bluuebunny/crossref_metadata_2025 huggingface dataset:
FLOWERING LOCUS T
mRNA is synthesized in specialized companion cells in
Arabidopsis
and Maryland Mammoth tobacco leaf veins
Authors: Chen Qingguo , Payyavula Raja S. , Chen Lin , Zhang Jing , Zhang Cankui , Turgeon Robert
Published: February 2018

Significance

Flowering in many plants begins with the perception of daylength in leaves. For example, some plants flower in short days, others in long days. In
Arabidopsis thaliana
, the leaves then transmit a small protein, FLOWERING TIME T (FT), to the shoot apex in the food-conducting cells, the phloem. Arrival of FT causes the apex to transition from leaf to flower formation. In this paper, we show that only two files of phloem cells in
A. thaliana
veins synthesize FT. This is also true for the Maryland Mammoth cultivar of tobacco (
Nicotiana tabacum
). Killing the cells specifically affects downstream, but not upstream, genes, indicating that an extensive intercellular signaling system regulates FT synthesis in the phloem.
Multiscale approach reveals that
Cloudina
aggregates are detritus and not in situ reef constructions
Authors: Mehra Akshay , Maloof Adam
Published: February 2018

Significance

Little is known about how the Ediacaran index fossil
Cloudina
lived and what impact it had on its surroundings. This uncertainty is due to the fact that
Cloudina
often is preserved with the same mineralogy as the rocks in which it is found; the lack of density contrast means that traditional imaging techniques cannot be used to reconstruct and measure in situ
Cloudina
populations. Recently, researchers have suggested that
Cloudina
was a framework reef builder that actively adapted to changing environmental conditions. In this paper, we use a serial grinding and imaging technique to produce 3D models of
Cloudina
aggregates. Along with detailed field observations, we demonstrate that
Cloudina
populations are detritus and not in situ growth.
Expanded cellular clones carrying replication-competent HIV-1 persist, wax, and wane
Authors: Wang Zheng , Gurule Evelyn E. , Brennan Timothy P. , Gerold Jeffrey M. , Kwon Kyungyoon J. , Hosmane Nina N. , Kumar Mithra R. , Beg Subul A. , Capoferri Adam A. , Ray Stuart C. , Ho Ya-Chi , Hill Alison L. , Siliciano Janet D. , Siliciano Robert F.
Published: February 2018

Significance

The HIV-1 latent reservoir cannot be eradicated by antiretroviral therapy (ART). The reservoir is a major barrier to cure. To characterize the mechanisms that contribute to persistence of the latent reservoir, we examined clonally expanded cell populations carrying replication-competent HIV-1 and followed them longitudinally. Expanded clones harboring replication-competent HIV-1 were identified in all study participants, but these clones emerge and wane on a time scale of years. A similar pattern was identified in viruses sampled from residual viremia. The findings suggest that the latent reservoir is likely to be maintained through expansion driven by antigens and cytokines, and that the expansion is balanced with a constant cell loss.
RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome
Authors: Van Treeck Briana , Protter David S. W. , Matheny Tyler , Khong Anthony , Link Christopher D. , Parker Roy
Published: February 2018

Significance

Stress granules, which are ubiquitous, non–membrane-bound assemblies of protein and RNA, form when translation initiation is inhibited, contribute to the regulation of gene expression, and are implicated in the pathologies of cancer and neurodegenerative disease. Understanding the mechanisms of stress granule assembly is crucial to gaining greater insight into their biological function and pathological misregulation. We provide evidence that RNA–RNA interactions contribute to the assembly of stress granules. Furthermore, we show that pathogenic dipeptides increase the propensity of RNA to assemble. Together, this argues that RNAs are assembly prone and must be carefully regulated. A summative model of stress granule assembly, which includes
trans
-RNA–RNA interactions, can be extended to other ribonucleoprotein granules in the cell.
Listener-adapted speech
Authors: Lorge Isabelle , Katsos Napoleon
Published: February 2018

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

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.
BBSome trains remove activated GPCRs from cilia by enabling passage through the transition zone
Authors: Ye Fan , Nager Andrew R. , Nachury Maxence V.
Published: February 2018

