bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence of near-death experiences and REM sleep intrusion in 1034 adults from 35 countries
Authors: Kondziella Daniel , Harboe Olsen Markus
Published: January 2019

Background

Near-death experiences have fascinated humans for centuries, but their origin and prevalence remain unknown.

Methods

Using an online crowdsourcing platform, we recruited 1034 lay people from 35 countries to investigate the prevalence of near-death experiences and self-reported REM sleep intrusion. Reports were validated using the Greyson Near-Death Experiences Scale (GNDES) with a score of ≥7 as cut-off point for identifying near-death experiences.

Results

Near-death experiences were reported by 106 of 1034 participants (10%; CI 95% 8.5-12%). REM sleep intrusion was more common in people with near-death experiences (n=50/106; 47%) than in people with experiences with 6 points or less on the GNDES (n=47/183; 26%) or in those without any such experience (n=107/744; 14%; p=<0.0001). Following multivariate regression analysis to adjust for age, gender, place of origin, employment status and perceived danger, this association remained highly significant; people with REM sleep intrusion were more likely to exhibit near-death experiences than those without REM sleep abnormalities (odds ratio 2.85; CI 95% 1.68-4.88; p=0.0001).

Conclusions

The prevalence of near-death experiences in the public is around 10%. While age, gender, place of residence, employment status and perceived threat do not seem to influence the prevalence of near-death experiences, there is a significant association with REM sleep intrusion. This finding is in line with the view that despite imminent threat to life, brain physiology must be well-preserved to perceive these fascinating experiences and store them as long-term memories.
Facilitating open-science with realistic fMRI simulation: validation and application
Authors: Ellis Cameron T. , Baldassano Christopher , Schapiro Anna C. , Cai Ming Bo , Cohen Jonathan D.
Published: January 2019

Background

With advances in methods for collecting and analyzing fMRI data, there is a concurrent need to understand how to reliably evaluate and optimally use these methods. Simulations of fMRI data can aid in both the evaluation of complex designs and the analysis of data.

New Method

We present fmrisim, a new Python package for standardized, realistic simulation of fMRI data. This package is part of BrainIAK: a recently released open-source Python toolbox for advanced neuroimaging analyses. We describe how to use fmrisim to extract noise properties from real fMRI data and then create a synthetic dataset with matched noise properties and a user-specified signal.

Results

We validate the noise generated by fmrisim to show that it can approximate the noise properties of real data. We further show how fmrisim can help researchers find the optimal design in terms of power.

Comparison with other methods

fmrisim ports the functionality of other packages to the Python platform while extending what is available in order to make it seamless to simulate realistic fMRI data.

Conclusions

The fmrisim package holds promise for improving the design of fMRI experiments, which may facilitate both the pre-registration of such experiments as well as the analysis of fMRI data.

Highlights

fmrisim can simulate fMRI data matched to the noise properties of real fMRI.

This can help researchers investigate the power of their fMRI designs.

This also facilitates open science by making it easy to pre-register analysis pipelines.
CAMITAX: Taxon labels for microbial genomes
Authors: Bremges Andreas , Fritz Adrian , McHardy Alice C.
Published: January 2019

The number of microbial genome sequences is growing exponentially, also thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to genomes is key and often a prerequisite for downstream analyses. We introduce CAMITAX, a scalable and reproducible workflow for the taxonomic labelling of microbial genomes recovered from isolates, single cells, and metagenomes. CAMI-TAX combines genome distance-, 16S rRNA gene-, and gene homology-based taxonomic assignments with phylogenetic placement. It uses Nextflow to orchestrate reference databases and software containers, and thus combines ease of installation and use with computational re-producibility. We evaluated the method on several hundred metagenome-assembled genomes with high-quality taxonomic annotations from the TARA Oceans project, and show that the ensemble classification method in CAMITAX improved on all individual methods across tested ranks. While we initially developed CAMITAX to aid the Critical Assessment of Metagenome Interpretation (CAMI) initiative, it evolved into a comprehensive software to reliably assign taxon labels to microbial genomes. CAMITAX is available under the Apache License 2.0 at: https://github.com/CAMI-challenge/CAMITAX
Financial implications of preterm birth during initial hospitalization: The extent and predictors of catastrophic health expenditure
Authors: Zainal Hadzri , Dahlui Maznah , Su Tin Tin
Published: January 2019

Preterm birth incidence has risen globally and the high cost of initial hospitalization poses financial burden to the family. This study assessed family cost at neonatal intensive care units of two hospitals in the state of Kedah, Malaysia. Family’s expenditure was obtained using a structured questionnaire. 126 families who were government employed spent a mean total cost of MYR 549 (MYR 0 - MYR 4,700) compared to MYR 650 (MYR 40 – MYR 9,300) for 244 families who were not government employed. Mean income loss was MYR 310 (MYR 0 – MYR 15,000) and MYR 348 (MYR 0 – MYR 5,500) respectively. Travel expenses was the cost driver for all families. 15% of families in this study were already living below the income poverty line and majority were not government employed. For the rest of the families, 21% became impoverished when one month household income was used for hospitalization cost but this lowered to 9% with cumulative household income by length of hospital stay. Overall incidence of catastrophic health expenditure among families was 38%. Using multivariable logistic regression household income and residential location were predictive factors for catastrophic health expenditure. Despite universal health coverage through subsidy of direct medical (hospital) cost, the high incidence of catastrophic health expenditure and impoverishment among families of preterm infants was attributable to out of pocket payment for direct non-medical cost (such as travel and food) and indirect cost from income loss. Government employed families with an array of employment benefits appear better protected against financial hardship compared to those in private sector or self-employed. Remedial measures include improving neonatal intensive care unit rooming-in service for mothers, complementary financial assistance for families and enhancing universal health coverage through affordable social health insurance for infant healthcare.
Plant growth regulators interact with elevated temperature to alter heat stress signaling via the Unfolded Protein Response in maize
Authors: Neill Elena M. , Byrd Michael C. R. , Billman Thomas , Brandizzi Federica , Stapleton Ann E.
Published: January 2019

