bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergent Simplicity in Microbial Community Assembly
Authors: Goldford Joshua E. , Lu Nanxi , Bajic Djordje , Estrela Sylvie , Tikhonov Mikhail , Sanchez-Gorostiaga Alicia , Segrè Daniel , Mehta Pankaj , Sanchez Alvaro 
Published: October 2017

AbstractMicrobes assemble into complex, dynamic, and species-rich communities that play critical roles in human health and in the environment. The complexity of natural environments and the large number of niches present in most habitats are often invoked to explain the maintenance of microbial diversity in the presence of competitive exclusion. Here we show that soil and plant-associated microbiota, cultivatedex situin minimal synthetic environments with a single supplied source of carbon, universally re-assemble into large and dynamically stable communities with strikingly predictable coarse-grained taxonomic and functional compositions. We find that generic, non-specific metabolic cross-feeding leads to the assembly of dense facilitation networks that enable the coexistence of multiple competitors for the supplied carbon source. The inclusion of universal and non-specific cross-feeding in ecological consumer-resource models is sufficient to explain our observations, and predicts a simple determinism in community structure, a property reflected in our experiments.
Distinct Epigenomic Patterns Are Associated with Haploinsufficiency and Predict Risk Genes of Developmental Disorders
Authors: Han Xinwei , Chen Siying , Flynn Elise , Wu Shuang , Wintner Dana , Shen Yufeng 
Published: October 2017

AbstractHaploinsufficiency is a major mechanism of genetic risk in developmental disorders. Accurate prediction of haploinsufficient genes is essential for prioritizing and interpreting deleterious variants in genetic studies. Current methods based on mutation intolerance in population data suffer from inadequate power for genes with short transcripts. Here we showed haploinsufficiency is strongly associated with epigenomic patterns, and then developed a new computational method (Episcore) to predict haploinsufficiency from epigenomic data from a broad range of tissue and cell types using machine learning methods. Based on data from recent exome sequencing studies of developmental disorders, Episcore achieved better performance in prioritizing loss of function de novo variants than current methods. We further showed that Episcore was less biased with gene size, and was complementary to mutation intolerance metrics for prioritizing loss of function variants. Our approach enables new applications of epigenomic data and facilitates discovery and interpretation of novel risk variants in studies of developmental disorders.
Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima
Authors: Morgunova Ekaterina , Yin Yimeng , Das Pratyush K. , Jolma Arttu , Popov Alexander , Xu You , Nilsson Lennart , Taipale Jussi 
Published: October 2017

SUMMARYMost transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (ΔG). To determine the molecular mechanism behind this effect, we solved the structures of human HOXB13 and CDX2 bound to their two optimal DNA sequences, CAATAAA and TCGTAAA. Thermodynamic analyses by isothermal titration calorimetry revealed that both sites were bound with similar ΔG. However, the interaction with the CAA sequence was driven by change in enthalpy (ΔH), whereas the TCG site was bound with similar affinity due to smaller loss of entropy (ΔS). The common presence of at least two local optima is general to all macromolecular interactions, as ΔG depends on two partially independent variables ΔH and ΔS according to the central equation of thermodynamics, ΔG = ΔH - TΔS.
PGE2production at sites of tissue injury promotes an anti-inflammatory neutrophil phenotype and determines the outcome of inflammation resolutionin vivo
Authors: Loynes Catherine A. , Lee Jou A. , Robertson Anne L. , Steel Michael JG. , Ellett Felix , Feng Yi , Levy Bruce D. , Whyte Moira K , Renshaw Stephen A. 
Published: October 2017

AbstractNeutrophils are the first immune cells recruited to a site of injury or infection, where they perform many functions. Having completed their role, neutrophils must be removed from the inflammatory site - either by apoptosis and efferocytosis or by reverse migration away from the wound - for restoration of normal tissue homeostasis. Disruption of these tightly controlled physiological processes of neutrophil removal can lead to a range of inflammatory diseases. We used anin vivozebrafish model to understand the role of lipid mediator production in neutrophil removal. Following tailfin amputation in the absence of macrophages, neutrophillic inflammation does not resolve. This is due to loss of macrophage-dependent production of eicosanoid prostaglandin E2, which drives neutrophil removal via promotion of reverse migration. Knockdown of endogenous prostaglandin E synthase gene reveals PGE2as essential for neutrophil inflammation resolution. Furthermore, PGE2is able to signal through EP4 receptors to enhance Alox15 production, causing a switch towards anti-inflammatory eicosanoid signalling, specifically Lipoxin A4. Our data confirm regulation of neutrophil migration by PGE2and LXA4in anin vivomodel of inflammation resolution. This pathway may contain therapeutic targets for driving inflammation resolution in chronic inflammatory disease.
The relationship between reinforcement and explicit strategies during visuomotor adaptation
Authors: Codol Olivier , Holland Peter J , Galea Joseph M 
Published: October 2017

