bluuebunny/crossref_metadata_2025 huggingface dataset:
atrB-Associated Fludioxonil Resistance in Botrytis fragariae Not Linked to Mutations in Transcription Factor mrr1
Authors: Hu Meng-Jun , Cosseboom Scott , Schnabel Guido
Published: December 2018

Resistance to fludioxonil in Botrytis cinerea and B. fragariae was previously found to be linked to either overexpression of the drug efflux pump atrB activated by mutations in transcription factor mrr1 or to mutations in the osmoregulation gene os1. In the present study, isolates of B. cinerea, Botrytis group S, or B. fragariae collected from strawberry fields in the United States were resistant to fludioxonil with half-maximal effective concentration values ranging from 0.04 to 0.43 µg/ml for B. cinerea, 0.03 to 1.03 µg/ml for Botrytis group S, and 0.28 to 3.48 µg/ml for B. fragariae. Analyses of mrr1 sequences revealed various mutations linked to fludioxonil resistance in B. cinerea and Botrytis group S isolates. However, no mutations in mrr1 correlated with atrB overexpression-mediated resistance in B. fragariae isolates. Neither nucleotide variations in the 1,370-bp upstream region of atrB nor increased atrB copy numbers could explain the atrB overexpression in these B. fragariae isolates. Mutations in os1 conferred resistance to iprodione in B. cinerea and Botrytis group S isolates; none correlated with resistance to fludioxonil in B. fragariae. In contrast to European isolates, U.S. B. fragariae isolates contained a 3-bp insertion in the coding region of os1. These isolates were more sensitive to osmotic stress but it is unclear whether the insertion is responsible for this phenotype. Our findings suggest that atrB overexpression-associated fludioxonil resistance is an across-species mechanism of resistance to fludioxonil that can be induced by mutations in mrr1 and other, still-unknown mechanisms.
Role of Vacuum-Assisted Closure in the Management of Crohn Anal Fistulas
Authors: Hermann Jacek , Banasiewicz Tomasz , Kołodziejczak Barbara
Published: December 2018

BACKGROUND:

Patients with Crohn disease–related anal fistulas are treated with debridement of fistulous tracts and the placement of noncutting setons (NCSs). However, to reduce the high recurrence rate, there is still a need to develop more effective treatment methods.

OBJECTIVE:

To compare NCS with vacuum-assisted closure (VAC) treatment.

METHODS:

Medical records of 47 patients with Crohn anal fistulas were retrospectively evaluated. They were divided into two groups (I, VAC; II, NCS), consisting of 24 and 23 patients, respectively. The fistulas in the former group were applied with VAC, whereas NCSs were placed in the latter group. Fistula healing was evaluated with the Fistula Drainage Assessment classification, Perianal Disease Activity Index, and the van Assche MRI-Based Score.

RESULTS:

There was a significant difference (P = .006) between the groups; closure of all fistulas at 6 months after treatment was achieved in 18 patients (75%) from group 1, compared with 8 patients (35%) from group 2. Partial response occurred in five patients (21%) from group 1 and in five patients (22%) from group 2. Closure of fistulous tracts was visualized via MRI in nine patients (37.50%) from group 1, more than twice as many patients as from group 2.

CONCLUSIONS:

Because preliminary results of the study showed a high rate of closure after application of VAC to Crohn anal fistulas, this method might be considered a novel sphincter-saving procedure.
Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy
Authors: Hartmann Felix J. , Babdor Joel , Gherardini Pier Federico , Amir El-Ad D. , Jones Kyle , Sahaf Bita , Marquez Diana M. , Krutzik Peter , O’Donnell Erika , Sigal Natalia , Maecker Holden T. , Meyer Everett , Spitzer Matthew H. , Bendall Sean C.
Published: December 2018

The success of immunotherapy has led to a myriad of new clinical trials. Connected to these trials are efforts to discover biomarkers providing mechanistic insight and predictive signatures for personalization. Still, the plethora of immune monitoring technologies can face investigator bias, missing unanticipated cellular responses in limited clinical material. We here present a mass cytometry workflow for standardized, systems-level biomarker discovery in immunotherapy trials. To broadly enumerate human immune cell identity and activity, we established and extensively assessed a reference panel of 33 antibodies to cover major cell subsets, simultaneously quantifying activation and immune checkpoint molecules in a single assay. The resulting assay enumerated ≥ 98% of peripheral immune cells with ≥ 4 positively identifying antigens. Robustness and reproducibility were demonstrated on multiple samples types, across research centers and by orthogonal measurements. Using automated analysis, we monitored complex immune dynamics, identifying signatures in bone-marrow transplantation associated graft-versus-host disease. This validated and available workflow ensures comprehensive immunophenotypic analysis, data comparability and will accelerate biomarker discovery in immunomodulatory therapeutics.
High-dimensional characterization of IL-10 production and IL-10 dependent regulation during primary gammaherpesvirus infection
Authors: Kimball Abigail K. , Oko Lauren M. , Kaspar Rachael E. , van Dyk Linda F. , Clambey Eric T.
Published: December 2018

