bluuebunny/crossref_metadata_2025_split huggingface dataset:
Listener-adapted speech
Authors: Lorge Isabelle , Katsos Napoleon 
Published: February 2018

Abstract
While a significant amount of research has focussed on whether bilingualism bestows advantages in cognitive skills, perspective-taking and Theory of Mind, less is known about the effect of bilingualism in communicative tasks where these and related skills may be called for. This study examines bilingual and monolingual adults’ communicative skills through their production of two types of listener-adapted speech (LAS): child-directed speech and foreigner-directed speech. 20 monolinguals and 20 bilingual adults were asked to explain a cooking recipe to a child, a non-native adult and a control native adult. Participants adapted their speech for the child and the foreigner compared to the native adult. Furthermore, bilinguals adapted some features of their speech to a greater extent and in a fine-tuned way (wider pitch range addressing the child and vowel hyperarticulation addressing the foreigner). The prevalence of these features in bilingual speech was not correlated with personality or cognitive measures. We discuss possible sources of this difference in speech adaptation and implications for theories of bilingual cognition.
South African business nanny state: the case of the automotive industrial policy post-apartheid, 1995–2010
Authors: Masondo David 
Published: February 2018

ABSTRACT
The automotive industry is used as a case study to examine why the attempts by the post-apartheid state to channel private investment along the lines of developmental states under conditions of globalisation have been not successful. Instead of building a developmental state, the post-apartheid state elite has built a nanny state which simply provides handouts to transnational companies.
Multimodal hard x-ray imaging with resolution approaching 10 nm for studies in material science
Authors: Yan Hanfei , Bouet Nathalie , Zhou Juan , Huang Xiaojing , Nazaretski Evgeny , Xu Weihe , Cocco Alex P , Chiu Wilson K S , Brinkman Kyle S , Chu Yong S 
Published: February 2018

Abstract
We report multimodal scanning hard x-ray imaging with spatial resolution approaching 10 nm and its application to contemporary studies in the field of material science. The high spatial resolution is achieved by focusing hard x-rays with two crossed multilayer Laue lenses and raster-scanning a sample with respect to the nanofocusing optics. Various techniques are used to characterize and verify the achieved focus size and imaging resolution. The multimodal imaging is realized by utilizing simultaneously absorption-, phase-, and fluorescence-contrast mechanisms. The combination of high spatial resolution and multimodal imaging enables a comprehensive study of a sample on a very fine length scale. In this work, the unique multimodal imaging capability was used to investigate a mixed ionic-electronic conducting ceramic-based membrane material employed in solid oxide fuel cells and membrane separations (compound of Ce0.8Gd0.2O2−x
and CoFe2O4) which revealed the existence of an emergent material phase and quantified the chemical complexity at the nanoscale.
Physical Functioning Decline and Mortality in Older Adults With Multimorbidity: Joint Modeling of Longitudinal and Survival Data
Authors: Wei Melissa Y , Kabeto Mohammed U , Galecki Andrzej T , Langa Kenneth M 
Published: February 2018

AbstractBackgroundMultimorbidity is common among older adults and strongly associated with physical functioning decline and increased mortality. However, the full spectrum of direct and indirect effects of multimorbidity on physical functioning and survival has not been quantified. We aimed to determine the longitudinal relationship of multimorbidity on physical functioning and quantify the impact of multimorbidity and multimorbidity-attributed changes in physical functioning on mortality risk.MethodsThe Health and Retirement Study (HRS) is a nationally representative population-based prospective cohort of adults aged 51 or older. In 2000, participants were interviewed about physician-diagnosed chronic conditions, from which their multimorbidity-weighted index (MWI) was computed. Between 2000 and 2011, participants reported their current physical functioning using a modified Short Form-36. With MWI as a time-varying exposure, we jointly modeled its associations with physical functioning and survival.ResultsThe final sample included 74,037 observations from 18,174 participants. At baseline, participants had a weighted mean MWI of 4.6 ± 4.2 (range 0–36.8). During follow-up, physical functioning declined: −1.72 (95% confidence interval [CI] −1.77, −1.67, p < .001) HRS physical functioning units per point MWI in adjusted models. Over follow-up, 6,362 (34%) participants died. Mortality risk increased 8% (hazard ratio 1.08, 95% CI 1.07–1.08, p < .001) per point MWI in adjusted models. Across all population subgroups, MWI was associated with greater physical functioning decline and mortality risk.ConclusionsMultimorbidity and its associated decline in physical functioning were significantly associated with increased mortality. These associations can be predicted with an easily interpreted and applied multimorbidity index that can better identify and target adults at increased risk for disability and death.
Developing a community-based intervention for Dutch older adults in a socioeconomically disadvantaged community
Authors: Luten Karla A , Dijkstra Arie , de Winter Andrea F , Reijneveld Sijmen A 
Published: February 2018

