bluuebunny/crossref_metadata_2025 huggingface dataset:
plyranges: A grammar of genomic data transformation
Authors: Lee Stuart , Cook Dianne , Lawrence Michael
Published: May 2018

The Bioconductor project provides many interoperable data abstractions for analyzing high-throughput genomics experiments; however implementing a typical genomic workflow with Bioconductor requires learning these abstractions and understanding them at an integrative level. This places a large cognitive burden on the user, especially for non-programmers. To reduce this burden we have created a grammar of genomic data transformation that operates on a single, central Bioconductor data structure, GRanges, which naturally represents genomic intervals and their associated measurements. The grammar defines verbs for performing actions on and between genomic interval data through a simplified, coherent interface to existing Bioconductor infrastructure, resulting in fluent analysis workflows. We have implemented this grammar as an R/Bioconductor package calledplyranges.
The RNA demethylase FTO targets m6Am in snRNA to establish distinct methyl isoforms that influence splicing
Authors: Mauer Jan , Sindelar Miriam , Guez Théo , Vasseur Jean-Jacques , Rentmeister Andrea , Gross Steven S. , Pellizzoni Livio , Debart Françoise , Goodarzi Hani , Jaffrey Samie R.
Published: May 2018

Small nuclear RNAs (snRNAs) are core spliceosome components and mediate pre-mRNA splicing. During their biogenesis, snRNAs acquire several constitutive nucleotide modifications. Here we show that snRNAs also contain a regulated and reversible nucleotide modification causing them to exist as two different methyl isoforms, m1 and m2, reflecting the methylation state of the adenosine adjacent to the snRNA cap. We find that snRNA biogenesis involves the formation of an initial m1-isoform with a single-methylated adenosine (2’-O-methyladenosine, Am), which is then converted to a dimethylated m2-isoform (N6,2’-O-dimethyladenosine, m6Am). The relative m1- and m2-isoform levels are determined by the RNA demethylase FTO, which selectively demethylates the m2-isoform. We show FTO is inhibited by endogenous metabolites, resulting in increased m2-snRNA levels. Furthermore, cells that exhibit high m2-snRNA levels show altered patterns of alternative splicing. Together, these data reveal that FTO has a central role in snRNA biogenesis and controls a previously unknown step of snRNA processing involving reversible methylation, thereby providing a potential link between reversible RNA modifications and mRNA splicing.
A tail of two sides: Artificially doubled false positive rates in neuroimaging due to the sidedness choice with t-tests
Authors: Chen Gang , Cox Robert W. , Glen Daniel R. , Rajendra Justin K. , Reynolds Richard C. , Taylor Paul A.
Published: May 2018

One-sided t-tests are widely used in neuroimaging data analysis. While such a test may be applicable when investigating specific regions and prior information about directionality is present, we argue here that it is often mis-applied, with severe consequences for false positive rate (FPR) control. Conceptually, a pair of one-sided t-tests conducted in tandem (e.g., to test separately for both positive and negative effects), effectively amounts to a two-sided t-test. However, replacing the two-sided test with a pair of one-sided tests without multiple comparisons correction essentially doubles the intended FPR of statements made about the same study; that is, the actual family-wise error (FWE) of results at the whole brain level would be 10% instead of the 5% intended by the researcher. Therefore, we strongly recommend that, unless otherwise explicitly justified, two-sided t-tests be applied instead of two simultaneous one-sided t-tests.
The timing and direction of introgression under the multispecies network coalescent
Authors: Hibbins Mark S. , Hahn Matthew W.
Published: May 2018

Introgression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics,D1andD2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively.D1may find use in evaluating cases of homoploid hybrid speciation, whileD2provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply theD1statistic to genomic data from the wild yeastSaccharomyces paradoxus, a proposed example of homoploid hybrid speciation, demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.
The y-ome defines the thirty-four percent ofEscherichia coligenes that lack experimental evidence of function
Authors: Ghatak Sankha , King Zachary A. , Sastry Anand , Palsson Bernhard O.
Published: May 2018

Experimental studies ofEscherichia coliK-12 MG1655 often implicate poorly annotated genes in cellular phenotypes. However, we lack a systematic understanding of these genes. How many are there? What informationisavailable for them? And what features do they share that could explain the gap in our understanding? Efforts to build predictive, whole-cell models ofE. coliinevitably face this knowledge gap. We approached these questions systematically by assembling annotations from the knowledge bases EcoCyc, EcoGene, UniProt, RefSeq, and RegulonDB. We identified the genes that lack direct experimental evidence of function (the “y-ome”) which include 1563 of 4653 unique genes (34%), of which 131 have absolutely no evidence of function. An additional 304 genes (6.6%) are pseudogenes or phantom genes. y-ome genes tend to have lower expression levels and are enriched in the termination region of theE. colichromosome. Where evidence is available for y-ome genes, it most often points to them being membrane proteins and transporters. We resolve the misconception that a gene inE. coliwhose primary name starts with “y” is unannotated, and we discuss the value of the y-ome for systematic improvement ofE. coliknowledge bases and its extension to other organisms.
Intermediate filaments control collective migration by restricting traction forces and sustaining cell-cell contacts
Authors: Pascalis Chiara De , Pérez-González Carlos , Seetharaman Shailaja , Boëda Batiste , Vianay Benoit , Burute Mithila , Leduc Cécile , Borghi Nicolas , Trepat Xavier , Etienne-Manneville Sandrine
Published: May 2018