Plants are increasingly exposed to high temperatures, which can cause accumulation of unfolded protein in the endoplasmic reticulum (ER). This condition, known as ER stress, evokes the unfolded protein response (UPR), a cytoprotective signaling pathway. One important branch of the UPR is regulated by splicing of bZIP60 mRNA by the IRE1 stress sensor. There is increasing evidence that commercial plant growth regulators may protect against abiotic stressors including heat stress and drought, but there is very little mechanistic information about these effects or about the regulatory pathways involved. We evaluated evidence in the B73 Zea mays inbred for differences in the activity of the UPR between permissive and elevated temperature in conjunction with plant growth regulator application. Treatment with elevated temperature and plant growth regulators increased UPR activation, as assessed by an increase in splicing of the mRNA of the IRE1 target bZIP60 following paclobutrazol treatment. We propose that plant growth regulator treatment induces bZIP60 mRNA splicing which ‘primes’ plants for rapid adaptive response to subsequent endoplasmic reticulum-stress inducing conditions.
Plumbagin-induced oxidative stress leads to inhibition of Na+/K+-ATPase (NKA) in canine cancer cells
Authors: Alharbi Yousef , Kapur Arvinder , Felder Mildred , Barroilhet Lisa , Stein Timothy , Pattnaik Bikash R. , Patankar Manish S.
Published: January 2019

The Na+/K+-ATPase (NKA) complex is the master regulator of membrane potential and a target for anti-cancer therapies. Here, we investigate the effect of drug-induced oxidative stress on NKA activity. The natural product, plumbagin increases oxygen radicals through inhibition of oxidative phosphorylation. As a result, plumbagin treatment results in decreased production of ATP and a rapid increase in intracellular oxygen radicals. We show that plumbagin induces apoptosis in canine cancer cells via oxidative stress. We use this model to test the effect of oxidative stress on NKA activity. Using whole-cell patch-clamp electrophysiology we demonstrate that short-term exposure (4 min) to plumbagin results in 48% decrease in outward current at +50 mV. Even when exogenous ATP was supplied to the cells, plumbagin treatment resulted in 46% inhibition outward current through NKA at +50 mV. In contrast, when the canine cancer cells were pre-treated with the oxygen radical scavenger, N-acetylcysteine, the NKA inhibitory activity of plumbagin was abrogated. These experiments demonstrate that the oxidative stress-causing agents such as plumbagin and its analogues, are a novel avenue to regulate NKA activity in tumors.
Quantifying the effect of experimental perturbations at single-cell resolution
Authors: Burkhardt Daniel B. , Stanley Jay S. , Tong Alexander , Perdigoto Ana Luisa , Gigante Scott A. , Herold Kevan C. , Wolf Guy , Giraldez Antonio J. , van Dijk David , Krishnaswamy Smita
Published: January 2019

Current methods for comparing scRNA-seq datasets collected in multiple conditions focus on discrete regions of the transcriptional state space, such as clusters of cells. Here, we quantify the effects of perturbations at the single-cell level using a continuous measure of the effect of a perturbation across the transcriptomic space. We describe this space as a manifold and develop a relative likelihood estimate of observing each cell in each of the experimental conditions using graph signal processing. This likelihood estimate can be used to identify cell populations specifically affected by a perturbation. We also develop vertex frequency clustering to extract populations of affected cells at the level of granularity that matches the perturbation response. The accuracy of our algorithm to identify clusters of cells that are enriched or depleted in each condition is on average 57% higher than the next best-performing algorithm tested. Gene signatures derived from these clusters are more accurate compared to six alternative algorithms in ground-truth comparisons.
The SUMO ligase Su(var)2-10 links piRNA-guided target recognition to chromatin silencing
Authors: Ninova Maria , Chen Yung-Chia Ariel , Godneeva Baira , Rogers Alicia K. , Luo Yicheng , Aravin Alexei A. , Tóth Katalin Fejes
Published: January 2019

Regulation of transcription is the main mechanism responsible for precise control of gene expression. While the majority of transcriptional regulation is mediated by a multitude of DNA-binding transcription factors that bind to regulatory gene regions, an elegant alternative strategy employs small RNA guides, piwi-interacting RNAs (piRNAs) to identify targets of transcriptional repression. Here we show that in Drosophila the small ubiquitin-like protein SUMO and the SUMO E3 ligase Su(var)2-10 are required for piRNA-guided deposition of repressive chromatin marks and transcriptional silencing of piRNA targets. Su(var)2-10 links the piRNA-guided target recognition complex to the silencing effector by binding the piRNA/Piwi complex and inducing SUMO-dependent recruitment of the SetDB1/Wde histone methyltransferase effector. We propose that in Drosophila, the nuclear piRNA pathway has co-opted a conserved mechanism of SUMO-dependent recruitment of the SetDB1/Wde chromatin modifier to confer repression of genomic parasites.