Interleukin (IL)-10 is a potent immunomodulatory cytokine produced by multiple cell types to restrain immune activation. Many herpesviruses use the IL-10 pathway to facilitate infection, but how endogenous IL-10 is regulated during primary infection in vivo remains poorly characterized. Here, we infected mice with murine gammaherpesvirus 68 (γHV68) and analyzed the production, and genetic contribution, of IL-10 using mass cytometry (cytometry by time-of-flight,CyTOF) analysis. γHV68 infection elicited a breadth of effector CD4 T cells in the lungs of acutely infected mice, including a highly activated effector subset that co-expressed IFNγ, TNFα, and IL-10. By using IL-10 green fluorescent protein (gfp) transcriptional reporter mice, we identified that IL-10 was primarily expressed within CD4 T cells during acute infection in the lungs. IL10gfp expressing CD4 T cells were highly proliferative and characterized by the expression of multiple co-inhibitory receptors including PD-1 and LAG-3. When we analyzed acute γHV68 infection of IL-10 deficient mice, we found that IL-10 limits the frequency of both myeloid and effector CD4 T cell subsets in the infected lung, with minimal changes at a distant mucosal site. These data emphasize the unique insights that high-dimensional analysis can afford in investigating antiviral immunity, and provide new insights into the breadth, phenotype and function of IL-10 expressing effector CD4 T cells during acute virus infection.
Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set
Authors: Zhao Zhirong , Huang Guohe , Wang Mingyuan , Zhou Nan , He Shishi , Dang Chenyuan , Wang Jiawen , Zheng Maosheng
Published: December 2018

Complete ammonia oxidizing bacteria (CAOB) have been recognized as a new member of ammonia-oxidizing microorganisms (AOMs) due to its single-step nitrification capability. However, the abundance and diversity of CAOB in environmental ecosystems were still far from known owing to the lack of specific molecular marker. Herein, a universal primer set specifically targeting the both clades of CAOBamoAgene with high specificity and coverage was successfully designed. Intriguingly, real-time quantitative PCR tests revealed that CAOB were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that clade A existed in all the five types of ecosystems, while clade B were only detected in soil and sediment samples. Four sub-clusters were further classified within clade A, in whichN. nitrosacluster dominated CAOBamoAin activated sludge samples while the new recognized soil cluster was the primary constitute in soils. Moreover, the niche specialization between different CAOB species and the environmental conditions were supposed to be the primary driven force to shape the diversity and community of CAOB. This study provided a strong evidence in support of the ubiquities and high abundances of CAOB in various environmental ecosystems and highlighted the significance of including CAOB as the new member of AOMs to re-evaluate the biogeochemical nitrogen cycle.
Man against machine: Do fungal fruitbodies and eDNA give similar biodiversity assessments across broad environmental gradients?
Authors: Frøslev Tobias Guldberg , Kjøller Rasmus , Bruun Hans Henrik , Ejrnæs Rasmus , Hansen Anders Johannes , Læssøe Thomas , Heilmann-Clausen Jacob
Published: December 2018

The majority of Earths biodiversity is unknown. This is particularly true for the vast part of soil biodiversity, which rarely can be observed directly. Metabarcoding of DNA extracted from the environment (eDNA) has become state-of-the-art in assessing soil biodiversity. Also for fungal community profiling eDNA is seen as an attractive alternative to classical surveying based on fruitbodies. However, it is unknown whether eDNA-metabarcoding provides a representative sample of fungal diversity and census of threatened species. Therefore conservation planning and assessment are still based on fruitbody inventories. Based on a dataset of unprecedented width and depth, representing both soil eDNA-metabarcoding and expert inventorying of fungal fruitbodies, we document for the first time the validity of eDNA as practical inventory method and measure of conservation value for fungi. Fruitbody data identified fewer species in total and per site, and had larger variance in site richness. Focusing on macrofungi – the class Agaricomycetes, and in turn the order Agaricales – metrics of total richness and compositional similarity converged between the methods. eDNA was suboptimal for recording the non-soil dwelling fungi. β-diversity was similar between methods, but more variation in community composition could be explained by environmental predictors in eDNA data. The fruitbody survey was slightly better in finding red-listed species. We find a better correspondence between biodiversity indices derived from fungal fruitbodies and DNA-based approaches than indicated in earlier studies. We argue that (historical) fungal community data based on fruitbody forays – with careful selection of taxonomic groups – may be interpreted together with modern DNA-based approaches.
Synergy and remarkable specificity of antimicrobial peptides in vivo using a systematic knockout approach
Authors: Hanson Mark Austin , Dostalova Anna , Ceroni Camilla , Poidevin Mickael , Kondo Shu , Lemaitre Bruno
Published: December 2018

Antimicrobial peptides (AMPs) are host-encoded antibiotics that combat invading microorganisms. These short, cationic peptides have been implicated in many biological processes, primarily involving innate immunity. In vitro studies have shown AMPs kill bacteria and fungi at physiological concentrations, but little validation has been done in vivo. We utilised CRISPR gene editing to delete all known immune inducible AMPs of Drosophila, namely: 4 Attacins, 4 Cecropins, 2 Diptericins, Drosocin, Drosomycin, Metchnikowin and Defensin. Using individual and multiple knockouts, including flies lacking all 14 AMP genes, we characterize the in vivo function of individual and groups of AMPs against diverse bacterial and fungal pathogens. We found that Drosophila AMPs act primarily against Gram-negative bacteria and fungi, acting either additively or synergistically. We also describe remarkable specificity wherein certain AMPs contribute the bulk of microbicidal activity against specific pathogens, providing functional demonstrations of highly specific AMP-pathogen interactions in an in vivo setting.
SVIM: Structural Variant Identification using Mapped Long Reads
Authors: Heller David , Vingron Martin
Published: December 2018