A diffusion barrier at the transition zone enables the compartmentalization of signaling molecules by cilia. The BBSome and the small guanosine triphosphatase Arl6, which triggers BBSome coat polymerization, are required for the exit of activated signaling receptors from cilia, but how diffusion barriers are crossed when membrane proteins exit cilia remains to be determined. In this study, we found that activation of the ciliary G protein–coupled receptors (GPCRs) Smoothened and SSTR3 drove the Arl6-dependent assembly of large, highly processive, and cargo-laden retrograde BBSome trains. Single-molecule imaging revealed that the assembly of BBSome trains enables the lateral transport of ciliary GPCRs across the transition zone. However, the removal of activated GPCRs from cilia was inefficient because a second periciliary diffusion barrier was infrequently crossed. We conclude that exit from cilia is a two-step process in which BBSome/Arl6 trains first move activated GPCRs through the transition zone before a periciliary barrier can be crossed.
Otopetrin-1: A sour-tasting proton channel
Authors: Ramsey I. Scott , DeSimone John A.
Published: February 2018

Ramsey and DeSimone highlight the recent discovery of a new family of proton channels.
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

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

Background

Multimorbidity 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.

Methods

The 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.

Results

The 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.

Conclusions

Multimorbidity 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

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

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

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

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.
Incidence of Nephrotoxicity Among Pediatric Patients Receiving Vancomycin With Either Piperacillin–Tazobactam or Cefepime: A Cohort Study
Authors: Cook Kathryn M , Gillon Jessica , Grisso Alison G , Banerjee Ritu , Jimenez-Truque Natalia , Phillips Elizabeth J , Van Driest Sara L
Published: February 2018

In this matched-cohort study of pediatric inpatients, 28.9% of those treated with a combination of piperacillin–tazobactam and vancomycin developed acute kidney injury, compared to 7.9% in those treated with cefepime and vancomycin (P < .001).
Discovery of pulsations from NGC 300 ULX1 and its fast period evolution
Authors: Carpano S , Haberl F , Maitra C , Vasilopoulos G
Published: February 2018

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.
Paecilomyces Rot: A New Apple Disease
Authors: Biango-Daniels Megan N. , Hodge Kathie T.
Published: February 2018

Paecilomyces niveus is an important food spoilage fungus that survives thermal processing in fruit products, where it produces the mycotoxin patulin. Spoilage of products has been attributed to soil contamination; however, little is known about the ecology of this organism. In this study, orchard soils and culled apple fruit were surveyed and the ability of P. niveus to infect apple was tested on two popular apple varieties. P. niveus was found in 34% of sampled orchard soils from across New York. Completing Koch’s postulates, P. niveus was demonstrated to cause postharvest disease in Gala and Golden Delicious apple. Symptoms of this disease, named Paecilomyces rot, resemble several other apple diseases, including black rot, bitter rot, and bull’s-eye rot. External symptoms of Paecilomyces rot include brown, circular, concentrically ringed lesions, with an internal rot that is firm and cone-shaped. Both Gala and Golden Delicious apple fruit inoculated with P. niveus developed lesions ≥43 mm in size at 22 days after inoculation. There is some evidence that the size of lesions and rate of infection differ between Gala and Golden Delicious, which may indicate differing resistance to P. niveus. This work shows that P. niveus is common in New York orchard soil and can cause a novel postharvest fruit disease. Whether infected fruit can serve as an overlooked source of inoculum in heat-processed apple products requires further study.
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

Observers 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

Coral-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

Sexual 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 statement

Rice 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

Interspecific 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

Altering 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

The 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.
C. elegans ADARs antagonize silencing of cellular dsRNAs by the antiviral RNAi pathway
Authors: Reich Daniel P. , Tyc Katarzyna M. , Bass Brenda L.
Published: February 2018

Cellular dsRNAs are edited by adenosine deaminases that act on RNA (ADARs). While editing can alter mRNA-coding potential, most editing occurs in noncoding sequences, the function of which is poorly understood. Using dsRNA immunoprecipitation (dsRIP) and RNA sequencing (RNA-seq), we identified 1523 regions of clustered A-to-I editing, termed editing-enriched regions (EERs), in four stages of Caenorhabditis elegans development, often with highest expression in embryos. Analyses of small RNA-seq data revealed 22- to 23-nucleotide (nt) siRNAs, reminiscent of viral siRNAs, that mapped to EERs and were abundant in adr-1;adr-2 mutant animals. Consistent with roles for these siRNAs in silencing, EER-associated genes (EAGs) were down-regulated in adr-1;adr-2 embryos, and this was dependent on associated EERs and the RNAi factor RDE-4. We observed that ADARs genetically interact with the 26G endogenous siRNA (endo-siRNA) pathway, which likely competes for RNAi components; deletion of factors required for this pathway (rrf-3 or ergo-1) in adr-1;adr-2 mutant strains caused a synthetic phenotype that was rescued by deleting antiviral RNAi factors. Poly(A)+ RNA-seq revealed EAG down-regulation and antiviral gene induction in adr-1;adr-2;rrf-3 embryos, and these expression changes were dependent on rde-1 and rde-4. Our data suggest that ADARs restrict antiviral silencing of cellular dsRNAs.
Transcription elongation rate affects nascent histone pre-mRNA folding and 3′ end processing
Authors: Saldi Tassa , Fong Nova , Bentley David L.
Published: February 2018

