bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterizing the Toxicity and Dose-Effect Profile of Tramadol Ingestions in Children
Authors: Stassinos Gina L. , Gonzales Lawrence , Klein-Schwartz Wendy
Published: February 2017

Objectives

Tramadol can cause life-threatening toxicity in overdose; however, data on its toxicity in children are lacking. This study investigates toxicity associated with tramadol ingestions in children. The hypothesis is that children will experience dose-related central nervous system and respiratory depression and seizures.

Methods

A retrospective evaluation of cases from the National Poison Center Data System between January 1, 2000, and December 31, 2013, was performed. Inclusion criteria were age below 6 years and single-substance acute tramadol ingestion. For dose-effect analysis, cases with sufficient dose quantity information were included.

Results

There were 7334 cases that met inclusion criteria. Outcomes were 84.8% no effect, 12.6% minor, 2.2% moderate, and 0.4% major effect. There was 1 fatality. Most of the children (36.4%) were treated/released from the emergency department; other management sites were home (36.4%), admission (5.9%), and others (3.2%). In the 1115 children with symptoms, drowsiness (N = 611) and vomiting (N = 178) occurred most frequently. More serious clinical effects included respiratory depression in 36 and seizures in 24 children. Of 2772 children with milligram dose recorded, there were 10 cases of respiratory depression and 6 of seizure. Median doses for respiratory depression and seizure were 225 (range, 50–600 mg) and 525 mg (range, 50–1050 mg), respectively. The minimum weight-based dose for respiratory depression/arrest was 7.9 mg/kg and for seizures, 4.8 mg/kg.

Conclusions

Seizure and respiratory depression are uncommon in pediatric tramadol ingestions. Given the small number of patients with dose data and lack of laboratory confirmation of dose, more studies are needed to determine the minimum dose at which medical management is recommended.
PANLAR Presidency, First Self-Assessment Report 2014–2016
Authors: Pineda Carlos , Sandoval Hugo , Sheen Rosa , Muñoz-Louis Roberto
Published: February 2017

We present here the first PANLAR Presidency Self-Assessment Report 2014–2016, emphasizing the challenges, opportunities, and results achieved in terms of (1) governance, (2) education and scientific research, (3) finance, and (4) communications throughout this tenure. The main result must be understood as a strategic planning exercise that strengthened institutional responsibility in policies, decisions, and actions, thanks to the teamwork of Latin America's National Rheumatology Societies, the PANLAR Executive Committee, and PANLAR Board Members.
High Hemoglobin A1c and Diabetes Predict Memory Decline in the Health and Retirement Study
Authors: Marden Jessica R. , Mayeda Elizabeth R. , Tchetgen Tchetgen Eric J. , Kawachi Ichiro , Glymour M. Maria
Published: February 2017

Background:

Type 2 diabetes (T2D) is an established risk factor for dementia, but evidence for T2D and memory decline is less consistent. Understanding how T2D and blood glucose relate to memory decline is crucial to elucidating the mechanisms linking T2D and dementia.

Materials and Methods:

For 8888 Health and Retirement Study participants aged 50+, glycosylated hemoglobin (HbA1c) was measured in either 2006 or 2008 and physician’s diagnosis of diabetes was self-reported in the same year. Composite memory (z scored) was assessed biennially through 2012 using immediate and delayed word list recall or the Informant Questionnaire for Cognitive Decline. Marginal mean regression models for repeated outcomes were specified to predict memory decline as a function of diabetes or HbA1c, using age as the timescale and adjusting for health and social confounders.

Results:

Diabetes was associated with a 10% faster rate of memory decline [β=−0.04 per decade; 95% confidence interval (CI), −0.06 to −0.01). A 1 U increase in HbA1c corresponded with a 0.05 SD decrease in memory score per decade (95% CI, −0.08 to −0.03). Even among individuals with HbA1c<6.5% (threshold for diabetes), higher HbA1c was associated with memory decline (β=−0.05 per decade; 95% CI, −0.08 to −0.03).

Discussion:

Diabetes accelerated memory loss and higher HbA1c predicted memory decline even in nondiabetics.
Parallel evolution of mound-building and grass-feeding in Australian nasute termites
Authors: Arab Daej A. , Namyatova Anna , Evans Theodore A. , Cameron Stephen L. , Yeates David K. , Ho Simon Y. W. , Lo Nathan
Published: February 2017