Motivation

Structural variants are defined as genomic variants larger than 50bp. They have been shown to affect more bases in any given genome than SNPs or small indels. Additionally, they have great impact on human phenotype and diversity and have been linked to numerous diseases. Due to their size and association with repeats, they are difficult to detect by shotgun sequencing, especially when based on short reads. Long read, single molecule sequencing technologies like those offered by Pacific Biosciences or Oxford Nanopore Technologies produce reads with a length of several thousand base pairs. Despite the higher error rate and sequencing cost, long read sequencing offers many advantages for the detection of structural variants. Yet, available software tools still do not fully exploit the possibilities.

Results

We present SVIM, a tool for the sensitive detection and precise characterization of structural variants from long read data. SVIM consists of three components for the collection, clustering and combination of structural variant signatures from read alignments. It discriminates five different variant classes including similar types, such as tandem and interspersed duplications and novel element insertions. SVIM is unique in its capability of extracting both the genomic origin and destination of duplications. It compares favorably with existing tools in evaluations on simulated data and real datasets from PacBio and Nanopore sequencing machines.

Availability and implementation

The source code and executables of SVIM are available on Github: github.com/eldariont/svim. SVIM has been implemented in Python 3 and published on bioconda and the Python Package Index.

Contact

heller_d@molgen.mpg.de
Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinson’s Disease in Mouse Midbrain
Authors: Kochmanski Joseph , VanOeveren Sarah E. , Bernstein Alison I.
Published: December 2018

Human and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson’s disease (PD). Despite previous work showing a link between developmental dieldrin exposure and increased neuronal susceptibility to MPTP toxicity in male C57BL/6 mice, the mechanism mediating this effect has not been identified. Here, we tested the hypothesis that developmental exposure to dieldrin increases neuronal susceptibility via genome-wide changes in DNA methylation. Starting at 8 weeks of age and prior to mating, female C57BL/6 mice were exposed to 0.3 mg/kg dieldrin by feeding (every 3 days) throughout breeding, gestation, and lactation. At 12 weeks of age, pups were sacrificed and midbrains were dissected. DNA was isolated and dieldrin-related changes in DNA methylation were assessed via reduced representation bisulfite sequencing (RRBS). We identified significant, sex-specific differentially methylated CpGs (DMCs) and regions (DMRs) by developmental dieldrin exposure (FDR<0.05), including DMCs at the Nr4a2 and Lmx1b genes, which are involved in dopaminergic neuron development and maintenance. Developmental dieldrin exposure had distinct effects on the male and female epigenome. Furthermore, a separate set of changes in DNA methylation was identified after adult exposure to dieldrin, suggesting that adult and developmental dieldrin toxicity may not act through a shared epigenetic mechanism. Together, our data suggest that developmental dieldrin exposure establishes sex-specific poised epigenetic states early in life. These poised epigenomes may mediate sensitivity to additional environmental stimuli and contribute to the development of late-life neurodegenerative disease, including PD.
Manganese influx and expression of ZIP8 is essential in primary myoblasts and contributes to activation of SOD2
Authors: Gordon Shellaina J. V. , Fenker Daniel E. , Vest Katherine E. , Padilla-Benavides Teresita
Published: December 2018

Trace elements such as copper (Cu), zinc (Zn), iron (Fe), and manganese (Mn) are enzyme cofactors and second messengers in cell signaling. Trace elements are emerging as key regulators of differentiation and development of mammalian tissues including blood, brain, and skeletal muscle. We previously reported an influx of Cu and dynamic expression of various metal transporters during differentiation of skeletal muscle cells. Here, we demonstrate that during differentiation of skeletal myoblasts an increase of additional trace elements such as Mn, Fe and Zn occurs. Interestingly the Mn increase is concomitant with increased Mn-dependent SOD2 levels. To better understand the Mn import pathway in skeletal muscle cells, we probed the functional relevance of the closely related proteins ZIP8 and ZIP14, which are implicated in Zn, Mn, and Fe transport. Partial depletion of ZIP8 severely impaired growth of myoblasts and led to cell death under differentiation conditions, indicating that ZIP8-mediated metal transport is essential in skeletal muscle cells. Moreover, knockdown ofZip8impaired activity of the Mn-dependent SOD2. Growth defects were partially rescued by Mn supplementation to the medium, suggesting additional functions for ZIP8 in the skeletal muscle lineage. Knockdown ofZip14, on the other hand, had only a mild effect on myotube size, consistent with a role for ZIP14 in muscle hypertrophy. This is the first report on the functional relevance of two members of the ZIP family of metal transporters in the skeletal muscle lineage, and further supports the paradigm that trace metal transporters are critical modulators of mammalian tissue development.
Chicory demonstrates substantial water uptake from below 2 m depth, but still did not escape topsoil drought
Authors: Rasmussen Camilla Ruø , Thorup-Kristensen Kristian , Dresbøll Dorte Bodin
Published: December 2018

Aims

Deep-rooted agricultural crops can potentially utilize deep water pools and thus reduce periods where growth is water limited. Chicory (Cichorium intybusL.) is known to be deep-rooted, but the contribution of deep roots to water uptake under well-watered and drought conditions by the deep root system has not been studied. The aim of this study was to investigate whether chicory could reach 3 m depth within a growing season and demonstrate significant water uptake from the deeper part of the root zone.