AbstractThe motor system’s ability to adapt to changes in the environment is essential for maintaining accurate movements. During such adaptation several distinct systems are recruited: cerebellar sensory-prediction error learning, success-based reinforcement, and explicit strategy-use. Although much work has focused on the relationship between cerebellar learning and strategy-use, there is little research regarding how reinforcement and strategy-use interact. To address this, participants first learnt a 20° visuomotor displacement. After reaching asymptotic performance, binary, hit-or-miss feedback (BF) was introduced either with or without visual feedback, the latter promoting reinforcement. Subsequently, retention was assessed using no-feedback trials, with half of the participants in each group being instructed to stop using any strategy. Although BF led to an increase in retention of the visuomotor displacement, instructing participants to remove their strategy nullified this effect, suggesting strategy-use is critical to BF-based reinforcement. In a second experiment, we prevented the expression or development of a strategy during BF performance, by either constraining participants to a short preparation time (expression) or by introducing the displacement gradually (development). As both strongly impaired BF performance, it suggests reinforcement requires both the development and expression of a strategy. These results emphasise a pivotal role of strategy-use during reinforcement-based motor learning.
Neural decoding of bistable sounds reveals an effect of intention on perceptual organization
Authors: Billig Alexander J. , Davis Matthew H. , Carlyon Robert P. 
Published: October 2017

AbstractAuditory signals arrive at the ear as a mixture that the brain must decompose into distinct sources, based to a large extent on acoustic properties of the sounds. An important question concerns whether listeners have voluntary control over how many sources they perceive. This has been studied using pure tones H and L presented in the repeating pattern HLH-HLH-, which can form a bistable percept, heard either as an integrated whole (HLH-) or as segregated into high (H-H-) and low (-L—) sequences. Although instructing listeners to try to integrate or segregate sounds affects reports of what they hear, this could reflect a response bias rather than a perceptual effect. We had human listeners (15 males, 12 females) continuously report their perception of such sequences and recorded neural activity using magneto-encephalography. During neutral listening, a classifier trained on patterns of neural activity distinguished between periods of integrated and segregated perception. In other conditions, participants tried to influence their perception by allocating attention either to the whole sequence, or to a subset of the sounds. They reported hearing the desired percept for a greater proportion of time than when listening neutrally. Critically, neural activity supported these reports; stimulus-locked brain responses in auditory cortex were more likely to resemble the signature of segregation when participants tried to hear segregation than when attempting to perceive integration. These results indicate that listeners can influence how many sound sources they perceive, as reflected in neural responses that track both the input and its perceptual organization.Significance StatementCan we consciously influence our perception of the external world? We address this question using sound sequences that can be heard either as coming from a single source, or as two distinct auditory streams. Listeners reported spontaneous changes in their perception between these two interpretations while we recorded neural activity to identify signatures of such integration and segregation. They also indicated that they could, to some extent, choose between these alternatives. This claim was supported by corresponding changes in responses in auditory cortex. By linking neural and behavioral correlates of perception we demonstrate that the number of objects we perceive can depend not only on the physical attributes of our environment, but also on how we intend to experience it.
spe-43is required for sperm activation inC. elegans
Authors: Krauchunas Amber R. , Mendez Ernesto , Ni Julie Zhouli , Druzhinina Marina , Mulia Amanda , Parry Jean , Gu Sam Guoping , Stanfield Gillian M. , Singson Andrew 
Published: October 2017

ABSTRACTSuccessful fertilization requires that sperm are activated prior to contacting an oocyte. InC. elegans, this activation process, called spermiogenesis, transforms round immobile spermatids into motile, fertilization-competent spermatozoa. We describe the phenotypic and genetic characterization ofspe-43, a new component of thespe-8pathway, which is required for spermiogenesis in hermaphrodites;spe-43hermaphrodites are self-sterile, whilespe-43males show wild-type fertility. When exposed to Pronase to activate spermin vitro,spe-43spermatids form long rigid spikes radiating outward from the cell periphery instead of forming a motile pseudopod, indicating that spermiogenesis initiates but is not completed. Using a combination of recombinant and deletion mapping and whole genome sequencing, we identified F09E8.1 asspe-43. SPE-43 is predicted to exist in two isoforms; one isoform appears to be a single-pass transmembrane protein while the other is predicted to be a secreted protein. SPE-43 can bind to other known sperm proteins, including SPE-4 and SPE-29, which are known to impact spermiogenesis. In summary, we have identified a membrane protein that is present inC. eleganssperm and is required for sperm activation via the hermaphrodite activation signal.
Managerial ability, tone of earnings announcements, and market reaction
Authors: Luo Yan , Zhou Linying 
Published: October 2017

Purpose
The purpose of this paper is to examine the effect of managerial ability on the tone of earnings announcements and on the market response to the tone.