Termite mounds built by representatives of the family Termitidae are among the most spectacular constructions in the animal kingdom, reaching 6–8 m in height and housing millions of individuals. Although functional aspects of these structures are well studied, their evolutionary origins remain poorly understood. Australian representatives of the termitid subfamily Nasutitermitinae display a wide variety of nesting habits, making them an ideal group for investigating the evolution of mound building. Because they feed on a variety of substrates, they also provide an opportunity to illuminate the evolution of termite diets. Here, we investigate the evolution of termitid mound building and diet, through a comprehensive molecular phylogenetic analysis of Australian Nasutitermitinae. Molecular dating analysis indicates that the subfamily has colonized Australia on three occasions over the past approximately 20 Myr. Ancestral-state reconstruction showed that mound building arose on multiple occasions and from diverse ancestral nesting habits, including arboreal and wood or soil nesting. Grass feeding appears to have evolved from wood feeding via ancestors that fed on both wood and leaf litter. Our results underscore the adaptability of termites to ancient environmental change, and provide novel examples of parallel evolution of extended phenotypes.
Functional optics of glossy buttercup flowers
Authors: van der Kooi Casper J. , Elzenga J. Theo M. , Dijksterhuis Jan , Stavenga Doekele G.
Published: February 2017

Buttercup (
Ranunculus
spp.) flowers are exceptional because they feature a distinct gloss (mirror-like reflection) in addition to their matte-yellow coloration. We investigated the optical properties of yellow petals of several
Ranunculus
and related species using (micro)spectrophotometry and anatomical methods. The contribution of different petal structures to the overall visual signal was quantified using a recently developed optical model. We show that the coloration of glossy buttercup flowers is due to a rare combination of structural and pigmentary coloration. A very flat, pigment-filled upper epidermis acts as a thin-film reflector yielding the gloss, and additionally serves as a filter for light backscattered by the strongly scattering starch and mesophyll layers, which yields the matte-yellow colour. We discuss the evolution of the gloss and its two likely functions: it provides a strong visual signal to insect pollinators and increases the reflection of sunlight to the centre of the flower in order to heat the reproductive organs.
Novel layers of RNA polymerase III control affecting tRNA gene transcription in eukaryotes
Authors: Leśniewska Ewa , Boguta Magdalena
Published: February 2017

RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Also, several factors required for assembly and nuclear import of Pol III complex have been identified recently. Models of Pol III based on cryo-electron microscopy reconstructions of distinct Pol III conformations reveal unique features distinguishing Pol III from other polymerases. Novel concepts concerning Pol III functioning involve recruitment of general Pol III-specific transcription factors and distinctive mechanisms of transcription initiation, elongation and termination. Despite the short length of Pol III transcription units, mapping of transcriptionally active Pol III with nucleotide resolution has revealed strikingly uneven polymerase distribution along all genes. This may be related, at least in part, to the transcription factors bound at the internal promoter regions. Pol III uses also a specific negative regulator, Maf1, which binds to polymerase under stress conditions; however, a subset of Pol III genes is not controlled by Maf1. Among other RNA polymerases, Pol III machinery represents unique features related to a short transcript length and high transcription efficiency.
1/
f
Noise and multifractality from bristlecone pine growth explained by the statistical convergence of random data
Authors: Kendal Wayne S.
Published: February 2017

Tree-ring growth records from bristlecone pines reveal an irregular pattern of fluctuations that have been linked to climatic change but otherwise have remained poorly understood. We find within these records evidence for a temporally related variance to mean power law, 1/
f
noise and multifractality that empirically resembles a fractal stochastic process and could be attributed to self-organized criticality. These growth records, however, also conformed to a non-Gaussian statistical distribution (the Tweedie compound Poisson distribution) characterized by an inherent variance to mean power law, that by itself implies 1/
f
noise. This distribution has a fundamental role in statistical theory as a focus of convergence for many types of random data, much like the Gaussian distribution has with the central limit theorem. The growth records were also multifractal, with the dimensional exponent of the Tweedie distribution critically balanced near the transition point between fractal stochastic processes and gamma distributed data, possibly consequent to a related convergence effect. Non-Gaussian random systems, like those related to bristlecone pine tree growth, may express 1/
f
noise and multifractality through mathematical convergence effects alone, without the dynamical assumptions of self-organized criticality.
Holocene selection for variants associated with cognitive ability: Comparing ancient and modern genomes
Authors: Woodley Menie Michael A. , Younuskunju Shameem , Balan Bipin , Piffer Davide
Published: February 2017

Human populations living in Eurasia during the Holocene experienced considerable microevolutionary change. It has been predicted that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene coevolution that favoured via directional selection genetic variants associated with higher general cognitive ability (GCA). To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4.56 to 1.21 kyr BP) with a sample of 503 modern European genomes, using three different cognitive polygenic scores. Significant differences favouring the modern genomes were found for all three polygenic scores (Odds Ratios=0.92,p=0.037; 0.81,p=0.001 and 0.81,p=0.02). Furthermore, a significant increase in positive allele count over 3.25 kyr was found using a subsample of 66 ancient genomes (r=0.217,pone-taiied=0.04).These observations are consistent with the expectation that GCA rose during the Holocene.
IcyTree: Rapid browser-based visualization for phylogenetic trees and networks
Authors: Vaughan Timothy G.
Published: February 2017

IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible.