Methods

We tested if chicory exposed to either topsoil drought or resource competition from the shallow-rooted species ryegrass(Lolium perenne L.)and black medic (Medicago lupulina L.)would increase deep water uptake in compensation for reduced topsoil water uptake. We grew chicory in 4 m deep soil filled rhizotrons and found that the roots reached 3 m depth within a growing season.

Results

Water uptake from below 1.7 m depth in 2016 and 2.3 m depth in 2017 contributed significantly to chicory water use. However, neither drought nor intercropping increased the deep water uptake.

Conclusion

Chicory benefits from being deep-rooted during drought events, yet deep water uptake cannot compensate for the reduced topsoil water uptake during drought.
Inhibitory microcircuits for top-down plasticity of sensory representations
Authors: Wilmes Katharina Anna , Clopath Claudia
Published: December 2018

Humans and animals are remarkable at detecting stimuli that predict rewards. While the underlying neural mechanisms are unknown, reward influences plasticity of sensory representations in early sensory areas. The underlying changes in excitatory and inhibitory circuitry are however unclear. Recently, experimental findings suggest that the inhibitory circuits can regulate learning. In addition, the inhibitory neurons in superficial layers are highly modulated by diverse long-range inputs, including reward signals. We, therefore, hypothesise that plasticity of interneuron circuits plays a major role in adjusting stimulus representations. We investigate how top-down modulation by rewards can interact with local excitatory and inhibitory plasticity to induce long-lasting changes in sensory circuitry. Using a computational model of layer 2/3 primary visual cortex, we demonstrate how interneuron networks can store information about the rewarded stimulus to instruct long-term changes in excitatory connectivity in the absence of further reward. In our model, stimulus-tuned somatostatin-positive interneurons (SSTs) develop strong connections to parvalbumin-positive interneurons (PVs) during reward presentation such that they selectively disinhibit the pyramidal layer henceforth. This triggers plasticity in the excitatory neurons, which leads to increased stimulus representation. We make specific testable predictions in terms of the activity of different neuron types. We finally show that this two-stage model allows for translation invariance of the learned representation.
Cryo-EM sample preparation method for extremely low concentration liposomes
Authors: Tonggu Lige , Wang Liguo
Published: December 2018

Liposomes are widely used as delivery systems in pharmaceutical, cosmetics and food industries, as well as a system for structural and functional study of membrane proteins. To accurately characterize liposomes, cryo-Electron Microscopy (cryo-EM) has been employed as it is the most precise and direct method to determine liposome lamellarity, size, shape and ultrastructure. However, its use is limited by the number of liposomes that can be trapped in the thin layer of ice that spans holes in the perforated carbon film on EM grids. We report a long-incubation method for increasing the density of liposomes in holes. By increasing the incubation time, high liposome density was achieved even with extremely dilute (in the nanomolar range) liposome solutions. This long-incubation method has been successfully employed to study the structure of an ion channel reconstituted into liposomes. This method will also be useful for preparing other biological macromolecules / assemblies for structural studies using cryo-EM.
Super-resolution modularity analysis shows polyhedral caveolin-1 oligomers combine to form scaffolds and caveolae
Authors: Khater Ismail M. , Liu Qian , Chou Keng C. , Hamarneh Ghassan , Nabi Ivan Robert
Published: December 2018

Caveolin-1 (Cav1), the coat protein for caveolae, also forms non-caveolar Cav1 scaffolds. Single molecule Cav1 super-resolution microscopy analysis previously identified caveolae and three distinct scaffold domains: smaller S1A and S2B scaffolds and larger hemispherical S2 scaffolds. Application here of network modularity analysis of SMLM data for endogenous Cav1 labeling in HeLa cells shows that small scaffolds combine to form larger scaffolds and caveolae. We find modules within Cav1 blobs by maximizing the intra-connectivity between Cav1 molecules within a module and minimizing the inter-connectivity between Cav1 molecules across modules, which is achieved via spectral decomposition of the localizations adjacency matrix. Features of modules are then matched with intact blobs to find the similarity between the module-blob pairs of group centers. Our results show that smaller S1A and S1B scaffolds are made up of small polygons, that S1B scaffolds correspond to S1A scaffold dimers and that caveolae and hemi-spherical S2 scaffolds are complex, modular structures formed from S1B and S1A scaffolds, respectively. Polyhedral interactions of Cav1 oligomers therefore leads progressively to the formation of larger and more complex scaffold domains and the biogenesis of caveolae.
An RNA-binding region regulates CTCF clustering and chromatin looping
Authors: Hansen Anders S. , Hsieh Tsung-Han S. , Cattoglio Claudia , Pustova Iryna , Darzacq Xavier , Tjian Robert
Published: December 2018