Highlights

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piRNA-induced transposon silencing requires SUMO and the SUMO E3 ligase Su(var)2-10

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Su(var)2-10 links the target recognition complex to the silencing effector

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Su(var)2-10 binds the piRNA-guided target recognition complex and deposits SUMO on target chromatin

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Su(var)2-10 induces SUMO-dependent recruitment of the SetDB1/Wde histone methyltransferase to target loci
Extinction-resistant attention to long-term conditioned threat is indexed by selective visuocortical alpha suppression in humans
Authors: Panitz Christian , Keil Andreas , Mueller Erik M.
Published: January 2019

While ERP studies have shown heightened early visual attention to conditioned threat, it is unknown whether this attentional prioritization is sustained throughout later processing stages and whether it is robust to extinction. To investigate sustained visual attention, we assessed visuocortical alpha suppression in response to conditioned and extinguished threat. N = 87 participants underwent a two-day threat conditioning paradigm with acquisition and extinction on one day and a critical recall test one day later. EEG time-frequency analyses revealed that, on Day 2, threat-conditioned vs. safety cues evoked stronger occipital alpha power suppression from 600 to 1200 ms. Notably, this suppression was resistant to extinction. The present study showed for the first time that threat conditioning enhances sustained modulation of visuocortical attention to threat in the long term. The long-term stability and extinction resistance of alpha suppression suggests a crucial role of visuocortical attention mechanisms in the maintenance of learned fears.
Pharmacological inhibition of GPR4 remediates intestinal inflammation in a mouse colitis model
Authors: Sanderlin Edward J. , Marie Mona , Velcicky Juraj , Loetscher Pius , Yang Li V.
Published: January 2019

Inflammatory bowel disease (IBD) is characterized by chronic, recurring inflammation of the digestive tract. Current therapeutic approaches are limited and include biologics and steroids such as anti-TNFα monoclonal antibodies and corticosteroids, respectively. Significant adverse drug effects can occur for chronic usage and include increased risk of infection in some patients. GPR4, a pH-sensing G protein-coupled receptor, has recently emerged as a potential therapeutic target for intestinal inflammation. We have assessed the effects of a GPR4 antagonist, 2-(4-((2-Ethyl-5,7-dimethylpyrazolo[1,5-a]pyrimidin-3-yl)methyl)phenyl)-5-(piperidin-4-yl)-1,3,4-oxadiazole (GPR4 antagonist 13, also known as NE 52-QQ57) in the dextran sulfate sodium (DSS)-induced acute colitis mouse model. The GPR4 antagonist 13 inhibited intestinal inflammation. The clinical parameters such as body weight loss and fecal score were reduced in the GPR4 antagonist 13 treatment group compared to vehicle control. Macroscopic disease indicators such as colon shortening, splenic expansion, and mesenteric lymph node enlargement were all reduced in severity in the GPR4 antagonist 13 treated mice. Histopathological features of active colitis were alleviated in GPR4 antagonist 13 treatment groups compared to vehicle control. Finally, inflammatory gene expression in the colon tissues and vascular adhesion molecule expression in the intestinal endothelia were attenuated by GPR4 antagonist 13. Our results indicate that GPR4 antagonist 13 provides a protective effect in the DSS-induced acute colitis mouse model, and inhibition of GPR4 can be explored as a novel anti-inflammatory approach.
Tubulin mRNA stability is sensitive to change in microtubule dynamics caused by multiple physiological and toxic cues
Authors: Gasic Ivana , Boswell Sarah A. , Mitchison Timothy J.
Published: January 2019

The localization, mass, and dynamics of microtubules are important in many processes. Cells may actively monitor the state of their microtubules and respond to perturbation, but how this occurs outside mitosis is poorly understood. We used gene expression analysis in quiescent cells to analyze responses to subtle and strong perturbation of microtubules. Genes encoding α-, β, and γ-tubulins, but not δ- or ε-tubulins, exhibited the strongest differential expression response to microtubule-stabilizing versus destabilizing drugs. Q-PCR of exon versus intron sequences confirmed that these changes were caused by regulation of tubulin mRNA stability and not transcription. Using tubulin mRNA stability as a signature to query the GEO database, we find that tubulin genes respond to toxins known to damage microtubules. Importantly, we find many other experimental perturbations, including multiple signaling and metabolic inputs that trigger tubulin differential expression, suggesting their novel role in the regulation of microtubule cytoskeleton. Mechanistic follow up confirms that one important physiological signal, phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) activity, indeed regulates tubulin mRNA stability via changes in microtubule dynamics. We propose that that tubulin gene expression is regulated as part of many coordinated biological responses, with wide implications in physiology and toxicology. Furthermore, we present a new way to discover microtubule regulation using genomics.
Stability of dynamic functional architecture differs between brain networks and states
Authors: Li Le , Lu Bin , Yan Chao-Gan
Published: January 2019