Summary
Unhealthy eating and low levels of physical activity are major health risks, especially for older adults and people with a low socioeconomic status. The aim of this article is to describe the development of a community-based intervention aimed at promoting physical activity and healthy eating among people aged 55 years and over, in a socioeconomically disadvantaged community. The Intervention Mapping protocol was used to develop the intervention. We conducted a literature search, consultation with community partners and inhabitants, and a quantitative study, in order to obtain insight into the determinants of the target population and to identify appropriate theory-based methods and practical strategies for behavioural change. An assessment was performed of the problem with respect to health behaviour and the underlying determinants. Findings were translated into program, performance and change objectives which specify determinants related to behavioural change. Theory-based methods and practical applications were selected, resulting in a plan for adoption and implementation. The intervention included a local media campaign, social environmental approaches and physical environmental activities in the community, with an intermediating role for inhabitants and health professionals in the promotion of the campaign. An evaluation plan was produced to evaluate the effectiveness of the intervention. The Intervention Mapping protocol was a helpful instrument in developing a feasible, theory and evidence-based intervention tailored to a specific target population in the area of health promotion. The systematic and structured approach provided insight into the relationship between the objectives, methods and strategies used to develop the comprehensive intervention.
A Structure Theorem for Level Sets of Multiplicative Functions and Applications
Authors: Bergelson Vitaly , Kułaga-Przymus Joanna , Lemańczyk Mariusz , Richter Florian K 
Published: February 2018

Abstract
Given a level set E of an arbitrary multiplicative function f, we establish, by building on the fundamental work of Frantzikinakis and Host [14, 15], a structure theorem that gives a decomposition of $1_{E}$ into an almost periodic and a pseudo-random part. Using this structure theorem together with the technique developed by the authors in [3], we obtain the following result pertaining to polynomial multiple recurrence.
UMLS to DBPedia link discovery through circular resolution
Authors: Cuzzola John , Bagheri Ebrahim , Jovanovic Jelena 
Published: February 2018

Abstract

Objective
The goal of this work is to map Unified Medical Language System (UMLS) concepts to DBpedia resources using widely accepted ontology relations from the Simple Knowledge Organization System (skos:exactMatch, skos:closeMatch) and from the Resource Description Framework Schema (rdfs:seeAlso), as a result of which a complete mapping from UMLS (UMLS 2016AA) to DBpedia (DBpedia 2015-10) is made publicly available that includes 221 690 skos:exactMatch, 26 276 skos:closeMatch, and 6 784 322 rdfs:seeAlso mappings.

Methods
We propose a method called circular resolution that utilizes a combination of semantic annotators to map UMLS concepts to DBpedia resources. A set of annotators annotate definitions of UMLS concepts returning DBpedia resources while another set performs annotation on DBpedia resource abstracts returning UMLS concepts. Our pipeline aligns these 2 sets of annotations to determine appropriate mappings from UMLS to DBpedia.

Results
We evaluate our proposed method using structured data from the Wikidata knowledge base as the ground truth, which consists of 4899 already existing UMLS to DBpedia mappings. Our results show an 83% recall with 77% precision-at-one (P@1) in mapping UMLS concepts to DBpedia resources on this testing set.