Mesenchymal cell migration relies on the coordinated regulation of the actin and microtubule networks which participate in polarised cell protrusion, adhesion and contraction. During collective migration, most of the traction forces are generated by the acto-myosin network linked to focal adhesions at the front of leader cells, which transmit these pulling forces to the followers. Here, using an in vitro wound healing assay to induce polarisation and collective directed migration of primary astrocytes, we show that the intermediate filament (IF) network composed of vimentin, GFAP and nestin contributes to directed collective movement by controlling the distribution of forces in the migrating cell monolayer. Together with the cytoskeletal linker plectin, these IFs control the organisation and dynamics of the acto-myosin network, promoting the actin-driven treadmilling of adherens junctions, thereby facilitating the polarisation of leader cells. Independently of their effect on adherens junctions, IFs influence the dynamics and localisation of focal adhesions and limit their mechanical coupling to the acto-myosin network. We thus conclude that IFs promote collective directed migration by restricting the generation of traction forces to the front of leader cells, preventing aberrant tractions in the followers and by contributing to the maintenance of lateral cell-cell interactions.
Integrated accounts of behavioral and neuroimaging data using flexible recurrent neural network models
Authors: Dezfouli Amir , Morris Richard , Ramos Fabio , Dayan Peter , Balleine Bernard W.
Published: May 2018

Neuroscience studies of human decision-making abilities commonly involve sub-jects completing a decision-making task while BOLD signals are recorded using fMRI. Hypotheses are tested about which brain regions mediate the effect of past experience, such as rewards, on future actions. One standard approach to this is model-based fMRI data analysis, in which a model is fitted to the behavioral data, i.e., a subject’s choices, and then the neural data are parsed to find brain regions whose BOLD signals are related to the model’s internal signals. However, the internal mechanics of such purely behavioral models are not constrained by the neural data, and therefore might miss or mischaracterize aspects of the brain. To address this limitation, we introduce a new method using recurrent neural network models that are flexible enough to be jointly fitted to the behavioral and neural data. We trained a model so that its internal states were suitably related to neural activity during the task, while at the same time its output predicted the next action a subject would execute. We then used the fitted model to create a novel visualization of the relationship between the activity in brain regions at different times following a reward and the choices the subject subsequently made. Finally, we validated our method using a previously published dataset. We found that the model was able to recover the underlying neural substrates that were discovered by explicit model engineering in the previous work, and also derived new results regarding the temporal pattern of brain activity.
Exploratory noise governs both flexibility and spontaneous errors and is regulated by cocaine
Authors: Ebitz R. Becket , Sleezer Brianna J. , Jedema Hank P. , Bradberry Charles W. , Hayden Benjamin Y.
Published: May 2018

In many cognitive processes, lapses (spontaneous errors) are attributed to nuisance processes like sensorimotor noise or disengagement. However, some lapses could also be caused by exploratory noise: behavioral randomness that facilitates learning in changing environments. If so, strategic processes would need only up-regulate (rather than generate) exploration to adapt to a changing environment. This view predicts that lapse rates should be correlated with flexibility because they share a common cause. We report that when macaques performed a set-shifting task, lapse rates were negatively correlated with perseverative error frequency. Furthermore, chronic exposure to cocaine, which impairs cognitive flexibility, increased perseverative errors, but, surprisingly, improved overall performance by reducing lapse rates. We reconcile these results with a model in which cocaine decreased exploration by deepening attractor basins corresponding to rules. These results support the idea that exploratory noise contributes to lapses, meaning that it affects rule-based decision-making even when it has no strategic value.
Heterogeneous Impacts of Protein-Stabilizing Osmolytes on Hydrophobic Interaction
Authors: Mukherjee Mrinmoy , Mondal Jagannath
Published: May 2018

Osmolytes’ mechanism of protecting proteins against denaturation is a longstanding puzzle, further complicated by the complex diversities inherent in protein sequences. An emergent approach in understanding osmolytes’ mechanism of action towards biopolymer has been to investigate osmolytes’ interplay with hydrophobic interaction, the major driving force of protein folding. However, the crucial question is whether all these protein-stabilizing osmolytes display asingle unifiedmechanism towards hydrophobic interactions. By simulating the hydrophobic collapse of a macromolecule in aqueous solutions of two such osmoprotectants, Glycine and Trimethyl N-oxide (TMAO), both of which are known to stabilize protein’s folded conformation, we here demonstrate that these two osmolytes can impart mutually contrasting effects towards hydrophobic interaction. While TMAO preserves its protectant nature across diverse range of polymer-osmolyte interactions, glycine is found to display an interesting cross-over from being a protectant at weaker polymer-osmolyte interaction to a denaturant of hydrophobicity at stronger polymer-osmolyte interactions. A preferential-interaction analysis reveals that a subtle balance ofconformation-dependentexclusion/binding of osmolyte molecules from/to the macromolecule holds the key to overall heterogenous behavior. Specifically, TMAO’s consistent stabilization of collapsed configuration of macromolecule is found to be a result of TMAO’s preferential binding to polymer via hydrophobic methyl groups. However, polar Glycine’s cross-over from being a protectant to denaturant across polymer-osmolyte interaction is rooted in its switch from preferential exclusion to preferential binding to the polymer with increasing interaction. Overall, by highlighting the complex interplay of osmolytes with hydrophobic interaction, this work puts forward the necessity of quantitative categorization of osmolytes’ action in protein.
The human cytomegalovirus ER resident glycoprotein UL148 activates the unfolded protein response
Authors: Siddiquey Mohammed N.A. , Zhang Hongbo , Nguyen Christopher C. , Domma Anthony J. , Kamil Jeremy P.
Published: May 2018