Stable representation of information in distributed neural connectivity is critical to function effectively in the world. Despite the dynamic nature of the brain’s functional architecture, characterizing its temporal stability has been largely neglected. Here we characterized stability of functional architecture for each brain voxel by measuring the concordance of dynamic functional connectivity (DFC) over time, and explored how stability was modified by movie watching. High-order association regions, especially the default mode network, demonstrated high stability during resting state scans, while primary sensory-motor cortices revealed relatively lower stability. During movie watching, stability in the primary visual cortex was decreased, which was associated with larger DFC variation with neighboring regions. By contrast, higher-order regions in the ventral and dorsal visual stream demonstrated increased stability. The distribution of functional stability and its modification describes a profile of the brain’s stability property, which may be useful reference for examining distinct mental states and disorders.
Flexible Experimental Designs for Valid Single-cell RNA-sequencing Experiments Allowing Batch Effects Correction
Authors: Song Fangda , Chan Ga Ming , Wei Yingying
Published: January 2019

Despite their widespread applications, single-cell RNA-sequencing (scRNA-seq) experiments are still plagued by batch effects and dropout events. Although the completely randomized experimental design has frequently been advocated to control for batch effects, it is rarely implemented in real applications due to time and budget constraints. Here, we mathematically prove that under two more flexible and realistic experimental designs—the “reference panel” and the “chain-type” designs—true biological variability can also be separated from batch effects. We develop Batch effects correction with Unknown Subtypes for scRNA-seq data (BUSseq), which is an interpretable Bayesian hierarchical model that closely follows the data-generating mechanism of scRNA-seq experiments. BUSseq can simultaneously correct batch effects, cluster cell types, impute missing data caused by dropout events, and detect differentially expressed genes without requiring a preliminary normalization step. We demonstrate that BUSseq outperforms existing methods with simulated and real data.
DNA double-strand breaks induced by reactive oxygen species promote DNA polymerase IV activity inEscherichia coli
Authors: Henrikus Sarah S. , Henry Camille , McDonald John P. , Hellmich Yvonne , Wood Elizabeth A. , Woodgate Roger , Cox Michael M. , Oijen Antoine M. van , Ghodke Harshad , Robinson Andrew
Published: January 2019

Under many conditions the killing of bacterial cells by antibiotics is potentiated by DNA damage induced by reactive oxygen species (ROS)1–3. A primary cause of ROS-induced cell death is the accumulation of DNA double-strand breaks (DSBs)1,4–6. DNA polymerase IV (pol IV), an error-prone DNA polymerase produced at elevated levels in cells experiencing DNA damage, has been implicated both in ROS-dependent killing and in DSBR7–15. Here, we show using single-molecule fluorescence microscopy that ROS-induced DSBs promote pol IV activity in two ways. First, exposure to the antibiotics ciprofloxacin and trimethoprim triggers an SOS-mediated increase in intracellular pol IV concentrations that is strongly dependent on both ROS and DSBR. Second, in cells that constitutively express pol IV, treatment with an ROS scavenger dramatically reduces the number of pol IV foci formed upon exposure to antibiotics, indicating a role for pol IV in the repair of ROS-induced DSBs.
Curated BLAST for Genomes
Authors: Price Morgan N. , Arkin Adam P.
Published: January 2019

“Curated BLAST for Genomes” finds candidate genes for a process or an enzymatic activity within a genome of interest. In contrast to annotation tools, which usually predict a single activity for each protein, Curated BLAST asks if any of the proteins in the genome are similar to characterized proteins that are relevant. Given a query such as an enzyme’s name or an EC number, Curated BLAST searches the curated descriptions of over 100,000 characterized proteins, and it compares the relevant characterized proteins to the predicted proteins in the genome of interest. In case of errors in the gene models, Curated BLAST also searches the six-frame translation of the genome. Curated BLAST is available at http://papers.genomics.lbl.gov/curated.
Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype
Authors: Yin Bojian , Balvert Marleen , van der Spek Rick A. A. , Dutilh Bas E. , Bohté Sander , Veldink Jan , Schönhuth Alexander
Published: January 2019

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by aberrations in the genome. While several disease-causing variants have been identified, a major part of heritability remains unexplained. ALS is believed to have a complex genetic basis where nonadditive combinations of variants constitute disease, which cannot be picked up using the linear models employed in classical genotype-phenotype association studies. Deep learning on the other hand is highly promising for identifying such complex relations. We therefore developed a deep-learning based approach for the classification of ALS patients versus healthy individuals from the Dutch cohort of the ProjectMinE dataset. Based on recent insight that regulatory regions on the genome play a major role in ALS, we employ a two-step approach: first promoter regions that are likely associated to ALS are identified, and second individuals are classified based on their genotype in the selected genomic regions. Both steps employ a deep convolutional neural network. The network architecture accounts for the structure of genome data by applying convolution only to parts of the data where this makes sense from a genomics perspective.

