibres activated by cyanuric chloride
Authors: Almulaiky Yaaser Q. , Aqlan Faisal M. , Aldhahri Musab , Baeshen Mohammed , Khan Tariq Jamal , Khan Khalid A. , Afifi Mohamed , AL-Farga Ammar , Warsi Mohiuddin Khan , Alkhaled Mohammed , Alayafi Aisha A. M.
Published: November 2018

Enzyme immobilization is one of the most important techniques for industrial applications. It makes the immobilized enzyme more stable and advantageous than the free form in different aspects. α-Amylase was immobilized on 4% cyanuric chloride-activated amidoximated acrylic fabric at pH 7.0 with (79%) maximum efficiency. A field emission scanning electron microscope and Fourier transform infrared were used to confirm the immobilization process. Even after being recycled 10 times, the immobilized enzyme lost just 28% of its initial activity. Owing to immobilization, the pH of the soluble α-amylase was shifted from 6.0 to 6.5. The immobilized α-amylases showed thermal stability at 60°C, and became more resistant to heavy metal ions. The
k
m
values of the immobilized and soluble α-amylases were 9.6 and 3.8 mg starch ml
−1
, respectively. In conclusion, this method shows that the immobilized α-amylase proved to be more efficient than its soluble form, and hence could be used during saccharification of starch.
What can associative learning do for planning?
Authors: Lind Johan
Published: November 2018

There is a new associative learning paradox. The power of associative learning for producing flexible behaviour in non-human animals is downplayed or ignored by researchers in animal cognition, whereas artificial intelligence research shows that associative learning models can beat humans in chess. One phenomenon in which associative learning often is ruled out as an explanation for animal behaviour is flexible planning. However, planning studies have been criticized and questions have been raised regarding both methodological validity and interpretations of results. Due to the power of associative learning and the uncertainty of what causes planning behaviour in non-human animals, I explored what associative learning can do for planning. A previously published sequence learning model which combines Pavlovian and instrumental conditioning was used to simulate two planning studies, namely Mulcahy & Call 2006 ‘Apes save tools for future use.’Science312, 1038–1040 and Kabadayi & Osvath 2017 ‘Ravens parallel great apes in flexible planning for tool-use and bartering.’Science357, 202–204. Simulations show that behaviour matching current definitions of flexible planning can emerge through associative learning. Through conditioned reinforcement, the learning model gives rise to planning behaviour by learning that a behaviour towards a current stimulus will produce high value food at a later stage; it can make decisions about future states not within current sensory scope. The simulations tracked key patterns both between and within studies. It is concluded that one cannot rule out that these studies of flexible planning in apes and corvids can be completely accounted for by associative learning. Future empirical studies of flexible planning in non-human animals can benefit from theoretical developments within artificial intelligence and animal learning.
Facile synthesis of Al-doped NiO nanosheet arrays for high-performance supercapacitors
Authors: Chen Jinping , Peng Xianyun , Song Lida , Zhang Lihan , Liu Xijun , Luo Jun
Published: November 2018

Electrode material design is the key to the development of asymmetric supercapacitors with high electrochemical performances and stability. In this work, Al-doped NiO nanosheet arrays were synthesized using a facile hydrothermal method followed by a calcination process, and the synthesized arrays exhibited a superior pseudocapacitive performance, including a favourable specific capacitance of 2253 ± 105 F g
−1
at a current density of 1 A g
−1
, larger than that of an undoped NiO electrode (1538 ± 80 F g
−1
). More importantly, the arrays showed a high-rate capability (75% capacitance retention at 20 A g
−1
) and a high cycling stability (approx. 99% maintained after 5000 cycles). The above efficient capacitive performance benefits from the large electrochemically active area and enhanced conductivity of the arrays. Furthermore, an assembled asymmetric supercapacitor based on the Al-doped NiO arrays and N-doped multiwalled carbon nanotube ones delivered a high specific capacitance of 192 ± 23 F g
−1
at 0.4 A g
−1
with a high-energy density of 215 ± 15 Wh kg
−1
and power density of 21.6 kW kg
−1
. Additionally, the asymmetric device exhibited a durable cyclic stability (approx. 100% retention after 5000 cycles). This work with the proposed doping method will be beneficial to the construction of high-performance supercapacitor systems.
From hand to mouth: monkeys require greater effort in motor preparation for voluntary control of vocalization than for manual actions
Authors: Koda Hiroki , Kunieda Takumi , Nishimura Takeshi
Published: November 2018