Eukaryotic cells are equipped with three sensors that respond to the accumulation of misfolded proteins within the lumen of the endoplasmic reticulum (ER) by activating the unfolded protein response (UPR), which functions to resolve proteotoxic stresses involving the secretory pathway. Here, we identify UL148, a viral ER resident glycoprotein from human cytomegalovirus (HCMV), as an inducer of the UPR. Metabolic labeling results indicate that global mRNA translation is markedly decreased when UL148 expression is induced in uninfected cells. Further, we find evidence suggesting that ectopic expression of UL148 is sufficient to activate at least two UPR sensors: the inositol requiring enzyme-1 (IRE1), as indicated by splicing ofXbp1mRNA, and the PKR-like ER kinase (PERK), as indicated by phosphorylation of eIF2αand accumulation of ATF4 protein. During wild-type HCMV infection,Xbp-1splicing, eIF2αphosphorylation and ATF4 accumulation neatly accompanied the onset of UL148 expression. However, the appearance of these UPR indicators was either markedly delayed or absent duringUL148-null infections. siRNA depletion of PERK dampened the extent of eIF2αphosphorylation and ATF4 induction observed during wild-type infection, implicating PERK as opposed to other eIF2αkinases. A virus disrupted forUL148showed statistically significant 2- to 4-fold decreases during infection in the levels of transcripts canonically regulated by PERK/ATF4 and by the ATF6 pathway.Taken together, our results argue that UL148 is sufficient to activate the UPR when expressed ectopically and that UL148 is an important cause of UPR activation in the context of the HCMV infected cell.

IMPORTANCE

The unfolded protein response (UPR) is an ancient cellular response to ER stress of broad importance to viruses. Certain consequences of the UPR, including mRNA degradation and translational shut-off, would presumably be disadvantageous to viruses, while other attributes of the UPR, such as ER expansion and upregulation of protein folding chaperones, might enhance viral replication. Although HCMV is estimated to express at least 200 distinct viral proteins, we show that the HCMV ER resident glycoprotein UL148 contributes substantially to the UPR during infection, and moreover is sufficient to activate the UPR in non-infected cells. Experimental activation of the UPR in mammalian cells is difficult to achieve without the use of toxins. Therefore, UL148 may provide a new tool to investigate fundamental aspects of the UPR. Furthermore, our findings may have implications for understanding the mechanisms underlying the effects of UL148 on HCMV cell tropism and evasion of cell mediated immunity.
The contribution of melanization toDrosophilasurvival changes withEnterococcus faecalisV583 genomic content
Authors: Teixeira Neuza , Jacinto António , Silva Lopes Maria de Fátima
Published: May 2018

Enterococcus faecalisis a human opportunist pathogen able to infect and killDrosophila. Previous studies proved thatE. faecaliscarrying the Fsr quorum sensing system are extremely virulent. Fsr is the regulator of two important virulence factors, gelatinase and serine protease, which cause death ofDrosophilaadult flies by decreasing its tolerance to infection. The exact mechanism underlying the toxicity of theseE. faecalisvirulence factors is nevertheless not known, in particular the way they interfere with the host immune response. In the present study, we investigated the influence of Fsr-GelE-SprE bacterial factors on different immunity responses, namely antimicrobial peptide production, phagocytosis and melanization. UsingE. faecalisV583 wild type andE. faecalisV583 ΔfsrBΔgelEΔsprEmutant we showed that both drosomycin production and phagocytosis were activated to similar levels by the two bacterial strains. However, fly pupae infected with the mutant strain showed less melanization and higher survival rates when compared to pupae infected with wild type bacteria. Using adult flies carrying thePPO1ΔPPO2Δmutation, we found that absence of melanization had a different impact in survival of the flies when infected with the twoE. faecalisstrains.PPO1Δ,PPO2Δmutant flies were more tolerant toE. faecalisdeprived of its major virulence factors. By showing that the presence of theE. faecalisproteases completely alters the impact of melanization activation onDrosophilatolerance, this study provides new clues on the interactions betweenE. faecalisvirulence factors and the fly´s immune system. Future studies onDrosophilaimmunity should consider the pathogen genomic content.
A particle-filter framework for robust cryoEM 3D reconstruction
Authors: Hu Mingxu , Yu Hongkun , Gu Kai , Wang Kunpeng , Ren Siyuan , Li Bing , Gan Lin , Xu Shizhen , Yang Guangwen , Shen Yuan , Li Xueming
Published: May 2018