Availability and Implementation

IcyTree is a web application and can be accessed directly athttp://tgvaughan.github.com/icytree. Currently-supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available athttp://github.com/tgvaughan/icytreeunder version 3 of the GNU General Public License.

Contact

tgvaughan@gmail.com
Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics
Authors: Léveillé-Bourret Étienne , Starr Julian R. , Ford Bruce A. , Lemmon Emily Moriarty , Lemmon Alan R.
Published: February 2017

Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur. In another contribution on anchored phylogenomics in angiosperms, we presented flowering plant-specific anchored enrichment probes for hundreds of conserved nuclear genes and demonstrated their use at the level of all angiosperms. In this contribution, we focus on a common problem in phylogenetic reconstructions below the family level: weak or unresolved backbone due to rapid radiations (≤ 10 million years) followed by long divergence, using the Cariceae-Dulichieae-Scirpeae clade (CDS, Cyperaceae) as a test case. By comparing our nuclear matrix of 461 genes to a typical Sanger-sequence dataset consisting of a few plastid genes (matK, ndhF) and an nrDNA marker (ETS), we demonstrate that our nuclear data is fully compatible with the Sanger dataset and resolves short backbone internodes with high support in both concatenated and coalescence-based analyses. In addition, we show that nuclear gene tree incongruence is inversely proportional to phylogenetic information content, indicating that incongruence is mostly due to gene tree estimation error. This suggests that large numbers of conserved nuclear loci could produce more accurate trees than sampling rapidly evolving regions prone to saturation and long-branch attraction. The robust phylogenetic estimates obtained here, and high congruence with previous morphological and molecular analyses, are strong evidence for a complete tribal revision of CDS. The anchored hybrid enrichment probes used in this study should be similarly effective in other flowering plant groups.[Carex,coalescent based species tree, flowering plants, low-copy nuclear genes, low-level phylogenetics, universal hybrid enrichment probes]
Global Proteomic Analyses of Macrophage Response toMycobacterium tuberculosisInfection
Authors: Poirier Valérie , Av-Gay Gal , Av-Gay Yossef
Published: February 2017

Alveolar macrophages serve as the first line of defence against microbial infection, yet provide a unique niche for the growth ofMycobacterium tuberculosis. To better understand the evasive nature of the tubercle bacilli and its molecular manifest on the macrophage response to infection, we conducted a global quantitative proteomic profile of infected macrophages. By examining four independent controlled infection experiments, we detected 42,007 peptides resulting in the characterization of 4,868 distinct proteins. Of these, we identified 845 macrophage proteins whose expression is modulated upon infection in all replicates. We showed that the macrophage’s response toM. tuberculosisinfection includes simultaneous and concerted upregulation of selected proteins. Using a number of statistical methods, we identified 27 proteins whose expression levels are significantly regulated outside of a 90% confidence interval about the mean. These host proteins represent the macrophage transcriptional, translational, and innate immune response to infection as well as its signaling capacity. The contribution of PtpA, anM. tuberculosissecreted virulence factor, modulated the expression levels of 11 host macrophage proteins, as categorized by RNA metabolism, translation, and cellular respiration.
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

Boron 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

The 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

2

Sorghum 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.
Understanding Tissue-specific Gene Regulation
Authors: Sonawane Abhijeet R. , Platig John , Fagny Maud , Chen Cho-Yi , Paulson Joseph N. , Lopes-Ramos Camila M. , DeMeo Dawn L. , Quackenbush John , Glass Kimberly , Kuijjer Marieke L.
Published: February 2017

Although all human tissues carry out common processes, tissues are distinguished by gene expres-sion patterns, implying that distinct regulatory programs control tissue-specificity. In this study, we investigate gene expression and regulation across 38 tissues profiled in the Genotype-Tissue Expression project. We find that network edges (transcription factor to target gene connections) have higher tissue-specificity than network nodes (genes) and that regulating nodes (transcription factors) are less likely to be expressed in a tissue-specific manner as compared to their targets (genes). Gene set enrichment analysis of network targeting also indicates that regulation of tissue-specific function is largely independent of transcription factor expression. In addition, tissue-specific genes arenothighly targeted in their corresponding tissue-network. However, they do assume bottleneck positions due to variability in transcription factor targeting and the influence of non-canonical regulatory interactions. These results suggest that tissue-specificity is driven by context-dependent regulatory paths, providing transcriptional control of tissue-specific processes.
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