Transcription elongation rate influences cotranscriptional pre-mRNA maturation, but how such kinetic coupling works is poorly understood. The formation of nonadenylated histone mRNA 3′ ends requires recognition of an RNA structure by stem–loop-binding protein (SLBP). We report that slow transcription by mutant RNA polymerase II (Pol II) caused accumulation of polyadenylated histone mRNAs that extend past the stem–loop processing site. UV irradiation, which decelerates Pol II elongation, also induced long poly(A)+ histone transcripts. Inhibition of 3′ processing by slow Pol II correlates with failure to recruit SLBP to histone genes. Chemical probing of nascent RNA structure showed that the stem–loop fails to fold in transcripts made by slow Pol II, thereby explaining the absence of SLBP and failure to process 3′ ends. These results show that regulation of transcription speed can modulate pre-mRNA processing by changing nascent RNA structure and suggest a mechanism by which alternative processing could be controlled.
A novel inhibitor stabilizes the inactive conformation of MAPK-interacting kinase 1
Authors: Matsui Yumi , Yasumatsu Isao , Yoshida Ken-ichi , Iimura Shin , Ikeno Yutaka , Nawano Takako , Fukano Hajime , Ubukata Osamu , Hanzawa Hiroyuki , Tanzawa Fumie , Isoyama Takeshi
Published: February 2018

Mitogen-activated protein kinase (MAPK)-interacting kinases 1 (Mnk1) and 2 (Mnk2) modulate translation initiation through the phosphorylation of eukaryotic translation initiation factor 4E, which promotes tumorigenesis. However, Mnk1 and Mnk2 are dispensable in normal cells, suggesting that the inhibition of Mnk1 and Mnk2 could be effective in cancer therapy. To provide a structural basis for Mnk1 inhibition, a novel Mnk1 inhibitor was discovered and the crystal structure of Mnk1 in complex with this inhibitor was determined. The crystal structure revealed that the inhibitor binds to the autoinhibited state of Mnk1, stabilizing the Mnk-specific DFD motif in the DFD-out conformation, thus preventing Mnk1 from switching to the active conformation and thereby inhibiting the kinase activity. These results provide a valuable platform for the structure-guided design of Mnk1 inhibitors.
Insurance prospects after the European dairy quota abolition
Authors: Schulte Hinrich , Musshoff Oliver
Published: February 2018

Purpose

The expected increase in milk price volatility after the milk quota abolition in the EU will lead to further planning uncertainty on dairy farms. Consequently, the modest supply of insurance and the hedging of milk prices through futures may increase. To shed more light on this possibility, the purpose of this paper is to calculate the additional willingness to pay (WTP) for risk-averse dairy farmers in order to cope with milk price volatility after the quota abolition.

Design/methodology/approach

After the European dairy quota abolition, European dairy farmers will be more dependent on the milk price of the world market. To reflect the world market, a time series of milk prices of a dairy processor from New Zealand (NZ) was used because NZ is exporting most of their dairy products under world market conditions. Based on the NZ price series, we approximated milk price volatility after the European dairy quota abolition and calculated the additional WTP of risk-averse dairy farmers in order to cope with milk price volatility.

Findings

Using a price series of NZ to approximate milk price volatility after the European dairy quota abolition and comparing it with a German milk price series before quota, the results suggest there might be increased WTP after the milk quota abolition in order to cope with milk price volatility. Following this assumption, the WTP of considerable risk-averse dairy farmers may exceed the initial transaction costs of hedging milk prices with futures on commodity exchanges. Nevertheless, a qualitative discussion of the results shows costs of education, basis risk, and the small size of farms could still keep dairy farmers from hedging the milk price.

