bluuebunny/crossref_metadata_2025_split huggingface dataset:
Boron Hyperaccumulation Mechanisms in Puccinellia distans as Revealed by Transcriptomic Analysis
Authors: Öztürk Saniye Elvan , Göktay Mehmet , Has Canan , Babaoğlu Mehmet , Allmer Jens , Doğanlar Sami , Frary Anne 
Published: February 2017

AbstractBoron is an essential plant micronutrient; but is toxic at high concentrations. Boron toxicity can severely affect crop productivity in arid and semi-arid environments. Puccinellia distans (Jacq.) Par1., common alkali grass, is found throughout the world and can survive under boron concentrations that are lethal for other plant species. In addition, P. distans can accumulate very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were analyzed by RNA sequencing to identify genes related to boron tolerance and hyperaccumulation. Abundance levels of selected differentially expressed transcripts were validated by real-time PCR. The results indicated that the hyperaccumulation mechanism of P. distans involves many transcriptomic changes including those that lead to: alterations in the malate pathway, changes in cell wall components that allow sequestration of excess boron without toxic effects, and increased expression of at least one putative boron transporter and two putative aquaporins. Elucidation of the boron accumulation mechanism is important to develop approaches for bioremediation of boron contaminated soils.
Variability of quantal NMDA to AMPA current ratio in nucleus tractus solitarii neurons
Authors: Strube Caroline , Gackière Florian , Saliba Layal , Tell Fabien , Kessler Jean-Pierre 
Published: February 2017

AbstractThe ratio between AMPA and NMDA receptors is a key factor governing integrative and plastic properties of excitatory glutamatergic synapses. To determine whether the respective proportions of AMPA and NMDA receptors are similar or vary across a neuron's synapse, we analyzed the variability of NMDA and AMPA currents in quantal responses recorded from neurons located in the nucleus tractus solitarii. We found that the average NMDA to AMPA current ratio strongly differed between recorded neurons and that most of the intra-neuronal current ratio variability was attributable to fluctuations in NMDA current. We next performed computer simulations with a Monte Carlo model of a glutamatergic synapse to estimate the part of AMPA and NMDA currents fluctuations induced by stochastic factors. We found that NMDA current variability mainly resulted from strong channel noise with few influence of release variations. On the contrary, partly because of the presence of subconductance states, AMPA receptor channel noise was low and AMPA current fluctuations tightly reflected changes in the amount of glutamate released. We next showed that these two factors, channel noise and fluctuations in glutamate release, were sufficient to explain the observed variability of the NMDA to AMPA current ratio in quantal events recorded from the same neuron. We therefore concluded that the proportion of AMPA and NMDA receptors was similar, or roughly similar, across synapses onto the same target cell.
TheSorghum bicolorreference genome: improved assembly and annotations, a transcriptome atlas, and signatures of genome organization
Authors: McCormick Ryan F. , Truong Sandra K. , Sreedasyam Avinash , Jenkins Jerry , Shu Shengqiang , Sims David , Kennedy Megan , Amirebrahimi Mojgan , Weers Brock , McKinley Brian , Mattison Ashley , Morishige Daryl , Grimwood Jane , Schmutz Jeremy , Mullet John 
Published: February 2017

2ABSTRACTSorghum bicoloris a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Sub-telomeric repeats with characteristics of Tandem Repeats In Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of the reference genome sequence to 56 resequenced genomes from diverse sorghum genotypes identified ~7.4M SNPs and 1.8M indels. Large scale variant features in euchromatin were identified with periodicities of ~25 kbp. An RNA transcriptome atlas of gene expression was constructed from 47 samples derived from growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.
Structural covariance networks in children with autism or ADHD
Authors: Bethlehem R.A.I. , Romero-Garcia R. , Mak E. , Bullmore E.T , Baron-Cohen Simon 
Published: February 2017

AbstractWhile autism and attention-deficit/hyperactivity disorder (ADHD) are considered distinct conditions from a diagnostic perspective, they share some phenotypic features and have high comorbidity. Taking a dual-condition approach might help elucidate shared and distinct neural characteristics.Graph theory was used to analyse properties of cortical thickness structural covariance networks across both conditions and relative to a neurotypical (NT; n=87) group using data from the ABIDE (autism; n=62) and ADHD-200 datasets (ADHD; n=69). This was analysed in a theoretical framework examining potential differences in long and short range connectivity.We found convergence between autism and ADHD, where both conditions show an overall decrease in CT covariance with increased Euclidean distance compared to a neurotypical population. The two conditions also show divergence: less modular overlap between the two conditions than there is between each condition and the neurotypical group. Lastly, the ADHD group also showed reduced wiring costs compared to the autism groups.Our results indicate a need for taking an integrated approach when considering highly comorbid conditions such as autism and ADHD. Both groups show a distance-covariance relation that more strongly favours short-range over long-range. Thus, on some network features the groups seem to converge, yet on others there is divergence.
Heritability of the structures and13C fractionation in tomato leaf wax alkanes: a genetic model system to inform paleoenvironmental reconstructions
Authors: Bender Amanda L.D. , Chitwood Daniel H. , Bradley Alexander S. 
Published: February 2017