Design/methodology/approach
This study constructs a model of the determinants of earnings announcement tone in order to examine whether managerial ability plays a significant role in determining earnings announcement tone. Further, to test whether the market response to the tone of earnings announcements is affected by managerial ability, this study also examines the interactive term between earnings announcement tone and managerial ability. The tone of earnings announcements is measured using the spread in the proportion of positive and negative words. Managerial ability is measured using the managerial ability rank developed by Demerjian et al. (2012).

Findings
More able management teams use a more positive tone in their earnings announcements. Stock markets have more pronounced positive reactions to positive tones in the earnings announcements issued by companies with more able management teams.

Originality/value
This study identifies managerial ability as a previously unrecognized determinant of tone in earnings announcements and of the stock price reaction to earnings announcements.
Deferred revenue changes as a leading indicator for future financial performance
Authors: Zhong Ke , Wang Fang , Zhou Lihui 
Published: October 2017

Purpose
The purpose of this paper is to investigate whether deferred revenue changes can serve as a leading indicator for firms listed on China’s stock markets, and whether China’s market participants can appropriately incorporate future performance implications of deferred revenue changes.

Design/methodology/approach
Empirical/archival/regression analysis.

Findings
The authors find that deferred revenue changes are positively associated with the next two years’ sales growth, gross profit margin, profit margin, and return on assets, suggesting that deferred revenue changes can serve as a valid leading indicator for future financial performance. The authors also find that Chinese investors tend to underweight future performance implications of deferred revenue changes.

Originality/value
To the authors’ knowledge, this study is among the first research to examine deferred revenue changes as a leading fundamental indicator and market underreaction to reported accounting information for firms listed on China’s stock markets.
What stops people on long-term opioid substitution from completing treatment?
Authors: Kondoni Tatenda , Kouimtsidis Christos 
Published: October 2017

Purpose
Opioid substitution treatment is effective in reducing harm for the person and society. However, the introduction of the recovery agenda has changed treatment philosophy. Associated targets such as successful treatment completions have introduced new expectations from treatment providers and service users. The purpose of this paper is to provide a service user-centred evaluation of underlying reasons that might prevent them from considering completion of treatment.

Design/methodology/approach
Ten service users who were stable on opioid substitution treatment for more than five years were interviewed face-to-face using a semi-structured format. Detailed inductive coding and thematic analysis of all transcripts was conducted.

Findings
Most participants expressed fear of change to their treatment and in particular reduction of the prescribed medication, due to past traumatic withdrawal experience, fear of relapse, fear of negative impact on their mental and physical health. Nevertheless all were optimistic about their future lives and were hoping to be able to complete their treatment at some point. A three-month follow-up revealed little change, with most participants not considering changing their medication dose in the future.

Practical implications
It could be argued that treatment providers, instead of focussing their efforts on stable service users in promoting treatment exit, should focus on new service users, avoiding coercion to treatment aims and rushed detoxifications.

Originality/value
This small qualitative study confirms results of other recent studies on the same theme and argues for the importance of the quality of the treatment experience of new people accessing treatment.
News media and the racialization of protest: an analysis of Black Lives Matter articles
Authors: Leopold Joy , Bell Myrtle P. 
Published: October 2017

PurposeThe purpose of this paper is to examine coverage of the Black Lives Matter (BLM) movement in seven US-based newspapers to determine whether the protest paradigm, “a pattern of news coverage that expresses disapproval toward protests and dissent,” and other marginalizing techniques are present, and racialized.Design/methodology/approachRelevant articles published during a six-month period of 2014 near the death of Michael Brown were retrieved from the selected outlets, including theNew York Times, theLos Angeles Times, and theSt Louis Post-Dispatch. Textual and content analyses were performed.FindingsThe articles heavily followed the paradigm. An additional characteristic, blame attribution, was also identified. Language of crime, lawlessness, violence, blame for nearby acts of violence, and inflammatory quotes from bystanders and official sources were often present. There was little discussion of key issues associated with the formation of BLM.Research limitations/implicationsMainstream outlets rather than social media or alternative outlets were examined. Future research should study coverage of BLM in other outlets.Practical implicationsMeasures to avoid marginalizing protests and racialization of coverage, including increased diversity in the newsroom and monitoring for racialized language are suggested.Social implicationsRacialization of news and coverage of BLM has widespread negative consequences, such as association of Blacks with criminality that may affect their quality of life. The protest paradigm has the ability to squelch participation in social movements, which have the possibility to bring about needed social change.Originality/valueThis interdisciplinary paper highlights the important role of mainstream media and news routines in affecting the BLM movement. It uses diversity research to make recommendations for media practitioners to avoid racialization of news.
Calling in Black: a dynamic model of racially traumatic events, resourcing, and safety
Authors: McCluney Courtney L. , Bryant Courtney M. , King Danielle D. , Ali Abdifatah A. 
Published: October 2017