Originality/value

In calculating the additional WTP for risk-averse dairy farmers to cope with milk price volatility, this is the first study to attempt to illustrate the expected influence of increasing milk price volatility at the dairy farm level after the dairy quota abolition in the EU. The additional WTP gives further insights into the need for and acceptance of insurance after the dairy quota abolition at the dairy farm level.
Exploring local and organic food consumption in a holistic sustainability view
Authors: Scalvedi Maria Luisa , Saba Anna
Published: February 2018

Purpose

The purpose of this paper is to identify sustainability aspects that overlap with local and organic consumer profiles in order to provide evidence that can be used to promote both kinds of foods in a sustainable food consumption (SFC) integrated framework.

Design/methodology/approach

Discriminant analysis was applied to a national sample of 3,004 respondents in Italy to separately depict local and organic consumers’ profiles based on personal values, eating habits, food purchase motivations, and involvement.

Findings

Organic consumption showed a lower penetration compared to local consumption. However, organic consumers adhered to more sustainable consumption principles. Adopting healthy diets and sharing self-transcendence values emerged as common traits of both consumers. Regular consumption made both consumers’ profiles look similar by sharing more sustainability-related traits.

Research limitations/implications

Only two out of the different types of foods promoted as sustainable were considered. Further insights could be made regarding fair trade foods and food promoted by voluntary sustainability standards.

Practical implications

The overlapping motivations of the two consumer profiles provided evidence of the potential efficacy of joint promotion in favour of sustainability and demonstrated that a synergic approach among food systems could foster more sustainable consumption.

Originality/value

This study identified common sustainability motivations among different consumer groups, based on sustainable food categories, adopting a holistic vision of SFC.
All insects are equal, but some insects are more equal than others
Authors: Fischer Arnout R.H. , Steenbekkers L.P.A. (Bea)
Published: February 2018

Purpose

Lack of acceptance of insects as food is considered a barrier against societal adoption of the potentially valuable contribution of insects to human foods. An underlying barrier may be that insects are lumped together as one group, while consumers typically try specific insects. The purpose of this paper is to investigate the ways in which Dutch consumers, with and without insect tasting experience, are more or less willing to eat different insects.

Design/methodology/approach

In a quasi-experimental study (n=140), the participants with and without prior experience in eating insects were asked to give their willingness to eat a range of insects, and their attitudes and disgust towards eating insects.

Findings

Insects promoted in the market were more preferred than the less marketed insects, and a subgroup of preferred insects for participants with experience in eating insects was formed.

Research limitations/implications

Although well-known insects were more preferred, general willingness to eat remained low for all participants. The results indicate that in future research on insects as food the specific insects used should be taken into account.

Practical implications

Continued promotion of specific, carefully targeted, insects may not lead to short-term uptake of insects as food, but may contribute to willingness to eat insects as human food in the long term.

Originality/value

The paper shows substantial differences between consumers who have and who have not previously tasted insects, with higher acceptance of people with experience in tasting insects for the specific insects that are frequently promoted beyond their generally more positive attitude towards eating insects.
Declining harmonization in maximum residue levels for pesticides
Authors: Yeung May , Kerr William A. , Coomber Blair , Lantz Matthew , McConnell Alyse
Published: February 2018

Purpose

Maximum residual limits (MRLs) for pesticides are based on science. This is true both for MRLs devised by national governments and multilaterally through the Codex. Science-based Codex MRLs are internationally harmonized to facilitate trade. Since the 1990s, an increasing number of countries have devised national MRLs and eschewed those of the Codex. These differing national standards are becoming important barriers to trade. The purpose of this paper is to explore the ramifications of these diverging MRLs for food security, investigate the reasons for the rise of national standards, and explore the role of science in regulatory processes.

Design/methodology/approach

The approach is an examination of the scientific basis for MRLs in the context of food safety outcomes.

Findings

It finds that there is no improvement in food safety from the move to national MRLs, only a loss of the benefits of trade. As all countries, along with the Codex, claim that their MRLs are based on science, suggesting that there is a need for an examination of the role of science in the making of public policy.