While 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

Leaf 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

Advances 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.
Natural variation and dosage of the HEI10 meiotic E3 ligase control Arabidopsis crossover recombination
Authors: Ziolkowski Piotr A. , Underwood Charles J. , Lambing Christophe , Martinez-Garcia Marina , Lawrence Emma J. , Ziolkowska Liliana , Griffin Catherine , Choi Kyuha , Franklin F. Chris H. , Martienssen Robert A. , Henderson Ian R.
Published: February 2017

During meiosis, homologous chromosomes undergo crossover recombination, which creates genetic diversity and balances homolog segregation. Despite these critical functions, crossover frequency varies extensively within and between species. Although natural crossover recombination modifier loci have been detected in plants, causal genes have remained elusive. Using natural Arabidopsis thaliana accessions, we identified two major recombination quantitative trait loci (rQTLs) that explain 56.9% of crossover variation in Col×Ler F2 populations. We mapped rQTL1 to semidominant polymorphisms in HEI10, which encodes a conserved ubiquitin E3 ligase that regulates crossovers. Null hei10 mutants are haploinsufficient, and, using genome-wide mapping and immunocytology, we show that transformation of additional HEI10 copies is sufficient to more than double euchromatic crossovers. However, heterochromatic centromeres remained recombination-suppressed. The strongest HEI10-mediated crossover increases occur in subtelomeric euchromatin, which is reminiscent of sex differences in Arabidopsis recombination. Our work reveals that HEI10 naturally limits Arabidopsis crossovers and has the potential to influence the response to selection.
Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence
Authors: Maheshwari Shamoni , Ishii Takayoshi , Brown C. Titus , Houben Andreas , Comai Luca
Published: February 2017

During cell division, spindle fibers attach to chromosomes at centromeres. The DNA sequence at regional centromeres is fast evolving with no conserved genetic signature for centromere identity. Instead CENH3, a centromere-specific histone H3 variant, is the epigenetic signature that specifies centromere location across both plant and animal kingdoms. Paradoxically, CENH3 is also adaptively evolving. An ongoing question is whether CENH3 evolution is driven by a functional relationship with the underlying DNA sequence. Here, we demonstrate that despite extensive protein sequence divergence, CENH3 histones from distant species assemble centromeres on the same underlying DNA sequence. We first characterized the organization and diversity of centromere repeats in wild-type Arabidopsis thaliana. We show that A. thaliana CENH3-containing nucleosomes exhibit a strong preference for a unique subset of centromeric repeats. These sequences are largely missing from the genome assemblies and represent the youngest and most homogeneous class of repeats. Next, we tested the evolutionary specificity of this interaction in a background in which the native A. thaliana CENH3 is replaced with CENH3s from distant species. Strikingly, we find that CENH3 from Lepidium oleraceum and Zea mays, although specifying epigenetically weaker centromeres that result in genome elimination upon outcrossing, show a binding pattern on A. thaliana centromere repeats that is indistinguishable from the native CENH3. Our results demonstrate positional stability of a highly diverged CENH3 on independently evolved repeats, suggesting that the sequence specificity of centromeres is determined by a mechanism independent of CENH3.
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

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.
Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis
Authors: Cole Jason C. , Giangreco Ilenia , Groom Colin R.
Published: February 2017

The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal–organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein–ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure refinement.
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

Purpose

The 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/approach

The 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.

Findings

Cognitive 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/implications

Several 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 implications

The 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/value

The 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

Purpose

In 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/approach

The establishment of this collaborative research space, helped to critically understand how this exclusion was maintained, and highlighted contradictory interpretations of policies and practices.

Findings

Proposing 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/value

The 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.
Security of classified information: one standard or many?
Authors: Weaver John Michael
Published: February 2017

Purpose

There should be one standard for those with access to classified data. Leadership by example should be required by all managers, supervisors and department heads. The paper aims to discuss this issue.

Design/methodology/approach

This paper is a viewpoint and does not have a methodology.

Findings

Leaders who work in the public sector have an inherent responsibility to earn and maintain the trust of the public for whom they serve. Regardless of whether one is a career government employee, a politician or a political appointee, all who have access to classified material should respect the necessity of safeguards to keep one’s nation’s secrets – secret.

Research limitations/implications

If leaders fail to set the example, then nations risk further breaches of their classified information.

Practical implications

This viewpoint applies to anyone who works in an environment dealing with classified material.

Social implications

This viewpoint serves to educate the public on maintaining a single standard for those who handle classified material.

Originality/value

The author has yet to see much covered in peer-reviewed publications on this topic and believe that the subject is particularly relevant at this time.