Electron cryo-microscopy (cryoEM) is now a powerful tool in determining atomic structures of biological macromolecules under nearly natural conditions. The major task of single-particle cryoEM is to estimate a set of parameters for each input particle image to reconstruct the three-dimensional structure of the macromolecules. As future large-scale applications require increasingly higher resolution and automation, robust high-dimensional parameter estimation algorithms need to be developed in the presence of various image qualities. In this paper, we introduced a particle-filter algorithm for cryoEM, which was a sequential Monte Carlo method for robust and fast high-dimensional parameter estimation. The cryoEM parameter estimation problem was described by a probability density function of the estimated parameters. The particle filter uses a set of random and weighted support points to represent such a probability density function. The statistical properties of the support points not only enhance the parameter estimation with self-adaptive accuracy but also provide the belief of estimated parameters, which is essential for the reconstruction phase. The implementation of these features showed strong tolerance to bad particles and enabled robust defocus refinement, demonstrated by the remarkable resolution improvement at the atomic level.
MicroRNA-196a is regulated by ER and is a prognostic biomarker in ER+ Breast Cancer
Authors: Milevskiy Michael J.G. , Gujral Udai , Lama Marques Carolina Del , Stone Andrew , Northwood Korinne , Burke Lez J. , Gee Julia M.W. , Nephew Kenneth , Clark Susan , Brown Melissa A.
Published: May 2018

MicroRNAs are potent post-transcriptional regulators involved in all hallmarks of cancer. Mir-196a is transcribed from two loci and has been implicated in a wide range of developmental and pathogenic processes, with targets including Hox, Fox, Cdk inhibitors and annexins. Genetic variants and altered expression of miR196a are associated with risk and progression of multiple cancers including breast cancer, however little is known about the regulation of the genes encoding this miRNA, nor the impact of variants therein. Here we demonstrate that MIR196A displays complex and dynamic expression patterns, in part controlled by long range transcriptional regulation between promoter and enhancer elements bound by ERα. Expression of this miRNA is significantly increased in models of hormone receptor positive disease resistance. The expression of MIR196A also proves to be a robust prognostic factor for patients with advanced and post-menopausal ER+ disease. This work sheds light on the normal and abnormal regulation of MIR196A and provides a novel stratification method for therapeutically resistant breast cancer.
Impact of Chronic Total Occlusion Lesion Length onSix-month Angiographic and 2-year Clinical Outcomes
Authors: Ahn Jihun , Rha Seung-Woon , Choi ByoungGeol , Choi Se Yeon , Byun Jae Kyeong , Mashaly Ahmed , Abdelshafi Kareem , Park Yoonjee , Jang Won Young , Kim Woohyeun , Choi Jah Yeon , Park EunJin , Na Jin Oh , Choi Cheol Ung Choi , Kim EungJu Kim , Park Chang Gyu , Seo HongSeog , Oh DongJoo , Byeon JinSu , Park SangHo , Yu HyeYon
Published: May 2018

Background

Successful chronic total occlusion (CTO) percutaneous coronary intervention (PCI) is known to be associated with improved clinical outcomes compared with failed CTO PCI. However, it is not clear whether the angiographic and clinical outcomes of long CTO lesionis different with those of short CTO lesion in the drug eluting stent (DES) era.

Method sand Results

A total of 235 consecutive patients underwent successful CTO intervention were divided into two groups according the CTO lesion length. Six-month angiographic and two-year clinical outcomes were compared between the two groups. The baseline clinical characteristics were similar between the two groups except prior PCI was more frequent in long CTO group whereas bifurcation lesion was more frequent in the short CTO group. In-hospital complications were similar between the two groups except intimal dissection was more frequent in long CTO group. Both groups had similar angiographic outcomes at 6 months and clinical outcomes up to 2 years except the incidence of repeat PCI, predominantly target vessel revascularization (TVR) was higher in long CTO group. In multivariate analysis, long CTO was an important predictor for repeat PCI (OR;4.26, CI 1.53-11.9, p=0.006).

Conclusion

The safety profile, angiographic and 2-year clinical outcomes were similar between the two groups except higher incidence of repeat PCI in long CTO group despite of successful PCI with DESs.
Linked mutations at adjacent nucleotides have shaped human population differentiation and protein evolution
Authors: Prendergast James G. D. , Pugh Carys , Harris Sarah E. , Hume David A. , Deary Ian J. , Beveridge Allan
Published: May 2018

Despite the fundamental importance of single nucleotide polymorphisms (SNPs) to human evolution there are still large gaps in our understanding of the forces that shape their distribution across the genome. SNPs have been shown to not be distributed evenly, with directly adjacent SNPs found unusually frequently. Why this is the case is unclear. We illustrate how neighbouring SNPs that can’t be explained by a single mutation event (that we term here sequential dinucleotide mutations, SDMs) are driven by distinct mutational processes and selective pressures to SNPs and multinucleotide polymorphisms (MNPs). By studying variation across multiple populations, including a novel cohort of 1,358 Scottish genomes, we show that, SDMs are over twice as common as MNPs and like SNPs, display distinct mutational spectra across populations. These biases are though not only different to those observed among SNPs and MNPs, but also more divergent between human population groups. We show that the changes that make up SDMs are not independent, and identify a distinct mutational profile, CA → CG → TG, that is observed an order of magnitude more often than other SDMs, including others that involve the gain and subsequent deamination of CpG sites. This suggests these specific changes are driven by a distinct process. In coding regions particular SDMs are favoured, and especially those that lead to the creation of single codon amino acids. Intriguingly selection has favoured particular pathways through the amino acid code, with epistatic selection appearing to have disfavoured sequential non-synonymous changes.
Bacteria associated with jellyfish during bloom and post-bloom periods
Authors: Kramar Maja Kos , Tinta Tinkara , Lučić Davor , Malej Alenka , Turk Valentina
Published: May 2018