Our approach identifies potential ALS-associated genetic variants, and generally outperforms other classification methods. Test results support the hypothesis that ALS is caused by non-additive combinations of variants. Our method can be applied to large-scale whole genome data. We consider this a first step towards genotype-phenotype association with deep learning that is tailored to genomics and can deal with genome-sized data.
Erosion of phylogenetic diversity in Neotropical bat assemblages: findings from a whole-ecosystem fragmentation experiment
Authors: Aninta Sabhrina G. , Rocha Ricardo , López-Baucells Adrià , Meyer Christoph F. J.
Published: January 2019

The traditional focus on taxonomic diversity metrics for investigating species responses to habitat loss and fragmentation has limited our understanding on how biodiversity is impacted by habitat modification. This is particularly true for taxonomic groups such as bats which exhibit species-specific responses. Here, we investigate phylogenetic alpha and beta diversity of Neotropical bat assemblages across two environmental gradients, one in habitat quality and one in habitat amount. We surveyed bats in 39 sites located across a whole-ecosystem fragmentation experiment in the Brazilian Amazon, representing a gradient of habitat quality (interior-edge-matrix, hereafter IEM) in both continuous forest and forest fragments of different sizes (1, 10, and 100 ha; forest size gradient). For each habitat category, we quantified alpha and beta phylogenetic diversity, then used linear models and cluster analysis to explore how forest area and IEM gradient affect phylogenetic diversity. We found that the secondary forest matrix harboured significantly lower total evolutionary history compared to the fragment interiors, especially the 1 ha fragments, containing bat assemblages with more closely related species. Forest fragments ≥ 10 ha had levels of phylogenetic richness similar to continuous forest, suggesting that large fragments retain considerable levels of evolutionary history. The edge and matrix adjacent to large fragments tend to have closely related lineages nonetheless, suggesting phylogenetic homogenization in these IEM gradient categories. Thus, despite the high mobility of bats, fragmentation still induces considerable levels of erosion of phylogenetic diversity, suggesting that the various evolutionary history might not be able to persist in present-day human-modified landscapes.
Towards a Gamete Matching Platform: Using Immunogenetics and Artificial Intelligence to Predict Recurrent Miscarriage
Authors: Mora-Sánchez Aldo , Aguilar-Salvador Daniel-Isui , Nowak Izabela
Published: January 2019

The degree of Allele sharing of the Human Leukocyte Antigen (HLA) genes has been linked with recurrent miscarriage (RM). However, no clear genetic markers of RM have yet been identified, possibly because of the complexity of interactions between paternal and maternal genes. We propose a methodology to analyse HLA haplotypes from couples either with histories of successful pregnancies or RM. This article describes, for the first time, a method of RM genetic-risk calculation. Novel HLA representation techniques allowed us to create an algorithm (IMMATCH) to retrospectively predict RM with an AUC = 0.71 (p = 0.0035) thanks to high-resolution typing and the use of linear algebra on peptide binding affinity data. The algorithm features an adjustable threshold to increase either sensitivity or specificity. Combining immunogenetics with artificial intelligence could create personalized tools to better understand the genetic causes of unexplained infertility and a gamete matching platform that could increase pregnancy success rates.
Identification of aggressive Gardner syndrome phenotype associated with a de novo APC variant, c.4666dup
Authors: Kiessling Patrick , Dowling Eric , Huang Yajue , Ho Mai Lan , Balakrishnan Karthik , Weigel Brenda J. , Highsmith W. Edward , Niu Zhiyv , Schimmenti Lisa A.
Published: January 2019

Gardner syndrome describes a variant phenotype of familial adenomatous polyposis (FAP), primarily characterized by extracolonic lesions including osteomas, dental abnormalities, epidermal cysts, and soft tissue tumors. We describe a 2-yr-old boy presenting with a 2-cm soft tissue mass of the forehead. Pathologic evaluation revealed a nuchal-type/Gardner-associated fibroma. Sequencing of the APC gene revealed a pathologic variant c.4666dupA. Parental sequencing of both blood and buccal tissue supported the de novo occurrence of this pathologic variant. Further imaging revealed a number of additional lesions including a large lumbar paraspinal desmoid, a 1-cm palpable lesion posterior to the left knee, firm lesions on bilateral heels, and multiple subdermal lesions. Colonoscopy was negative. This case illustrates a genetic variant of Gardner syndrome resulting in an aggressive early childhood phenotype and highlights the need for an individualized approach to treatment.
Structural insights into methyl- or methoxy-substituted 1-(α-aminobenzyl)-2-naphthol structures: the role of C—H...π interactions
Authors: Capozzi Maria Annunziata M. , Terraneo Giancarlo , Cardellicchio Cosimo
Published: January 2019

Aminobenzylnaphthols are a class of compounds containing a large aromatic molecular surface which makes them suitable candidates to study the role of C—H...π interactions. We have investigated the effect of methyl or methoxy substituents on the assembling of aromatic units by preparing and determining the crystal structures of (S,S)-1-{(4-methylphenyl)[(1-phenylethyl)amino]methyl}naphthalen-2-ol, C26H25NO, and (S,S)-1-{(4-methoxyphenyl)[(1-phenylethyl)amino]methyl}naphthalen-2-ol, C26H25NO2. The methyl group influenced the overall crystal packing even if the H atoms of the methyl group did not participate directly either in hydrogen bonding or C—H...π interactions. The introduction of the methoxy moiety caused the formation of new hydrogen bonds, in which the O atom of the methoxy group was directly involved. Moreover, the methoxy group promoted the formation of an interesting C—H...π interaction which altered the orientation of an aromatic unit.
Intermolecular interactions in a phenol-substituted benzimidazole
Authors: Geiger David K. , Geiger H. Cristina , Moore Shawn M.
Published: January 2019