Originality/value

This study identifies a potential risk to food security for food policy makers. Given future food security challenges and that pesticides are used almost universally in conventional agriculture, trade barriers based on divergent interpretations of science need to be addressed by food policy makers.
Non-alcoholic beverage marketing in 100 highest grossing movies in 2010-2014
Authors: Cockburn Nicole , Schubert Lisa , Nguyen Nam-Phuong Quoc , Ford Pauline
Published: February 2018

Purpose

Australian sales of hyperpalatable beverages (HPB) (a term used to describe naturally or artificially sweet beverages) have followed a consistent upward trend since 2000. The purpose of this paper is to examine HPB brand placements in the top 20 annual highest grossing movies in Australia in 2010-2014.

Design/methodology/approach

A content analysis was undertaken on the 20 highest grossing movies annually from 2010 to 2014. Movies were analysed according to the prevalence and portrayal of branded beverages.

Findings

In total, 35 per cent of movies contained an HPB brand placement. Movies were more likely to be classified M, MA15+, R/R18+, and categorised as comedy, or action/adventure genre. Soft drinks were the most prevalent category (60.9 per cent), and Coca Cola Company manufactured 40.6 per cent of the brands that were embedded throughout the movies.

Originality/value

This study revealed some of industry’s non-direct marketing strategies through HPB placement in movies. Findings suggest that further scrutiny is needed of the relatively underresearched medium of beverage advertising.
Who knows more about food allergies – restaurant managerial staff or employees?
Authors: Lee Yee Ming , Sozen Erol
Published: February 2018

Purpose

The purpose of this paper is to compare restaurant managerial staff and employees’ attitudes toward food allergies, their food allergy knowledge and food allergy-related training.

Design/methodology/approach

An online questionnaire was administered through a market research company (Qualtrics® Inc.). A total of 110 managerial staff and 229 restaurant employees completed this questionnaire.

Findings

Most restaurants were willing to modify recipes for customers with food allergies. Respondents felt that the customers should be responsible for expressing their food allergy needs. Both groups were able to identify certain symptoms of allergic reactions to food but lacked knowledge of allergen-handling practices. The managerial staff and employees had knowledge differences about how to respond to an allergic reaction (p<0.001) and how to identify peanut derivatives on food labels (p<0.000). In total, 70 percent of the managerial staff indicated that they provided employee food allergy training but only 40 percent of employees indicated receiving such training. The managerial staff identified a lack of employee commitment and interest as barriers to training provision. However, the employees identified different reasons (i.e. it is unnecessary and not beneficial).

Practical implications

Restaurants should have policies in place to accommodative customers with food allergies and make sure food allergy-related information is communicated to their customers via different outlets (i.e. restaurants’ websites and printed menus). Food allergy training should be designed based on the areas that need improvement, as knowledge may differ based on the position in the restaurants (managerial staff vs employees) and types of the restaurants (quick service vs casual dining). Pragmatic strategies need to be identified to better encourage and motivate restaurant employees to attend a food allergy training.

Originality/value

Understanding the similarities and differences in attitudes, knowledge and training on food allergies between restaurant managerial staff and employees would help restaurants to plan and implement policies and training that best fit both managerial staff and employees.
A graphical equivalent to mandated nutrition information tables
Authors: Young Owen , Kantono Kevin , Waiguny Martin , Hung Li-Fan , Hamid Nazimah
Published: February 2018

Purpose

The purpose of this paper is to explore understanding of a graphic equivalent to mandatory nutrition information tables.

Design/methodology/approach

The horizontal bar graphic’s single number shows the per cent content of the dominant nutrient, marked “Most”, contrasting with “Least” at the origin. A separate bar for energy is expressed as percentage of 3,700 kJ, the energy in 100 g of fat. Six randomised table and equivalent graph images were shown to subjects who answered questions about the foods’ energy, dominant nutrient and per cent content, and relative abundance of seven mandated nutrients. One trial tested 40 food science students, another 100 online Australasian consumers. Scores were compared by the χ2 test. Liking of the two formats was compared by t-test.

Findings

Correct online consumer responses were: energy – 18 per cent (tables), 71 per cent (graphics); dominant nutrient – 81, 96 per cent; per cent dominant nutrient – 43, 82 per cent. All differences were highly significant. Relative abundance questions created a 7 nutrient × 6 food matrix (42 combinations) where tables were more accurately understood 14 times (3 significant) and graphics 28 times (12 significant). Responses in the student trial paralleled the consumer trial; differences were less marked but with similar statistical significances. Consumers liked the graphic more.

Practical implications

The graphic format was more understandable than the table format, and would be useful in internet-based applications.

Originality/value

The graphic format represents a huge advance in understanding of mandatory nutrient information.