Mammalian genomes are folded into Topologically Associating Domains (TADs), consisting of cell-type specific chromatin loops anchored by CTCF and cohesin. Since CTCF and cohesin are expressed ubiquitously, how cell-type specific CTCF-mediated loops are formed poses a paradox. Here we show RNase-sensitive CTCF self-association in vitro and that an RNA-binding region (RBR) mediates CTCF clustering in vivo. Intriguingly, deleting the RBR abolishes or impairs almost half of all chromatin loops in mouse embryonic stem cells. Disrupted loop formation correlates with abrogated clustering and diminished chromatin binding of the RBR mutant CTCF protein, which in turn results in a failure to halt cohesin-mediated extrusion. Thus, CTCF loops fall into at least 2 classes: RBR-independent and RBR-dependent loops. We suggest that evidence for distinct classes of RBR-dependent loops may provide a mechanism for establishing cell-specific CTCF loops regulated by RNAs and other RBR partner.
The topology of DNA entrapment by cohesin rings
Authors: Chapard Christophe , Jones Robert , van Oepen Till , Scheinost Johanna C , Nasmyth Kim
Published: December 2018

Cohesin entraps sister DNAs within tripartite rings created by pairwise interactions between Smc1,Smc3, and Scc1. Because the ATPase heads of Smc1 and Smc3 can interact with each other, cohesin rings in fact have the potential to form a variety of sub-compartments. Using in vivo cysteine crosslinking,we show that when Smc1 and Smc3 ATPases are engaged in the presence of ATP (E heads)cohesin rings generate a “SMC (S) compartment” between hinge and E heads and a “kleisin (K)compartment” between E heads and their associated kleisin subunit. Upon ATP hydrolysis, cohesin’s heads associate with each other in a very different mode, in which their signature motifs and their coiled coils are closely juxtaposed (J heads), creating alternative S and K compartments. We show that all four sub-compartments exist in vivo, that acetylation of Smc3 during S phase is accompanied by an increase in the ratio of J to E heads, and that sister DNAs are entrapped in J-K but not E-K compartments or in either type of S compartment.
Liquid-crystal organization of liver tissue
Authors: Morales-Navarrete Hernán , Nonaka Hidenori , Scholich André , Segovia-Miranda Fabián , de Back Walter , Meyer Kirstin , Bogorad Roman L. , Koteliansky Victor , Brusch Lutz , Kalaidzidis Yannis , Jülicher Frank , Friedrich Benjamin M. , Zerial Marino
Published: December 2018

Functional tissue architecture originates by self-assembly of distinct cell types, following tissue-specific rules of cell-cell interactions. In the liver, a structural model of the lobule was pioneered by Elias in 1949. This model, however, is in contrast with the apparent random 3D arrangement of hepatocytes. Since then, no significant progress has been made to derive the organizing principles of liver tissue. To solve this outstanding problem, we computationally reconstructed 3D tissue geometry from microscopy images and analyzed it applying soft-condensed-matter-physics concepts. Surprisingly, analysis of the spatial organization of cell polarity revealed that hepatocytes are not randomly oriented but follow a long-range liquid-crystal order. This does not depend exclusively on hepatocytes receiving instructive signals by endothelial cells as generally assumed, since silencing Integrin-ß1 disrupted both liquid-crystal order and organization of the sinusoidal network. Our results suggest that bi-directional communication between hepatocytes and sinusoids underlies the self-organization of liver tissue.
A gene expression programming model for economy growth using knowledge-based economy indicators
Authors: Ahmadi Mohsen , Taghizadeh Rahim
Published: December 2018

Purpose

The purpose of this paper is to focus on modeling economy growth with indicators of knowledge-based economy (KBE) introduced by World Bank for a case study in Iran during 1993-2013.

Design/methodology/approach

First, for grouping and reducing the number of variables, Tukey method and the principal component analysis are used. Also for modeling, 67 per cent of data is used for training in the two approaches of ARDL bounds testing and gene expression programming (GEP) and 33 per cent of them for testing the models. Then, the result models are compared with fitness function and Akaike information criteria (AIC).

Findings

The GEP model with fitness 945.7461 for training data and 954.8403 for testing data from 1000 is better than ARDL bounds testing model with fitness 335.5479 from 1000. In addition, according to model comparison tools (AIC), the GEP model has an extremely larger weight in comparison with ARDL bounds model. Therefore, the GEP model is introduced for future use in academia.

Practical implications

Knowledge and information is one of the most basic sources of wealth in economists’ sight. Thus, using KBE indicators appears essential in economic growth regarding daily progress in knowledge processes and its different theories. It is also extremely important to determine an appropriate model for KBE indicators which play a highly important role in the allocation of the economic resources of the country in an optimal manner.

Originality/value

This paper introduced a novel expression for economy growth using KBE indicators. All the data and the indicators are extracted from Word Bank service between 1993 and 2013.
Community policing and intelligence-led policing
Authors: Carter Jeremy G. , Fox Bryanna
Published: December 2018

Purpose

Despite increased scholarly inquiry regarding intelligence-led policing (ILP) and popularity among law enforcement agencies around the globe, ambiguity remains regarding the conceptual foundation and appropriate measurement of ILP. Although most scholars agree that ILP is indeed a unique policing philosophy, there is less consensus regarding the relationship between ILP and the ever-present model of community-oriented policing (COP). Consequently, there is a clear need to study the empirical distinctions and overlaps in these policing philosophies as implemented by US law enforcement agencies. The paper aims to discuss these issues.