PurposeRacially traumatic events – such as police violence and brutality toward Blacks – affect individuals in and outside of work. Black employees may “call in Black” to avoid interacting with coworkers in organizations that lack resources and perceived identity and psychological safety. The paper aims to discuss this issue.Design/methodology/approachThe paper integrates event system theory (EST), resourcing, and psychological safety frameworks to understand how external, racially traumatic events impact Black employees and organizations. As racially traumatic events are linked to experienced racial identity threat, the authors discuss the importance of both the availability and creation of resources to help employees to maintain effective workplace functioning, despite such difficult circumstances.FindingsOrganizational and social-identity resourcing may cultivate social, material, and cognitive resources for black employees to cope with threats to their racial identity after racially traumatic events occur. The integration of organizational and social-identity resourcing may foster identity and psychologically safe workplaces where black employees may feel valued and reduce feelings of racial identity threats.Research limitations/implicationsImplications for both employees’ social-identity resourcing practice and organizational resource readiness and response options are discussed.Originality/valueThe authors present a novel perspective for managing diversity and inclusion through EST. Further, the authors identify the interaction of individual agency and organizational resources to support Black employees.
Political tensions: English teaching, standards, and postsecondary readiness
Authors: Hungerford-Kresser Holly , Vetter Amy 
Published: October 2017

Purpose
The purpose of this paper was to highlight ways two novice secondary English teachers negotiated the politics of college and career readiness along with the literacy needs of students, in the age of accountability.

Design/methodology/approach
This three-year longitudinal qualitative case study focused on two participants in English teacher preparation and their first two years in the classroom.

Findings
The findings focus on participants’ definitions of college and career readiness as it pertains to their English Language Arts classrooms. Next, the focus is on two themes: tensions these novice teachers experienced as they attempted to build classrooms focused on postsecondary readiness, and the ways in which they worked to bridge the gap between their definitions of college and career readiness and the realities of their classrooms.

Research limitations/implications
Connections among high stakes testing environments, postsecondary readiness and literacy teacher education are important to the field. Studying the experiences of novice teachers can fill a present gap at the intersection of these concepts.

Practical implications
Curriculum in teacher education should introduce standards, as well as provide a platform for negotiating and critiquing them. Three focus areas to help pre-service teachers mitigate tensions between minimum skills assessments, college readiness and literacy are personal experience, collaboration and reflective partnerships.

Originality/value
There has been little to no research done on the tensions between preparing all students to be college and career ready and the minimum skills based priorities that govern many school systems and its impact on novice teachers. This classroom reality is important to literacy teacher education.
Addressing English teachers’ concerns about decentering Standard English
Authors: Metz Mike 
Published: October 2017

PurposeThis paper aims to address concerns of English teachers considering opening up their classrooms to multiple varieties of English.Design/methodology/approachDrawing on the author’s experience as a teacher educator and professional developer in different regions of the USA, this narrative paper groups teachers’ concerns into general categories and offers responses to the most common questions.FindingsTeachers want to know why they should make room in their classrooms for multiple Englishes; what they should teach differently; how they learn about English variation; how to balance Standardized English and other Englishes; and how these apply to English Learners and/or White speakers of Standardized English.Practical implicationsThe study describes the author’s approach to teaching about language as a way to promote social justice and equality, the value of increasing students’ linguistic repertoires and why it is necessary to address listeners as well as speakers. As teachers attempt to adopt and adapt new approaches to teaching English language suggested in the research literature, they need to know their challenges and concerns are heard and addressed. Teacher educators working to support these teachers need ways to address teachers’ concerns.Social implicationsThis paper emphasizes the importance of teaching mainstream, White, Standard English-speaking students about English language variation. By emphasizing the role of the listener and teaching students to hear language through an expanded language repertoire, English teachers can reduce the prejudice attached to historically stigmatized dialects of English.Originality/valueThis paper provides a needed perspective on how to work with teachers who express legitimate concerns about what it means to decenter Standardized English in English classrooms.