This study is the first to investigate bacterial community associated with live medusaAurelia sp. in the Gulf of Trieste (northern Adriatic Sea) using both culture independent and culture-based methods. We have analysed bacterial community composition of different body parts of medusa: exumbrella surface, oral arms (‘outer’ body parts) and of gastric cavity (‘inner’ body part) and investigated possible differences in medusa associated bacterial community structure at the time of jellyfish population peak and during senescent phase at the end of bloom, when jellyfish start to decay. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we demonstrated significant difference between bacterial community associated withAureliaand the ambient seawater bacterial assemblage. Comparing bacterial community composition between differentAureliamedusa body parts, communities differed significantly, especially the one within the gastral cavity. The pronounced difference is dominance ofBetaproteobacteria(Burkholderia, CupriavidusandAchromobacter) in gastral cavity of medusa andAlpha- (Phaeobacter, Ruegeria) andGamma-proteobacteria(Stenotrophomonas, Alteromonas, PseudoalteromonasandVibrio) on ‘outer’ body parts. This suggests that body-part specific bacterial association might have an important functional roles for the host. The results of bacterial isolates showed the dominance ofGammaproeteobacteria, especiallyVibrioandPseudoalteromonasin all body parts. Finally, comparison of medusa associated bacterial community structure, at the time of jellyfish population peak and during senescent phase at the end of bloom showed increased abundance ofGammaproteobacteria, especiallyVibrio. Our results suggest members ofVibriogroup are possible commensal opportunistic visitors, later becoming consumer of moribund jellyfish biomass and that the structure of jellyfish bacterial community might be affected by anthropogenic pollution in the marine environment.
Synthesis, Biological Activity and Molecular Docking of New Tricyclic Series as α-glucosidase Inhibitors
Authors: Abuelizz Hatem A. , Iwana Nor Azman N. I , Ahmad Rohaya , El-Hassane Anouar , Marzouk Mohamed , Al-Salahi Rashad
Published: May 2018

Diabetes is an emerging metabolic disorder. α-Glucosidase inhibitors, such as acarbose, delay the hydrolysis of carbohydrates by interfering with the digestive enzymes. This action decreases the glucose absorption and the postprandial glucose level. We have synthesized 25 tricyclic 2-phenoxypyrido[3,2-e][1,2,4]triazolo[1,5-a]pyrimidin-5(4H)-ones hybrids and evaluated their α-glucosidase inhibitory activity. Compounds 6h and 6d have shown stronger activity than that of acarbose. Compound 6h exhibited the highest inhibition with an IC50 of 104.07 mM. Molecular modelling studies revealed that compound 6h inhibits α-glucosidase due to the formation of a stable ligand–α-glucosidase complex and extra hydrogen bond interactions, and directed in the binding site by Trp329.
Influence of plant growth regulators and nitrogen sources on the production and development of Brachiaria decumbens cv. Basilisk
Authors: Rocha Leone Campos , Teixeira Fábio Andrade , dos Santos Pedreira Márcio , Fries Daniela Deitos , Costa Evely Giovanna Leite , Cláudia Maia Soares Ana , Dias Daniel Lucas Santos , José de Figueiredo Abdias , Seixas Angel Amaral , Pacheco Camile Carvalho
Published: May 2018

The aim was to evaluate the effect of seed treatment with plant growth regulators and nitrogen fertilization methods in Brachiaria decumbens cv. Basilisk on the growth and development through germinative characteristics, dry matter yield and physiological composition. Plant growth regulators increased germination and mass yields of plant structures in coated seeds. From the regression estimates, higher germination percentages and root dry mass production were obtained with the use of Plant growth regulators for the initial growth (10.3; 12.8 mL.kg−1 seed, respectively). Leaf and pseudostem mass production had a significant interaction effect between seed type and the use of growth regulator. Coated seeds had greater performance with absence or at lower levels of growth regulators, and embryo quality contributed to the greater formation of plant tissues. More efficient levels (8.85 and 9.57 mL.kg−1 seed) were observed for the yields of plant structures (leaf and pseudostem). Soil N-fertilization resulted in higher dry mass productions of leaf, stem, shoot and root, as well as for root volume. Rates of photoassimilate were increased by soil fertilization and use of plant growth regulators. The use of exogenous hormonal compounds acts on the organogenesis of plant tissues and increases the development of Brachiaria decumbens cv. Basilisk. Soil N-fertilization increase mass yields as it maximizes photosynthetic processes and growth rates.
Two hydrazones derived from 1-aryl-3-(p-substituted phenyl)prop-2-en-1-one: synthesis, crystal structure, Hirshfeld surface analysis andin vitrobiological properties
Authors: Dammene Debbih Ouafa , Sid Assia , Bouchene Rafika , Bouacida Sofiane , Mazouz Wissam , Gherraf Noureddine
Published: May 2018