Conclusions
The proposed circular resolution method is a simple yet effective technique for linking UMLS concepts to DBpedia resources. Experiments using Wikidata-based ground truth reveal a high mapping accuracy. In addition to the complete UMLS mapping downloadable in n-triple format, we provide an online browser and a RESTful service to explore the mappings.
Using clinician text notes in electronic medical record data to validate transgender-related diagnosis codes
Authors: Blosnich John R , Cashy John , Gordon Adam J , Shipherd Jillian C , Kauth Michael R , Brown George R , Fine Michael J 
Published: February 2018

Abstract

Objective
Transgender individuals are vulnerable to negative health risks and outcomes, but research remains limited because data sources, such as electronic medical records (EMRs), lack standardized collection of gender identity information. Most EMR do not include the gold standard of self-identified gender identity, but International Classification of Diseases (ICDs) includes diagnostic codes indicating transgender-related clinical services. However, it is unclear if these codes can indicate transgender status. The objective of this study was to determine the extent to which patients’ clinician notes in EMR contained transgender-related terms that could corroborate ICD-coded transgender identity.

Methods
Data are from the US Department of Veterans Affairs Corporate Data Warehouse. Transgender patients were defined by the presence of ICD9 and ICD10 codes associated with transgender-related clinical services, and a 3:1 comparison group of nontransgender patients was drawn. Patients’ clinician text notes were extracted and searched for transgender-related words and phrases.

Results
Among 7560 patients defined as transgender based on ICD codes, the search algorithm identified 6753 (89.3%) with transgender-related terms. Among 22 072 patients defined as nontransgender without ICD codes, 246 (1.1%) had transgender-related terms; after review, 11 patients were identified as transgender, suggesting a 0.05% false negative rate.

Conclusions
Using ICD-defined transgender status can facilitate health services research when self-identified gender identity data are not available in EMR.
Discovery of pulsations from NGC 300 ULX1 and its fast period evolution
Authors: Carpano S , Haberl F , Maitra C , Vasilopoulos G 
Published: February 2018

Abstract
The supernova impostor SN 2010da located in the nearby galaxy NGC 300, later identified as a likely supergiant B[e] high-mass X-ray binary, was simultaneously observed by NuSTAR and XMM–Newton between 2016 December 16 and 20, over a total time span of ∼310 ks. We report the discovery of a strong periodic modulation in the X-ray flux with a pulse period of 31.6 s and a very rapid spin-up, and confirm therefore that the compact object is a neutron star. We find that the spin period is changing from 31.71 s to 31.54 s over that period, with a spin-up rate of −5.56 × 10−7 s s−1, likely the largest ever observed from an accreting neutron star. The spectrum is described by a power-law and a disc blackbody model, leading to a 0.3–30 keV unabsorbed luminosity of 4.7 × 1039 erg s−1. Applying our best-fitting model successfully to the spectra of an XMM–Newton observation from 2010, suggests that the lower fluxes of NGC 300 ULX1 reported from observations around that time are caused by a large amount of absorption, while the intrinsic luminosity was similar as seen in 2016. A more constant luminosity level is also consistent with the long-term pulse period evolution approaching an equilibrium value asymptotically. We conclude that the source is another candidate for the new class of ultraluminous X-ray pulsars.
Serial Dependence in Position Perception Occurs at the Time of Perception
Authors: Manassi Mauro , Liberman Alina , Kosovicheva Anna , Zhang Kathy , Whitney David 
Published: February 2018