Design/methodology/approach

Data were gleaned from the 2007 LEMAS and 2009 NIJ Intelligence surveys. A total of 227 unique police agencies in the USA are included. A series of bivariate, exploratory factor analyses and structural models are used to determine discriminatory or convergent validity across COP and ILP constructs.

Findings

The goal was to answer the question: are these two policing philosophies are being implemented as separate and distinct strategies? Results of our exploratory and structural models indicate that COP and ILP loaded on unique latent constructs. This affirms the results of the bivariate correlations, and indicates that COP and ILP have discriminant measurement validity. In other words, COP and ILP are conceptually distinct, even when implemented in police departments across the USA. Implications of these findings and suggestions for future research are discussed.

Originality/value

This is the first study to empirically test the discriminant or convergent validity of COP and ILP.
The role of stressors in altering eco‐evolutionary dynamics
Authors: Theodosiou Loukas , Hiltunen Teppo , Becks Lutz
Published: December 2018

We review and synthesize evidence from the fields of ecology, evolutionary biology and population genetics to investigate how the presence of abiotic stress can affect the feedback between ecological and evolutionary dynamics.

To obtain a better insight of how, and under what conditions, an abiotic stressor can influence eco‐evolutionary dynamics, we use a conceptual predator–prey model where the prey can rapidly evolve antipredator defences and stress resistance.

We show how abiotic stress influences eco‐evolutionary dynamics by changing the pace and in some case the potential for evolutionary change and thus the evolution‐to‐ecology link. Whether and how the abiotic stress influences this link depends on the effect on population sizes, mutation rates, the presence of gene flow and the genetic architecture underlying the traits involved.

Overall, we report ecological and population genetic mechanisms that have so far not been considered in studies on eco‐evolutionary dynamics and suggest future research directions and experiments to develop an understanding of the role of eco‐evolutionary dynamics in more complex ecological and evolutionary scenarios.

Aplain language summaryis available for this article.
Carry‐over effects of early thermal conditions on somatic and germline oxidative damages are mediated by compensatory growth in sticklebacks
Authors: Kim Sin‐Yeon , Noguera José C. , Velando Alberto
Published: December 2018

Most studies of climate change impacts focus on the effects of summer temperatures, which can immediately impact fitness of breeders, but winter temperatures are expected to have a greater impact on development and growth of animals with long‐lasting consequences. Exposure to warmer temperatures can increase cellular oxidative damage in ectotherms. Yet, it is unknown whether thermal stress during early life has prolonged effects on oxidative status during adulthood.

In an experiment using F1 fish originated from a wild three‐spined stickleback population at the southern edge of its European distribution, we examined whether experimental thermal conditions experienced in winter had carry‐over effects on oxidative status and telomere length, a marker of accumulated stress, in the soma and germline during adulthood. For this, oxidative DNA damage, enzymatic antioxidant activities and telomere length were measured three months after the termination of the temperature manipulation. In addition, we tested whether such delayed effects, if any, were due to individuals’ compensatory growth after experiencing unfavourable growth conditions in winter.

Warm acclimation during winter induced increased levels of oxidative DNA damage in muscle and sperm and increased enzymatic antioxidant defences in muscle during the breeding season. Telomere length of adult fish was not influenced by thermal conditions experienced during early life.

Winter temperature manipulation influenced fish to alter the temporal pattern of growth trajectories across the juvenile and adult stages. Fish reared in warm winter conditions grew at a slower rate than the controls during the period of temperature manipulation then accelerated body mass gain to catch up during the breeding season. Faster somatic growth during the breeding season incurred a higher cost in terms of oxidative damage in the warm‐treated individuals.

For the first time, we experimentally show the long‐lasting detrimental effects of thermal stress on and the positive link between catch‐up growth and oxidative DNA damage in the soma and germline. Winter temperature increases due to climate change can reduce fertility and survival of fish by inducing catch‐up growth. The detrimental effects of winter climate change may accumulate across generations through the pre‐mutagenic DNA damage in the germline.
Linking the vectorial capacity of multiple vectors to observed patterns of West Nile virus transmission
Authors: McMillan Joseph R. , Blakney Rebekah A. , Mead Daniel G. , Koval William T. , Coker Sarah M. , Waller Lance A. , Kitron Uriel , Vazquez‐Prokopec Gonzalo M.
Published: December 2018

Theoretical models suggest that increased vector species participation in pathogen transmission significantly increases the prevalence of vector and host infections. However, there has been a lack of empirical evidence to support this.

We linked transmission potential of multiple vector species to observed patterns of enzootic pathogen transmission by conducting longitudinal field surveillance of West Nile virus (WNv) infections in Culex spp. mosquitoes and avian host communities in the southeast U.S. We then used a temperature‐dependent vectorial capacity model as a predictor of WNv infections in mosquitoes and birds using general linear mixed effects models.

Two WNv‐competent Culex spp. mosquitoes were present in our study sites, Culex restuans Theobald during the spring and Culex quinquefasciatus Say during the summer. Empirical evidence of WNv transmission was limited exclusively to time periods when night time temperatures were suitable for accelerated within‐vector viral replication, susceptible avian hosts (i.e. hatch year birds) were abundant and Cx. quinquefasciatus was the primary Culex spp. vector in the mosquito community.

Contrary to theoretical predictions, increased presence of competent vector species through time did not significantly increase the prevalence of infections in the WNv enzootic system.