AbstractLeaf waxn-alkanes are broadly used to reconstruct paleoenvironmental information. However, the utility of then-alkane paleoclimate proxy is modulated by the extent to which genetic as well as environmental factors influence the structural and isotopic variability of leaf waxes. In paleoclimate applications, there is an implicit assumption that most variation of leaf wax traits through a time series can be attributed to environmental change and that biological sources of variability within plant communities are small. For example, changes in hydrology affect the δ2H of waxes though rainwater and the δ13C of leaf waxes by changing plant communities (i.e., C3versus C4input). Here we test the assumption of little genetic control over 5 C variation of leaf wax by presenting the results of an experimental greenhouse growth study in which we estimate the role of genetic variability on structural and isotopic leaf wax traits in a set of 76 introgression lines (ILs) between two interfertileSolanum(tomato) species:S. lycopersicumcv M82 (hereafter cv M82) andS. pennellii.We found that the leaves ofS. pennellii,a wild desert tomato relative, produces significantly moreiso-alkanes than cv M82, a domesticated tomato cultivar adapted to water-replete conditions; we introduce a methylation index to summarize the ratio of branched (iso- andanteiso-) to total alkanes. BetweenS. pennelliiand cv M82, theiso-alkanes were found to be enriched in13C by 1.2–1.4%o overn-alkanes. By modeling our results from the ILs, we report the broad-sense heritability values (H2) of leaf wax traits to describe the degree to which genetic variation contributes to variation of these traits. Individual carbon isotope values of alkanes are of low heritability (H2= 0.13–0.19), suggesting that δ13C of leaf waxes from this study are strongly influenced by environmental variance, which supports the interpretation that variation in the 5 C of wax compounds recorded in sediments reflects paleohydrological changes. Average chain length (ACL) values ofn-alkanes are of intermediate heritability (H2= 0.30), suggesting that ACL values are strongly influenced by genetic cues.
MODELING MECHANICAL INTERACTIONS IN GROWING POPULATIONS OF ROD-SHAPED BACTERIA
Authors: Winkle James J. , Igoshin Oleg , Bennett Matthew R. , Josić Krešimir , Ott William 
Published: February 2017

AbstractAdvances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular fluid flow lead to complex, changing arrangements of cells within the population. To rationally engineer and control the behavior of cell collectives we need theoretical and computational tools to understand their emergent spatiotemporal dynamics. Here, we present an agent-based model that allows growing cells to detect and respond to mechanical interactions. Crucially, our model couples the dynamics of cell growth to the cell’s environment: Mechanical constraints can affect cellular growth rate and a cell may alter its behavior in response to these constraints. This coupling links the mechanical forces that influence cell growth and emergent behaviors in cell assemblies. We illustrate our approach by showing how mechanical interactions can impact the dynamics of bacterial collectives growing in microfluidic traps.
Sumoylation of Turnip mosaic virus RNA Polymerase Promotes Viral Infection by Counteracting the Host NPR1-Mediated Immune Response
Authors: Cheng Xiaofei , Xiong Ruyi , Li Yinzi , Li Fangfang , Zhou Xueping , Wang Aiming 
Published: February 2017

Abstract
Sumoylation is a transient, reversible dynamic posttranslational modification that regulates diverse cellular processes including plant-pathogen interactions. Sumoylation of NPR1, a master regulator of basal and systemic acquired resistance to a broad spectrum of plant pathogens, activates the defense response. Here, we report that NIb, the only RNA-dependent RNA polymerase of Turnip mosaic virus (TuMV) that targets the nucleus upon translation, interacts exclusively with and is sumoylated by SUMO3 (SMALL UBIQUITIN-LIKE MODIFIER3), but not the three other Arabidopsis thaliana SUMO paralogs. TuMV infection upregulates SUMO3 expression, and the sumoylation of NIb by SUMO3 regulates the nuclear-cytoplasmic partitioning of NIb. We identified the SUMO-interacting motif in NIb that is essential for its sumoylation and found that knockout or overexpression of SUMO3 suppresses TuMV replication and attenuates viral symptoms, suggesting that SUMO3 plays dual roles as a host factor of TuMV and as an antiviral defender. Sumoylation of NIb by SUMO3 is crucial for its role in suppressing the host immune response. Taken together, our findings reveal that sumoylation of NIb promotes TuMV infection by retargeting NIb from the nucleus to the cytoplasm where viral replication takes place and by suppressing host antiviral responses through counteracting the TuMV infection-induced, SUMO3-activated, NPR1-mediated resistance pathway.
Goodwill impairment loss and bond credit rating
Authors: Sun Li , Zhang Joseph H. 
Published: February 2017

Purpose
The purpose of this study is to examine the impact of goodwill impairment losses on bond credit ratings.