Hydrogen bonding plays an important role in the design of solid-state structures and gels with desirable properties. 1-(4-Hydroxybenzyl)-2-(4-hydroxyphenyl)-5,6-dimethyl-1H-benzimidazole was isolated as the acetone disolvate, C22H20N2O2·2C3H6O. O—H...N hydrogen bonding between benzimidazole molecules results in chains parallel to [010]. One of the acetone solvate molecules participates in O—H...O hydrogen bonding with the benzimidazole derivative. C—H...π interactions are observed in the extended structure. Hirshfeld surface analysis was used to explore the intermolecular interactions and density functional theory was used to estimate the strength of the hydrogen bonds.
(Z)-3-Butyl-5-(4-nitrobenzylidene)thiazolidine-2,4-dione
Authors: Faizi Md. Serajul Haque , Lone Mohammad Nadeem , Dege Necmi , Iskenderov Turganbay , Malinkin Sergey
Published: January 2019

In the title compound, C14H14N2O4S, the benzene and thiazolidine rings are almost coplanar with a dihedral angle of 2.98 (14)°. The butyl chain is directed almost perpendicular to the plane of the rest of the molecule. In the crystal, a combination of C—H...O hydrogen bonds and offset π–π interactions leads to the formation of a three-dimensional structure.
Relationship between novice versus experienced EFL teacher’s Big Five personality traits and their ambiguity tolerance and risk taking
Authors: Rezaei Omid , Vasheghani Farahani Mehrdad , Musaei Sejzehei Fatemeh
Published: January 2019

Purpose

The purpose of this paper is to investigate the possible relationship between novice vs experienced EFLs teachers’ Big Five personality traits, ambiguity tolerance and risk taking. To this purpose, 30 teachers of TEFL courses were randomly selected, and three instruments of NEO Five-Factor Inventory, Ambiguity Tolerance Scale and Risk-taking Propensity Measure were employed to measure their Big Five personality traits, their ambiguity tolerance and risk taking, respectively.

Design/methodology/approach

The study was a quantitative ex post facto study. The first phase of the study was to investigate the relationship among variables of the study. On the other hand, the second phase of the study examined the impact of experience of teachers on their risk taking and ambiguity tolerance.

Findings

The results showed that the more experienced the teachers are, the less risk they take and the more ambiguity tolerant they are. On the other hand, the less experienced the teachers are, the more risk they will take and the less they can tolerate ambiguity. The findings of this research can have useful implications for teacher training programs as well as teaching practices.

Originality/value

This study can add to the circle of knowledge and enhance theoretical assumptions of the field. Moreover, considering the Iranian context, a few studies have focused on the importance of uncovering relationship between five big personality traits and teachers’ personality factors. Therefore, this study is an attempt to investigate the relationship between the Big Five personality traits of teachers and their ambiguity tolerance and risk taking.
Leadership style, occupational perception and organizational citizenship behavior in the Arab education system in Israel
Authors: Arar Khalid , Abu Nasra Muhammed
Published: January 2019

Purpose

The field of educational systems has witnessed an increase in studies of organizational citizenship behavior (OCB) as it contributes to the effectiveness and success of schools and achieving their objectives and goals. The purpose of this paper is to examine the relationships between principals’ leadership style, occupational perceptions and OCB.

Design/methodology/approach

The research hypothesis holds that the leadership style (transformational or transactional) have a direct and indirect effect on OCB (through occupation perception). These hypotheses have been tested on data collected from 620 Arab Israeli teachers.

Findings

The results reveal that: transformational and transactional leadership have no direct effect on OCB, an indirect effect of occupational perception on the relationship between transformational leadership and OCB, occupational perception did not mediate the effect between transactional leadership and OCB.

Originality/value

The results of the study contribute to the understanding of the way leadership style and OCB interact in schools, and the importance of teachers’ occupational perception in explaining this relationship. Future research should further investigate the teachers’ occupational perceptions and its effect on their performance as little research has been conducted to date.
Of time and the city: curating urban fragments for the purposes of place marketing
Authors: Warnaby Gary
Published: January 2019

Purpose

This paper aims to analyse the place marketing potential of historic urban “fragments”, with particular reference to old corporate identity symbols still extant in urban space.

Design/methodology/approach

Following a discussion of theoretical context, specifically incorporating spatial semiotics and psychogeography, the paper constitutes an interpretive account of a “tour” around the city of Manchester, UK, apprehending and discussing various historic corporate identity fragments still visible in the city.

Findings

Historic corporate identity fragments are identified and outlined, and issues arising from their continued existence, in terms of, for example, what constitutes heritage, and how this heritage can be used for the creation of urban distinctiveness (or genius loci) for the purposes of place marketing/branding are discussed.