Synthesis and applications. We extend a common theoretical model to both estimate the transmission potential of a mosquito community for West Nile virus (WNv) and quantify the relative contribution of two Culex mosquito species (Culex quinquefasciatus and Culex restuans) to observed patterns of WNv in the southeast U.S. Our findings suggest that to reduce the risk of human exposure to WNv in urban environments, vector control should focus on the primary WNv vector, Cx. quinquefasciatus. Additionally, vector control may be more effective if it coincides with the onset of the avian breeding season, when most WNv amplification occurs. Moreover, our results highlight relevant knowledge gaps pertaining to WNv transmission by secondary mosquito species that coexist either in time or space with Cx. quinquefasciatus. A better understanding of secondary WNv vector species is greatly needed in order to appropriately gauge their role in pathogen transmission dynamics.
Quality of life is significantly impaired in both secretory and non‐functioning pituitary adenomas
Authors: Vega‐Beyhart Arturo , Enriquez‐Estrada Víctor M. , Bello‐Chavolla Omar Y. , Torres‐Victoria Tania R. , Martínez-Sánchez Froylan D. , López-Navarro Juan M. , Pérez-Guzmán Mireya C. , Hinojosa‐Amaya Jose M. , León‐Suárez Andrés , Espinoza‐Salazar Hector D. , Roldán‐Sarmiento Paola , Gómez-Sámano Miguel A. , Gómez-Pérez Francisco J. , Cuevas‐Ramos Daniel
Published: December 2018

Objective

To evaluate the quality of life (QoL) in patients with pituitary adenomas in comparison with healthy Mexican population QoL scores.

Design & Measurements

Cross‐sectional study using the short form 36 questionnaire (SF‐36) in 175 patients with pituitary adenomas grouped by adenoma subtype and disease activity, and compared them with the healthy Mexican population normative QoL scores.

Patients

A total of 44 patients with non‐functioning pituitary adenomas (NFPA), 48 with acromegaly, 53 with prolactinomas and 30 with Cushing disease (CD) were enrolled in this study.

Results

Mental and physical components scores (MCS & PCS) of SF‐36 questionnaire were lower in patients with active disease in all adenoma subtypes (P < 0.03). A significant negative relationship between prolactin levels and MCS (r = −0.30, P < 0.01) and PCS (r = −0.41, P < 0.01) were found in prolactinomas. Patients with CD showed 24 hours urine‐free cortisol levels negatively correlated with MCS (r = −0.43, P < 0.01) but not with PCS. No significant correlation was found between IGF‐1 ULN and QoL scores in acromegaly. NFPA patients had lower QoL scores than patients with controlled CD, acromegaly or prolactinoma (P < 0.02). Active CD and prolactinoma have lower QoL scores in comparison of NFPA (P < 0.05). Having an adenoma, secretory or non‐functioning, decrease QoL scores in comparison of results in the healthy Mexican population register. Using an adjusted‐multivariate model, we confirmed that disease activity in all secretory adenomas is an independent risk factor, reducing SF‐36 scores significantly.

Conclusion

Activity in all secretory pituitary adenomas’ patients decrease mental and physical QoL. However, independently of disease activity, secretory and NFPA significantly decrease QoL in comparison with healthy Mexican population QoL register.
Proximity to canopy mediates changes in the defensive chemistry and herbivore loads of an understory tropical shrub, Piper kelleyi
Authors: Glassmire Andrea E. , Philbin Casey , Richards Lora A. , Jeffrey Christopher S. , Snook Joshua S. , Dyer Lee A.
Published: December 2018

Phytochemical traits are a key component of plant defense theory. Chemical ecology has been biased towards studying effects of individual metabolites even though effective plant defenses are comprised of diverse mixtures of metabolites. We tested the phytochemical landscape hypothesis, positing that trophic interactions are contingent upon their spatial location across a phytochemically diverse landscape. Specifically, intraspecific phytochemical changes associated with vertical strata in forests were hypothesised to affect herbivore communities of the neotropical shrub Piper kelleyi Tepe (Piperaceae). Using a field experiment, we found that phytochemical diversity increased with canopy height, and higher levels of phytochemical diversity located near the canopy were characterised by tradeoffs between photoactive and non‐photoactive biosynthetic pathways. For understory plants closer to the ground, phytochemical diversity increased as direct light transmittance decreased, and these plants were characterised by up to 37% reductions in herbivory. Our results suggest that intraspecific phytochemical diversity structures herbivore communities across the landscape, affecting total herbivory.
Sex differences in 1‐year mortality risks in older patients experiencing a first acute heart failure hospitalization
Authors: Formiga Francesc , Moreno‐Gonzalez Rafael , Chivite David , Yun Sergi , Franco Jonathan , Ariza‐Solé Albert , Corbella Xavier
Published: December 2018

Aim

To assess whether 1‐year mortality in older patients experiencing a first admission for acute heart failure was related to sex, and to explore differential characteristics according to sex.

Methods

We reviewed the medical records of 1132 patients aged >70 years of age admitted within a 3‐year period because of a first episode of acute heart failure. We analyzed sex differences. Mortality was assessed using multivariate Cox analysis.