Two chalcones were synthesized by the aldolic condensation of enolizable aromatic ketones with substituted benzaldehydes under Claisen–Schmidt reaction conditions and then treated with 2,4-dinitrophenylhydrazine to yield their corresponding hydrazones. The two (E,Z)-2,4-dinitrophenylhydrazone structures, namely (Z)-1-(2,4-dinitrophenyl)-2-[(E)-3-(4-methylphenyl)-1-phenylallylidene]hydrazine, C22H18N4O4, (H1), and (Z)-1-[(E)-3-(4-chlorophenyl)-1-(naphthalen-1-yl)allylidene]-2-(2,4-dinitrophenyl)hydrazine, C25H17ClN4O4, (H2), were isolated by recrystallization and characterized by FT–IR, UV–Vis, single-crystal and powder X-ray diffraction methods. The UV–Vis spectra of the hydrazones have been studied in two organic solvents of different polarity. It was found that (H2) has a molar extinction coefficient larger than 40000. Single-crystal X-ray diffraction analysis reveals that the molecular zigzag chains of (H1) and (H2) are interconnected through noncovalent contacts. A quantitative analysis of the intermolecular interactions in the crystal structures has been performed using Hirshfeld surface analysis. All the synthesized chalcones and hydrazones were evaluated for their antibacterial and antioxidant activities. Results indicate that the studied compounds show significant activity against Gram negativeEscherichia colistrain and the chalcone 3-(4-methylphenyl)-1-phenylprop-2-en-1-one, (C1), was the most effective. In addition, only hydrazone (H1) displayed a moderate DPPH (2,2-diphenyl-1-picryl hydrazyl) scavenging efficiency.
M+M3+2As(HAsO4)6and α- and β-M+M3+(HAsO4)2(M+M3+= RbAl or CsFe): six new compounds crystallizing in three closely related structure types
Authors: Schwendtner Karolina , Kolitsch Uwe
Published: May 2018

The crystal structures of hydrothermally synthesized (T= 493 K, 7–9 d) rubidium aluminium bis[hydrogen arsenate(V)], RbAl(HAsO4)2, caesium iron bis[hydrogen arsenate(V)], CsFe(HAsO4)2, rubidium dialuminium arsenic(V) hexakis[hydrogen arsenate(V)], RbAl2As(HAsO4)6, and caesium diiron arsenic(V) hexakis[hydrogen arsenate(V)], CsFe2As(HAsO4)6, were solved by single-crystal X-ray diffraction. The four compounds with the general formulaM+M3+(HAsO4)2adopt the RbFe(HPO4)2structure type (R\overline{3}c) and a closely related new structure type, which is characterized by a different stacking order of the building units, leading to noncentrosymmetric space-group symmetryR32. The second new structure type, with the general formulaM+M3+2As(HAsO4)6(R\overline{3}c), is also a modification of the RbFe(HPO4)2structure type, in which one third of theM3+O6octahedra are replaced by AsO6octahedra, and two thirds of the voids in the structure, which are usually filled byM+cations, remain empty to achieve charge balance.
Crystal structure ofEscherichia colipurine nucleoside phosphorylase in complex with 7-deazahypoxanthine
Authors: Timofeev Vladimir I. , Zhukhlistova Nadezhda E. , Abramchik Yuliya A. , Fateev Ilya I. , Kostromina Maria A. , Muravieva Tatiana I. , Esipov Roman S. , Kuranova Inna P.
Published: May 2018

Purine nucleoside phosphorylases (EC 2.4.2.1; PNPs) reversibly catalyze the phosphorolytic cleavage of glycosidic bonds in purine nucleosides to generate ribose 1-phosphate and a free purine base, and are key enzymes in the salvage pathway of purine biosynthesis. They also catalyze the transfer of pentosyl groups between purine bases (the transglycosylation reaction) and are widely used for the synthesis of biologically important analogues of natural nucleosides, including a number of anticancer and antiviral drugs. Potent inhibitors of PNPs are used in chemotherapeutic applications. The detailed study of the binding of purine bases and their derivatives in the active site of PNPs is of particular interest in order to understand the mechanism of enzyme action and for the development of new enzyme inhibitors. Here, it is shown that 7-deazahypoxanthine (7DHX) is a noncompetitive inhibitor of the phosphorolysis of inosine by recombinantEscherichia coliPNP (EcPNP) with an inhibition constantKiof 0.13 mM. A crystal ofEcPNP in complex with 7DHX was obtained in microgravity by the counter-diffusion technique and the three-dimensional structure of theEcPNP–7DHX complex was solved by molecular replacement at 2.51 Å resolution using an X-ray data set collected at the SPring-8 synchrotron-radiation facility, Japan. The crystals belonged to space groupP6122, with unit-cell parametersa=b= 120.370,c= 238.971 Å, and contained three subunits of the hexameric enzyme molecule in the asymmetric unit. The 7DHX molecule was located with full occupancy in the active site of each of the three crystallographically independent enzyme subunits. The position of 7DHX overlapped with the positions occupied by purine bases in similar PNP complexes. However, the orientation of the 7DHX molecule differs from those of other bases: it is rotated by ∼180° relative to other bases. The peculiarities of the arrangement of 7DHX in theEcPNP active site are discussed.
Visual trends in the annual report: the case of Ericsson 1947-2016
Authors: Havemo Emelie
Published: May 2018