Design/methodology/approach
The authors use regression analysis to examine the relationship between goodwill impairment losses and bond credit ratings.

Findings
The empirical results show a negative relationship between the amount of goodwill impairment losses and bond credit ratings, suggesting that firms with goodwill impairment losses receive lower credit ratings. The authors perform various additional tests, including subsamples in good or bad market time, changes analysis, first time goodwill impairment firms vs subsequent impairment and the two-stage least squares regression analysis to address potential endogeneity issues. The main results persist.

Originality/value
This paper links and contributes to two streams of literature: goodwill impairment in accounting literature and bond credit ratings in finance literature. Whether a firm’s goodwill impairment losses affect the firm’s bond credit rating remains an interesting question that has not been examined previously. To the best of the authors’ knowledge, this is the first study that directly examines the relationship between goodwill impairment losses and bond ratings at the firm level.
An integrated framework for ERP system implementation
Authors: Jagoda Kalinga , Samaranayake Premaratne 
Published: February 2017

Purpose
The purpose of this paper is to propose an alternative integrated approach based on the stage-gate method to implement enterprise resource planning (ERP) systems which will enhance the effectiveness of ERP projects.

Design/methodology/approach
A literature review was conducted on ERP system implementation and its effectiveness. The need for improving implementation approaches and methodologies was examined. Based on the insights gained, a conceptual framework for ERP system implementation is presented by combining the state-gate approach with the pre-implementation roadmap.

Findings
The proposed framework aims to enhance the overall ERP implementation outcomes, ensuring critical success factors and eliminating common causes of failures. A pre-implementation roadmap is identified as a key element for eliminating many causes of failure including lack of organisations’ readiness for ERP. The post-implementation stage can be used for further improvements to the system through internal research and development.

Research limitations/implications
The development of the framework is an attempt to contribute to improving ERP implementation. This research is expected to motivate researchers to work in this area, and it will be beneficial to practicing managers in the identification of opportunities for improvements in ERP systems. Case studies will be valuable to refine and validate the proposed model.

Originality/value
This paper explores research in a needy area and offers a framework to help researchers and practitioners in improving ERP implementation. This framework is expected to reduce the implementation project duration, strengthen critical success factors and minimise common problems of ERP implementation projects.
Burning hearts in conflict
Authors: Hjerto Kjell B. , Kuvaas Bård 
Published: February 2017

PurposeThe purpose of this study is to investigate the relationships between three conflict types, cognitive task conflict, emotional relationship conflict and emotional task conflict, and team effectiveness (team performance and team job satisfaction).Design/methodology/approachThe authors conducted a group-level ordinary least square regression analysis of 61 working teams to investigate the study variables, and possible interaction effects among them. In an auxiliary analysis (36 teams), they analyzed the role of mood dimensions (hedonic valence and general conflict activation) as mediators to the relationship between cognitive task conflict and team effectiveness.FindingsCognitive task conflict was negatively related to team performance, emotional relationship conflict was negatively related to team job satisfaction and emotional task conflict was positively related to team performance, all controlled for the effect of each other. The relationship between cognitive task conflict and team job satisfaction was negatively moderated by team size. Mood valence mediated the relationship between cognitive task conflict and team performance, and between cognitive task conflict and team job satisfaction.Research limitations/implicationsSeveral possible research lines emanate from the current field study. First of all, the authors suggest that emotional task conflict may be of particular interest, as this is hypothesized and found to be incrementally positively related to team performance. Second, their auxiliary study of the mediating effect of mood valence on the relationship between cognitive task conflict and performance may spur curiosity concerning the role of mood as a mediator of the relationship between task or cognitive conflicts and team effectiveness.Practical implicationsThe practitioner should be advised to try to facilitate the distribution of intragroup conflict in their teams in the direction of an increased level of emotional task conflict (positive for performance) at the expense of cognitive task conflict (negative for performance) and emotional relationship conflict (negative for satisfaction). The practitioner should allow intragroup conflicts to be highly activated (intense), as long as the interactions are strictly directed to the task in hand, and not being personal. In addition, a positive mood in teams may significantly strengthen the team's resilience against adverse consequences of conflicts.Originality/valueThe three conflict types in this three-dimensional intragroup conflict model (3IC) have never been tested before, and the findings open for a conflict type – emotional task conflict – that may generally be conducive for the teams’ performance, evaluated by the teams’ supervisors. This is a conflict type where people simultaneously are emotional and yet task oriented. To the authors’ knowledge, this is a novelty, and they hope that it may encourage further research on this conflict type.
Exploration of factors leading to successful mediation
Authors: Zhang Yafei , Chen Li 
Published: February 2017