AbstractObservers perceive objects in the world as stable over space and time, even though the visual experience of those objects is often discontinuous and distorted due to masking, occlusion, camouflage, noise, etc. How are we able to easily and quickly achieve stable perception in spite of this constantly changing visual input? It was previously shown that observers experience serial dependence in the perception of features and objects, an effect that extends up to 15 seconds back in time. Here, we asked whether the visual system utilizes an object’s prior physical location to inform future position assignments in order to maximize location stability of an object over time. To test this, we presented subjects with small targets at random angular locations relative to central fixation in the peripheral visual field. Subjects reported the perceived location of the target on each trial by adjusting a cursor’s position to match its location. Subjects made consistent errors when reporting the perceived position of the target on the current trial, mislocalizing it toward the position of the target in the preceding two trials (Experiment 1). This pull in position perception occurred even when a response was not required on the previous trial (Experiment 2). In addition, we show that serial dependence in perceived position occurs immediately after stimulus presentation, and is a fast stabilization mechanism that does not require a delay (Experiment 3). This indicates that serial dependence occurs for position representations and facilitates the stable perception of objects in space. Taken together with previous work, our results show that serial dependence occurs at many stages of visual processing, from initial position assignment to object categorization.
Relationship between Acropora millepora juvenile fluorescence and composition of newly established Symbiodinium assemblage
Authors: Quigley KM , Strader ME , Matz MV 
Published: February 2018

AbstractCoral-dinoflagellate symbiosis is the key biological interaction enabling existence of modern-type coral reefs, but the mechanisms regulating initial host–symbiont attraction, recognition and symbiont proliferation thus far remain largely unclear. A common reef-building coral, Acropora millepora, displays conspicuous fluorescent polymorphism during all phases of its life cycle, due to the differential expression of fluorescent proteins (FPs) of the green fluorescent protein family. In this study, we examine whether fluorescent variation in young coral juveniles exposed to natural sediments is associated with the uptake of disparate Symbiodinium assemblages determined using ITS-2 deep sequencing. We found that Symbiodinium assemblages varied significantly when redness values varied, specifically in regards to abundances of clades A and C. Whether fluorescence was quantified as a categorical or continuous trait, clade A was found at higher abundances in redder juveniles. These preliminary results suggest juvenile fluorescence may be associated with Symbiodinium uptake, potentially acting as either as an attractant to ecologically specific types or as a mechanism to modulate the internal light environment to control Symbiodinium physiology within the host.
MCRiceRepGP: a framework for identification of sexual reproduction associated coding and lincRNA genes in rice
Authors: Golicz Agnieszka A. , Bhalla Prem L. , Singh Mohan B. 
Published: February 2018

AbstractSexual reproduction in plants underpins global food production and evolution. It is a complex process, requiring intricate signalling pathways integrating a multitude of internal and external cues. However, key players and especially non-coding genes controlling plant sexual reproduction remain elusive. We report the development of MCRiceRepGP a novel machine learning framework, which integrates genomic, transcriptomic, homology and available phenotypic evidence and employs multi-criteria decision analysis and machine learning to predict coding and non-coding genes involved in rice sexual reproduction.The rice genome was re-annotated using deep sequencing transcriptomic data from reproduction-associated tissues/cell types identifying novel putative protein coding genes, transcript isoforms and long intergenic non-coding RNAs (lincRNAs). MCRiceRepGP was used for genome-wide discovery of sexual reproduction associated genes in rice; 2,275 protein-coding and 748 lincRNA genes were predicted to be involved in sexual reproduction. The annotation performed and the genes identified, especially the ones for which mutant lines with phenotypes are available provide a valuable resource. The analysis of genes identified gives insights into the genetic architecture of plant sexual reproduction. MCRiceRepGP can be used in combination with other genome-wide studies, like GWAS, giving more confidence that the genes identified are associated with the biological process of interest. As more data, especially about mutant plant phenotypes will become available, the power of MCRiceRepGP with grow providing researchers with a tool to identify candidate genes for future experiments. MCRiceRepGP is available as a web application (http://mcgplannotator.com/MCRiceRepGP/)Significance statementRice is a staple food crop plant for over half of the world’s population and sexual reproduction resulting in grain formation is a key process underpinning global food security. Despite considerable research efforts, much remains to be learned about the molecular mechanisms involved in rice sexual reproduction. We have developed MCRiceRepGP, a novel framework which allows prediction of sexual reproduction associated genes using multi-omics data, multicriteria decision analysis and machine learning. The genes identified and the methodology developed will become a significant resource for the plant research community.
Comparative metabolomics of forest communities: Species differences in foliar chemistry are greater in the tropics
Authors: Sedio Brian E. , Parker John D. , McMahon Sean M. , Wright S. Joseph 
Published: February 2018