Results

There were 648 (57.2%) women (mean age 82.1 years) and 484 men (mean age 80.1 years). There were some differences in risk factors: women more often had hypertension, and less frequently had coronary heart disease and comorbidities (women more often had dementia, and men more often had chronic obstructive pulmonary disease, chronic kidney disease and stroke). Women were treated more frequently with spironolactone. The 1‐year all‐cause mortality rate was 30.2% (30.7% women and 29.5% men). Multivariate Cox analysis identified an association between reduced heart failure (hazard ratio [HR] 0.35, 95% confidence interval [95% CI] 0.21–0.59), hemoglobin <10 g/dL (HR 1.99, 95% CI 1.16–3.40), systolic blood pressure (HR 0.98, 95% CI 0.97–0.99), previous diagnosis of dementia (HR 2.07, 95% CI 1.12–3.85), number of chronic therapies (HR 1.12, 95% CI 1.05–1.19) and 1‐year mortality in women. In men, an association with mortality was found for low systolic blood pressure (HR 0.97, 95% CI 0.97–0.98) and higher potassium values (HR 1.42, 95% CI 1.01–2.00).

Conclusions

Among older patients hospitalized for the first acute heart failure episode, there is a slightly higher predominance of women. There are sex differences in risk factors and comorbidities. Although the mortality rate is similar, the factors associated with it according to sex are different. Geriatr Gerontol Int 2019; 19: 184–188.
Illness Perception and Job Satisfaction in Patients Suffering from Migraine Headaches: Trait Anxiety and Depressive Symptoms as Potential Mediators
Authors: Rogante Elena , Sarubbi Salvatore , Lamis Dorian A. , Canzonetta Valeria , Sparagna Alice , De Angelis Valerio , Erbuto Denise , Martelletti Paolo , Pompili Maurizio
Published: December 2018

Background and Objectives

Migraine headache is the seventh leading cause of disability worldwide causing adverse outcomes in many aspects of an individual’s life. Many psychological aspects affect chronic migraine (CM): illness perception, anxiety, depressive symptoms, and job satisfaction. This observational study aimed to examine the association among illness perception, anxiety, depressive symptoms, and job satisfaction, connected to migraine and its features.

Methods

Ninety‐eight individuals with CM treated with OnabotulinumtoxinA were recruited from the Regional Referral Headache Centre of Sant’Andrea Hospital in Rome. They completed 4 questionnaires (Brief Illness Perception Quality of Life, Enjoyment and Satisfaction Questionnaire, State‐Trait Anxiety Inventory, Beck Depression Inventory‐II) and a socio‐anamnestic form.

Results

This cross‐sectional study examined 2 mediational models. The first one demonstrated an indirect mediating effect of trait anxiety on the association between illness perception and job satisfaction (ab = −0.217, 95% CI [−0.37, −0.09]). In the second model, depressive symptoms mediated the association between illness perception and job satisfaction (ab = −0.186, 95% CI [−0.33, −0.04]).

Conclusions

In our study, levels of anxiety and depressive symptoms showed a mediational effect on the association between illness perception and job fulfillment. It is important to develop interventions aimed at improving the quality of life of individuals with CM and to increase knowledge about headache and psychological consequences.
Systemic disruption of the homeostasis of transfer RNA isopentenyltransferase causes growth and development abnormalities in Bombyx mori
Authors: Chen Y. , Bai B. , Yan H. , Wen F. , Qin D. , Jander G. , Xia Q. , Wang G.
Published: December 2018

Isopentenylation at A37 (i6A37) of some transfer RNAs (tRNAs) plays a vital role in regulating the efficiency and fidelity of protein synthesis. However, whether insects, which are well known for their highly efficient protein synthesis machinery, employ this regulatory mechanism remains uninvestigated. In the current study, a candidate tRNA isopentenyltransferase (IPT) gene with three alternative splicing isoforms (BmIPT1–BmIPT3) was identified in Bombyx mori (silkworm). Only BmIPT1 could complement a yeast mutant lacking tRNA IPT. Phylogenetic analysis showed that silkworm tRNA IPT is conserved in the Lepidoptera. BmIPT was expressed in all B. mori tissues and organs that were investigated, but was expressed at a significantly higher level in silk glands of the fourth instar compared to the first day of the fifth instar. Interestingly, BmIPT was expressed at a significantly higher level in the domesticated silkworm, B. mori, than in wild Bombyx mandarina in multiple tissues and organs. Knock‐down of BmIPT by RNA interference caused severe abnormalities in silk spinning and metamorphosis. Constitutive overexpression of BmIPT1 using a cytoplasmic actin 4 promoter in B. mori raised its messenger RNA level more than sixfold compared with nontransgenic insects and led to significant decreases in the body weight and cocoon shell ratio. Together, these results confirm the first functional tRNA IPT in insects and show that a suitable expression level of tRNA IPT is vital for silk spinning, normal growth, and metamorphosis. Thus, i6A modification at position A37 in tRNA probably plays an important role in B. mori protein synthesis.
Some Variants of Constrained Estimation in Finite Population Sampling
Authors: Ghosh Malay , Steorts Rebecca C.
Published: December 2018

This is a review article that unifies several important examples using constrained optimisation techniques. The basic tools are three simple mathematical optimisation results subject to certain constraints. Applications include calibration, benchmarking in small area estimation and imputation. A final illustration is constrained optimisation under a general divergence loss.