Purpose
The purpose of this study is to explore possible factors leading to a successful mediation in Chinese mediation shows. In China, media always play an indispensable role in information dissemination, morality advocacy and policy explanation.

Design/methodology/approach
This paper employed content analysis of 166 episodes of one representative mediation show, Gold Medal Mediation, and regression technique in data analysis.

Findings
Results of ordinal regression suggested that “secret talking”, rather than transparency, between disputants had significant influence on successful mediation. Function of mediators is limited in reaching full mediation. The effective factors leading to full mediation include compromise of rights, secret talking, attitude of the observer cohort. It suggests that the role of mediator is limited, rather than being over-exaggerated, in successful mediation. The successful mediation is largely dependent on disputants’ motivations. Additionally, “compromise of rights” by disputants is a key factor in solving disputes.

Research limitations/implications
Findings of this study revealed the role of Chinese mediation shows in propagating mediation in contemporary Chinese society and supporting upheld morality values. Due to the nature of the chosen mediation show, some disputes take more than one episode to solve. However, this study looks at each episode without considering the integrity of the dispute. That is, if the disputes take two episodes, the coder codes the two episodes as two separate disputes instead of looking at it as one dispute.

Originality/value
By exploring various aspects of mediations shows, including the role of mediators, disputants and a cohort of observers, this study can both explicitly show predicted factors to successful mediations on the shows, and can implicitly examine the power and perceived justification of mediation in contemporary China via media.
Invisible students: institutional invisibility and access to education for undocumented children
Authors: Meloni Francesca , Rousseau Cécile , Ricard-Guay Alexandra , Hanley Jill 
Published: February 2017

PurposeIn Canada, undocumented children are “institutionally invisible” – their access to education to be found in unwritten and discretionary practices. Drawing on the experience of a three-year university-community partnership among researchers, institutional and community stakeholders, the purpose of this paper is to examine how undocumented children are constructed as excluded from school.Design/methodology/approachThe establishment of this collaborative research space, helped to critically understand how this exclusion was maintained, and highlighted contradictory interpretations of policies and practices.FindingsProposing the analytical framework of “institutional invisibility”, the authors argue that issues of access and entitlement for undocumented children have to be often understood within unwritten and ambiguous policies and practices that make the lives of young people invisible to the institutional entities with which they interact.Originality/valueThe notion of institutional invisibility allows the authors to integrate the missing link between questions of access and deservingness. The paper also reflects on the role of action research in both documenting dynamics and pathways of institutional invisibility, as well as in initiating social change – as both horizontal, and vertical mobilisation.
Immigrant home-school information flows in Finnish comprehensive schools
Authors: Säävälä Minna , Turjanmaa Elina , Alitolppa-Niitamo Anne 
Published: February 2017

Purpose
School is an institution that provides an opportunity to improve children’s equity and wellbeing and to bridge the potential disadvantage related to ethnic- or language-minority backgrounds. Information sharing between immigrant homes and school can enhance school achievement, support positive identity formation and provide early support when needed. In this paper, the perspectives of immigrant parents, school welfare personnel and school-going adolescents are analysed in order to understand how they see their respective roles in information flows between home and school. The paper aims to discuss these issues.

Design/methodology/approach
The data consist of qualitative group and individual interviews of 34 representatives of school personnel, 13 immigrant parents and 81 young people who have experienced immigration, in the metropolitan area of Helsinki, Finland.

Findings
Despite general goodwill, school personnel may fail to secure the flow of information. Due to structural power imbalance, school personnel are often incapable of engaging the parents in dialogical discourse. Young people of immigrant background in turn try to manipulate the information flow in order to protect their family and ethnic group and to cope with pressures from parents. The patterns of information flows in school as a social field reproduce immigrant homes as subaltern. Adolescents act in a strategically important juncture of information flows between immigrant home and school, which indicates that home-school interaction is actually a triad.

Social implications
Awareness building among school personnel is vital for equity and wellbeing of children of immigrant families.

Originality/value
This triangulated analysis of patterned information flows in school as a social field provides a fresh perspective to those working with children of immigrant families.