AbstractInterspecific variation in the secondary metabolites of plants constrains host specificity of insect herbivores and microbial pathogens. The intensity and specificity of these plant-pest interactions is widely believed to increase towards the Equator, leading to the prediction that secondary metabolites should differ more among co-occurring plant species in tropical communities than in temperate communities. To evaluate this prediction, we quantified metabolomic similarity for 203 tree species that represent >89% of all individuals in large forest plots in Maryland and Panama. We constructed molecular networks based on mass spectrometry of all 203 species, quantified metabolomic similarity for all pairwise combinations of species, and evaluated how pairwise metabolomic similarity varies phylogenetically. Leaf metabolomes exhibited clear phylogenetic signal for the temperate plot, with high similarity among congeneric species. In contrast, leaf metabolomes lacked phylogenetic signal for the tropical plot, with low similarity among congeners. Our results suggest that species differences in secondary chemistry comprise important axes of niche differentiation among tropical trees, especially within species-rich genera, and that the contribution of species differences in secondary chemistry to niche differences increases towards the equator in forest tree communities.
Bacterial cyclopropane fatty acid synthase mRNA is targeted by activating and repressing small RNAs
Authors: Bianco Colleen M. , Fröhlich Kathrin S. , Vanderpool Carin K. 
Published: February 2018

AbstractAltering membrane protein and lipid composition is an important strategy for maintaining membrane integrity during environmental stress. Many bacterial small RNAs (sRNAs) control membrane protein production, but sRNA-mediated regulation of membrane fatty acid composition is less understood. The sRNA RydC was previously shown to stabilize cfa (cyclopropane fatty acid synthase) mRNA, resulting in higher levels of cyclopropane fatty acids in the cell membrane. Here, we report that three additional sRNAs, ArrS, CpxQ, and GadF also regulate cfa post-transcriptionally. RydC, ArrS, and GadF act through masking an RNase E cleavage site in the cfa mRNA 5’ untranslated region (UTR), and all three sRNAs post-transcriptionally activate cfa. In contrast, CpxQ binds to a different site in the cfa mRNA 5’ UTR and represses cfa. Alteration of membrane lipid composition is a key mechanism for bacteria to survive low pH environments, and we show that cfa translation increases in an sRNA-dependent manner when cells are subjected to mild acid stress. This work suggests an important role for sRNAs in the acid stress response through regulation of cfa mRNA.
Dbx1 pre-Bötzinger complex interneurons comprise the core inspiratory oscillator for breathing in adult mice
Authors: Vann Nikolas C. , Pham Francis D. , Dorst Kaitlyn E. , Del Negro Christopher A. 
Published: February 2018

ABSTRACTThe brainstem pre-Bötzinger complex (preBötC) generates inspiratory breathing rhythms, but which neurons comprise its rhythmogenic core? Dbx1-derived neurons may play the preeminent role in rhythm generation, an idea well founded at perinatal stages of development but not in adulthood. We expressed archaerhodopsin or channelrhodopsin in Dbx1 preBötC neurons in intact adult mice to interrogate their function. Prolonged photoinhibition slowed down or stopped breathing, whereas prolonged photostimulation sped up breathing. Brief inspiratory-phase photoinhibition evoked the next breath earlier than expected, whereas brief expiratory-phase photoinhibition delayed the subsequent breath. Conversely, brief inspiratory-phase photostimulation increased inspiratory duration and delayed the subsequent breath, whereas brief expiratory-phase photostimulation evoked the next breath earlier than expected. Because they govern the frequency and precise timing of breaths in awake adult mice with sensorimotor feedback intact, Dbx1 preBötC neurons constitute an essential core component of the inspiratory oscillator, knowledge directly relevant to human health and physiology.