Voluntary control of vocal production is an essential component of the language faculty, which is thought to distinguish humans from other primates. Recent experiments have begun to reveal the capability of non-human primates to perform vocal control; however, the mechanisms underlying this ability remain unclear. Here, we revealed that Japanese macaque monkeys can learn to vocalize voluntarily through a different mechanism than that used for manual actions. The monkeys rapidly learned to touch a computer monitor when a visual stimulus was presented and showed a capacity for flexible adaptation, such that they reacted when the visual stimulus was shown at an unexpected time. By contrast, successful vocal training required additional time, and the monkeys exhibited difficulty with vocal execution when the visual stimulus appeared earlier than expected; this occurred regardless of extensive training. Thus, motor preparation before execution of an action may be a key factor in distinguishing vocalization from manual actions in monkeys; they do not exhibit a similar ability to perform motor preparation in the vocal domains. By performing direct comparisons, this study provides novel evidence regarding differences in motor control abilities between vocal and manual actions. Our findings support the suggestion that the functional expansion from hand to mouth might be a critical evolutionary event for the acquisition of voluntary control of vocalizations.
Bracketing phenogenotypic limits of mammalian hybridization
Authors: Savriama Yoland , Valtonen Mia , Kammonen Juhana I. , Rastas Pasi , Smolander Olli-Pekka , Lyyski Annina , Häkkinen Teemu J. , Corfe Ian J. , Gerber Sylvain , Salazar-Ciudad Isaac , Paulin Lars , Holm Liisa , Löytynoja Ari , Auvinen Petri , Jernvall Jukka
Published: November 2018

An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material, and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian palaeontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between grey and ringed seals. We analysed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human–Neanderthal distance, but still within that of morphologically similar species pairs known to hybridize. By contrast, morphological and developmental analyses show grey and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that grey–ringed seal hybridization is not limited to captivity. Taken together, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.
Top carnivore decline has cascading effects on scavengers and carrion persistence
Authors: Cunningham Calum X. , Johnson Christopher N. , Barmuta Leon A. , Hollings Tracey , Woehler Eric J. , Jones Menna E.
Published: November 2018

Top carnivores have suffered widespread global declines, with well-documented effects on mesopredators and herbivores. We know less about how carnivores affect ecosystems through scavenging. Tasmania's top carnivore, the Tasmanian devil
(Sarcophilus harrisii)
, has suffered severe disease-induced population declines, providing a natural experiment on the role of scavenging in structuring communities. Using remote cameras and experimentally placed carcasses, we show that mesopredators consume more carrion in areas where devils have declined. Carcass consumption by the two native mesopredators was best predicted by competition for carrion, whereas consumption by the invasive mesopredator, the feral cat (
Felis catus
), was better predicted by the landscape-level abundance of devils, suggesting a relaxed landscape of fear where devils are suppressed. Reduced discovery of carcasses by devils was balanced by the increased discovery by mesopredators. Nonetheless, carcasses persisted approximately 2.6-fold longer where devils have declined, highlighting their importance for rapid carrion removal. The major beneficiary of increased carrion availability was the forest raven (
Corvus tasmanicus
). Population trends of ravens increased 2.2-fold from 1998 to 2017, the period of devil decline, but this increase occurred Tasmania-wide, making the cause unclear. This case study provides a little-studied potential mechanism for mesopredator release, with broad relevance to the vast areas of the world that have suffered carnivore declines.