Purpose

Disclosure research has argued that visuals are increasingly used in annual reports as a way to increase readability of the annual report, but comparatively little is known about of diagrams compared to graphs and photographs. The purpose of this paper is to provide a historical account of visuals use in corporate disclosure, with an emphasis on diagrams, to show changes from the 1940s until present-day reporting.

Design/methodology/approach

Visual research methods were applied to analyze how diagrams, photographs and graphs were used in 69 annual reports of the Swedish telecom company Ericsson.

Findings

Photographs have been used with increasing frequency since the 1950s. Graph and diagram use has increased significantly since the 1990s while photograph use remained stable, suggesting that graphs and diagrams increasingly complement photographs for visually representing the organization in corporate disclosure. Factors explaining the case company’s development include both internal (performance, individual preferences, shifting from a manufacturing-based strategy to a service-based strategy) and external (legislation, transformation of the telecom industry).

Originality/value

Visual elements in annual reports are increasingly oriented toward immaterial representations of the organization’s standings and identity and diagrams are increasingly used and contribute to this. This finding motivates further research about diagram use in corporate communication, such as how different diagram types convey accounting messages, and whether diagrams serve as impression management devices. For regulators, it will be important to follow the emerging trend of diagram use, since it is becoming part of reporting practice.
The German medical cannabis law of 2017
Authors: Grotenhermen Franjo
Published: May 2018

Purpose

The purpose of this paper is to give a review on the developments leading to the 2017 law on the medical use of cannabis and cannabinoids in Germany, and to present the major advances arising from this law for the supply of patients with cannabis-based drugs and its major limitations.

Design/methodology/approach

This paper used an Analysis of the major political statements and documents as well as court decisions of the past 20 years, which can be regarded as the major steps of this development.

Findings

Since 1998, when dronabinol/THC was made available in Germany on prescription there have been continuous improvements of the access to cannabis-based medicines. The law of 2017, which made cannabis flowers available to patients on a doctor’s prescription and forced health insurers to pay for a treatment under certain circumstances was a major step. However, many patients, who profit from a treatment with cannabis still do not get access.

Originality/value

The German law on the medical use of cannabis and cannabinoids of 2017 is unique in its kind in the world. Compared to the legal framework in other countries it has several disadvantages, for example with regard to the high prices of cannabis flowers (€20-€25 per gram), and several advantages, for example with regard to the role of health insurers.
The establishing of a European industrial relations system
Authors: Begega Sergio González , Aranea Mona
Published: May 2018

Purpose

The purpose of this paper is to examine European Union (EU) industrial relations in their development over time. It describes and analyzes their main constituent parts, which are deployed along four interlinked institutional dimensions: tripartite concertation; cross-industry social dialogue; sectoral social dialogue; and employee representation and negotiation at the transnational company level. The focus lies strictly on the emerging EU layer of industrial relations, which is common to the different Member States and not on comparative European industrial relations.

Design/methodology/approach

The paper is conceptual in nature. It considers the differences and mutually interdependent legal and political processes, policies and institutions between EU industrial relations and national industrial relations.

Findings

The findings substantiate that EU industrial relations constitute an incomplete but perfectly traceable transnational reality distinct from industrial relations in the Member States. EU industrial relations are not to supersede but to supplement national industrial relations. Neither the EU institutional framework nor the European social partners have the mandate, legitimation or desire to perform a more ambitious role.

Research limitations/implications

More empirically oriented research would further support the findings in the paper.

Originality/value

The paper presents a conceptual review based on a comprehensive and critical reading of the literature on EU industrial relations. It also puts labor strategies at the forefront of the analysis in corporate relocation.
“Life-changing things happen”
Authors: Clancy Sharon Louise , Holford John
Published: May 2018

Purpose

The purpose of this paper is to examine the implications for adults of learning in a residential context and whether the residential aspect intensifies the learning process, and can lead to enhanced personal transformation, moving beyond professional skills and training for employability.

Design/methodology/approach

The paper reports on research, conducted in 2017, with 41 current and former staff and students (on both short courses and longer access courses) in four residential colleges for adults: Ruskin, Northern, Fircroft and Hillcroft Colleges.

Findings

Key findings include the powerful role residential education plays in accelerating and deepening learning experiences, particularly for adults who have faced extraordinary personal and societal challenges and are second chance learners. The colleges, all in historic settings, confer feelings of worth, security and sanctuary and the staff support – pastoral and academic, bespoke facilities and private rooms are vital enabling mechanisms. Seminar-style learning creates opportunity for experiential group learning, helping to foster critical thinking and challenge to mainstream views.