Originality/value

The potential of heritage to be incorporated into the “representation work” of those responsible for urban management/marketing is highlighted, along with the need for such heritage fragments to be “curated”, if their full potential in this regard is to be realised.
‘The SEND Code of Practice has given me clout’: a phenomenological study illustrating how SENCos managed the introduction of the SEND reforms
Authors: Curran Helen
Published: January 2019

The introduction of the Special Educational Needs and Disabilities (SEND) reforms were hailed in 2014, by the then Government, as the most significant change to SEND policy for 30 years. Despite the changes introduced, the 2015 Code continued to place responsibility for the co‐ordination of provision for children with special educational needs within the remit of the SENCo. This article forms part of a wider study which examined the role of the SENCo at this time of significant reform; the study aimed to understand the role of the SENCo as a policy actor tasked with policy implementation, as well as their perceptions of the impact during the first year of reform. This article discusses the themes that arose from the in‐depth semi‐structured interviews carried out with SENCo participants during 2014/2015, which explored reflections on the SENCo role, SENCo activities undertaken across the year, and how SENCos facilitated the implementation of the 2015 Code.
The Left's New Urbanism
Authors: Cruddas Jon
Published: January 2019

The idea of suburbia, or the suburban, or the suburbs, can imply a number of different things. Suburbia suggests a physical place, in general the outskirts of a city or large town; suburban can infer a certain lifestyle; and the idea of the suburbs is often used to identify a community or class of people who inhabit a specific territory. In politics, these terms can also retain various meanings in terms of geography, culture or community. Alongside the ideas of the urban or the rural, they are often used to debate questions of political strategy and shifting electoral coalitions. In this article, ideas of urban and suburban places, cultures and communities are used to consider wider debate regarding future coalitions and strategy within the modern left, specifically a renewed urban politics that can be identified. This new ‘urbanism’ suggests a geographical realignment—partly on cultural or lifestyle grounds—which is significant within an overall attempt to redefine the ‘base’ of the left in terms of class and community. This article considers these issues with reference to what historically has been described as the ‘Progressive Dilemma’.
Public Meets Private: Conversations Between Coca‐Cola and the CDC
Authors: MAANI HESSARI NASON , RUSKIN GARY , McKEE MARTIN , STUCKLER DAVID
Published: January 2019

Policy Points

There is growing understanding of how manufacturers of harmful products influence health policy. The strategies, approaches, and influences from such manufacturers that are detrimental to health have been termed the “corporate” or “commercial” determinants of health. However, while partnerships with the tobacco industry are clearly unacceptable for public health organizations, ties to other industries continue to be pursued.

Such partnerships may influence health organizations in a number of ways detrimental to population health. However, with the exception of tobacco industry tactics as revealed by internal documents, we know relatively little about how this influence operates.

This article uses emails between the Coca‐Cola Company and the Centers for Disease Control and Prevention, which we obtained through Freedom of Information Act requests, to explore the nature of corporate influence, conflicts of interest, and lobbying “in their own words,” and highlights the need for greater transparency and clearer policies on engaging with such industries.

Context

There is a continuing debate about the appropriateness of contacts between manufacturers of some harmful products and health researchers, as well as practitioners and policymakers. Some argue that such contacts may be a means of exerting undue influence, while others present them as an opportunity to pursue shared health goals. This article examines interactions between the Centers for Disease Control and Prevention (CDC) and the Coca‐Cola Company (Coca‐Cola) as revealed by communications obtained through Freedom of Information Act (FOIA) requests.

Methods

We sent 10 US FOIA requests in 2016/2017 for communications between employees at the CDC and Coca‐Cola. We then performed a thematic content analysis of the documents provided.

Findings

Of our 10 FOIA requests, 3 requests are still pending (at the time of this publication); 5 were rejected as too broad or because no records were found; and 3 returned 295 pages from 86 emails. The CDC withheld 102 pages to “protect commercial or financial information which is privileged or confidential.” The returned emails demonstrate three main themes in Coca‐Cola's contact with CDC employees: to gain and expand access, to lobby, and to shift attention and blame away from sugar‐sweetened beverages.

Conclusions

The emails we obtained using FOIA requests reveal efforts by Coca‐Cola to lobby the CDC to advance corporate objectives rather than health, including to influence the World Health Organization. Our findings provide a rare example of the ways in which corporate interests attempt to influence public health practitioners “in their own words,” and they demonstrate a need for clearer policies on avoiding partnerships with manufacturers of harmful products.
Contemporary issues in the surgical management of pancreatic neuroendocrine tumours
Authors: Sham Jonathan G. , Gage Michele M. , He Jin
Published: January 2019

Pancreatic neuroendocrine tumours (PNET) are relatively rare entities, accounting for 1–2 per cent of pancreatic neoplasms. However, rates of diagnosis have recently increased, in part due to incidental discovery on the widespread use of cross‐sectional imaging. While general consensus exists regarding the treatment of large and/or functional PNET, the management of smaller (<2 cm) asymptomatic lesions is less clear. Recent updates in staging guidelines have improved classification of high‐ and low‐risk tumours, and additional genetic analysis (e.g. Death domain‐associated protein 6 Gene, Alpha Thalassemia/Mental Retardation Syndrome X‐Linked Gene) offers the possibility of enhanced risk stratification to further guide surgical management. In patients who do ultimately require pancreatectomy, the role of minimally‐invasive surgery (laparoscopic or robotic) continues to expand.
Putting a price on drugs: An economic sociological study of price formation in illegal drug markets
Authors: Moeller Kim , Sandberg Sveinung
Published: January 2019

Prices in illegal drug markets are difficult to predict. Based on qualitative interviews with 68 incarcerated drug dealers in Norway, we explore dealers’ perspectives on fair prices and the processes that influence their pricing decisions. Synthesized through economic sociology, we draw on perspectives from traditions as different as behavioral economics and cultural analysis to demonstrate how participants in illicit drug distribution base their pricing decisions on institutional context, social networks, and drug market cultures. We find that dealers take institutional constraints into consideration and search for niches with high earnings and low risks. The use of transactions embedded in social networks promotes a trusting form of governance, which enables strategic network management and expedient distribution but also uncompetitive pricing. Finally, dealers’ pricing decisions are embedded in three different cultures narratives: business, friendship, and street cultural stories, with widely varying implications for prices. Our findings demonstrate how an economic sociology of illicit drug distribution can extend insights from behavioral economics and cultural studies into a coherent criminology of illegal drug markets.
A new species of Macrophya Dahlbom (Hymenoptera: Tenthredinidae) with a key to species of the Macrophya coxalis group from China
Authors: Li Ze‐Jian , Liu Meng‐Meng , Wei Mei‐Cai
Published: January 2019

A new species, Macrophyra pseudocoxalis Li, Liu & Wei, sp. nov., of the genus Macrophya Dahlbom (Hymenptera: Tenthredinidae) from China is described. A key to known Chinese species of the Macrophya coxalis group is provided. The type specimens of the new species are deposited in the Lishui Academy of Forestry, Lishui, Zhejiang, China.
Review and audit of the post‐surgical MRI breast: Pictorial essay
Authors: Muir Tracey , Ebrahim Lamya , Wylie Elizabeth , Taylor Donna
Published: January 2019

Audit of contrast‐enhanced breast MRI performed over a 3‐year period in a single institution to describe and summarise the changes seen after surgery and radiation therapy for primary breast cancer, breast augmentation and oncoplastic surgery. Seventy women were identified and reviewed (100 breast MRIs in total). The most common change seen was haemosiderin deposition. The early changes of skin thickening, oedema, seroma and background parenchymal enhancement decreased with time leaving residual breast shrinkage, haemosiderin/calcification and architectural distortion due to fibrosis and scarring.
Usefulness of marker‐assisted selection to improve maize for increased resistance to Sesamia nonagrioides attack with no detrimental effect on yield
Authors: Samayoa Luis F. , Butrón Ana , Malvar Rosa A.
Published: January 2019

Two decades of investigations on maize resistance to Mediterranean corn borer (Sesamia nonagrioides Lefebvre; MCB) have shown that breeding for increased resistance to stem tunnelling by MCB often resulted in reduced yield because significant genetic correlation between both traits exists in some backgrounds. Unlike phenotypic selection, marker‐assisted selection (MAS) could differentiate markers linked only to one trait from those linked simultaneously to yield potential and susceptibility to the pest. In the current study, the suitability of MAS for improving resistance to stem tunnelling without adverse effects on yield has been tested. The unfavourable genetic relationship between yield potential and susceptibility could be overcome using MAS. Gains obtained using MAS were weak, because genetic variance explained by the quantitative trait loci (QTL) was low but results encourage us to persevere in using marker information for simultaneous improvement of resistance and yield especially if genome‐wide approaches are applied. Approaches to detect QTL are widely used, but studies on the suitability of markers linked to QTL for performing MAS have been mostly neglected.
Identification and characterisation of the tomato parthenocarpic mutant high fruit set under stress (hfs) exhibiting high productivity under heat and salt stress
Authors: Meco Victoriano , Egea Isabel , Albaladejo Irene , Campos Juan F. , Morales Belen , Ortíz‐Atienza Ana , Capel Carmen , Angosto Trinidad , Bolarín María C. , Flores Francisco B.
Published: January 2019

Pollination and therefore fruit set in tomato (Solanum lycopersicum) is very sensitive to temperature. Parthenocarpy can be a very useful trait in tomato breeding in sustainable agriculture faced with global warming. Within a collection of Moneymaker tomato mutants a monogenic and recessive mutant with high fruit number was identified in heat stress conditions and named high fruit set under stress (hfs). No morphological alterations in vegetative and reproductive organs were observed except the bigger size of ovary. hfs is parthenocarpic, pollination not being required for fruit set, although this trait was not absolute since it produced some under‐seeded fruit. When plants were grown under extreme temperatures (higher than 35°C), hfs exhibits higher fruit yield than wild‐type (WT) due to increased fruit number. Another very interesting characteristic of hfs is its improved fruit quality under heat stress, exhibiting a better sweetness/acidity balance than WT. Interestingly, hfs was also tolerant to the combination of heat and salt stress, and the positive effect on production was due to both components of yield, fruit number and fruit weight. The generation of mostly seedless fruit and the high productivity and fruit quality under extreme temperatures make hfs a very interesting mutant to obtain new breeding high‐yield lines in adverse environmental conditions.