Social implications

The colleges’ ethos, curricula and traditions foster among students an “ethic of service” and a desire to offer “emotional labour” to their own communities, through working for instance in health and social care or the voluntary sector.

Originality/value

Little research has been undertaken in contemporary settings on the impact of learning in a residential environment, particularly for second chance learners and vulnerable adults. Still less research has examined the wider implications of learning in a historic building setting and of learning which extends into critical thinking, intellectual growth, transformation and change.
Inter-organizational fit and environmental innovation in supply chains
Authors: Shou Yongyi , Che Wen , Dai Jing , Jia Fu
Published: May 2018

Purpose

Through examining the two constructs of inter-organizational complementarity and inter-organizational compatibility in supply chains, the purpose of this paper is to develop a taxonomy of focal firms’ inter-organizational fit (IOF) configurations with their suppliers and customers, and examine the relationship between these configurations and environmental innovation (EI) in order to answer the question of “with whom” to collaborate for EI development.

Design/methodology/approach

A survey instrument was elaborated and data from a sample of 171 US firms were collected. The authors adopted cluster analysis to identify the IOF taxonomy. Canonical discriminant analysis was employed to uncover underlying dimensions between clustering variables and cluster membership. Then, ANOVA tests were conducted to investigate relationships between IOF configurations in the context of EI in supply chains.

Findings

Three configurations were identified based on the complementarity and compatibility between focal firms and their supply chain partners. It is observed that the overall IOF level is positively related to firms’ EI outcomes. Moreover, inter-organizational complementarity facilitates incremental EI while inter-organizational compatibility plays a more crucial role in radical EI. Both are required to achieve the best innovation outcome.

Originality/value

This research develops the first taxonomy for depicting IOF in a supply chain innovation context and also clarifies different rationale behind the development of incremental and radical EI through examining distinctive effects of the complementarity and compatibility with supply chain partners.
How public sport centers can improve the sport consumer experience
Authors: Cepeda-Carrión Ignacio , Cepeda-Carrion Gabriel
Published: May 2018

Purpose

The sport consumer experience is becoming an important aspect to sport center’s management. From this point, the purpose of this paper is to explore and examine the relationship between sport centers’ absorptive capacity and sport consumer experience, proposing that internal knowledge management processes act as mediators in this relationship.

Design/methodology/approach

The study offers empirical insights by applying the consistent PLS algorithm (PLSc-SEM) in an analysis of data from 156 sport centers in Andalusia (Spain) and a sample of 3,150 sport users from these sport centers.

Findings

The results demonstrate that a sport center’s absorptive capacity for external knowledge is crucial for enhancing the sport consumer experience and also that this effect requires additional knowledge management, such as the sport center’s knowledge storage and knowledge application.

Practical implications

The practical implication for sport center managers is that knowledge management processes have a very strong influence on the sport consumer experience, when they are managed in a sequential way.

Originality/value

The main value of this paper is draw conclusions using a study of sport managers and sport consumers to increase value experience of those ones.
Roadmap to collaboration: journey from silos to enterprise
Authors: LugoSantiago José A.
Published: May 2018

Purpose

Collaboration facilitates competitive advantages. That’s the reason why every leader should be concerned with whether his or her part of the organization embraces collaboration or not. Collaboration in itself is an instrumental value, and it should be pursued as part of an organization’s enterprise-wide strategy, especially in merged organizations. Unfortunately, the natural inclination in merged organizations is for the merged entities to continue the past practice of independent, autonomous operations. When merged, the separate entities of the new organization naturally resist integration. The leader must infuse collaboration to enable knowledge sharing and the integration and employment of the new organization’s capabilities. The following discussion presents a roadmap to collaboration focused on the leader’s employment of seven critical practices.

Design/methodology/approach

Concept Paper

Findings

Scholarly study points to collaboration as an instrumental value. If it must become a value in the organization, then leaders must use seven practices as part of an enterprise-wide strategy and carefully follow the implementation of the seven practices until collaboration becomes a value and the natural instinct of the organization.

Originality/value

Leaders struggle with how to bring collaboration into an environment where inertial forces impede it. The following discussion presents a roadmap to infuse collaboration and grow an appreciation for it because this process will facilitate the development and implementation of goals, objectives and action plans for the organization. Seven practices are discussed and integrated into an operational design-like method just like the one commanders use to achieve victories in military campaign planning and execution.
Staples: strategic evolution and decline in retailing
Authors: Strong John S.
Published: May 2018

Purpose

This paper aims to analyze strategic decline in office supply retailing. The paper describes how inconsistent and biased internal decisions and perspectives can lead to decline, even for retailers, once dominant in their sector.

Design/methodology/approach

This paper is a case study of Staples and the US office supply industry over a 30-year period.

Findings

A series of inconsistent and contradictory strategic decisions led to the decline of Staples, the world’s largest office supply retailer. With a backdrop of increasing online competition, Staples failed to rethink the role of its store network, lost its value positioning and embarked on an inconsistent and flawed acquisition strategy.

Originality/value

This paper shows the need for retail companies to continue to develop strategies for traditional formats while moving into a multichannel competitive environment. The paper concludes with nine lessons for retailers, involving the need for distinct channel strategies, reinforcing of value positioning and the importance of an internal focus on strategic evolution.