bluuebunny/crossref_metadata_2025_split huggingface dataset:
IMMUNOLOGICAL INVESTIGATIONS OF HHV-6 U12 AND U51 ENCODED PROTEINS INVOLVEMENT IN AUTOIMMUNE THYROIDITIS DEVELOPMENT
Authors: Sultanova Alina , Cistjakovs Maksims , Sokolovska Liba , Cunskis Egils , Murovska Modra 
Published: July 2020

AbstractHuman herpesvirus 6 (HHV-6) is a human pathogen with a wide cell tropism and many immunomodulating properties. HHV-6 has been linked to the development of multiple diseases, among them – autoimmune. Conflicting evidence implicates HHV-6 in autoimmune thyroiditis (AIT). HHV-6 contains two genes (U12 and U51) that encode putative homologues of human G-protein-coupled receptors (GPCR) like CCR1, CCR3 and CCR5. It has been shown that proteins encoded by HHV-6 U12 and U51 genes can be expressed on the surface of epithelial and some peripheral blood mononuclear cells populations, which makes them a potential cause for evoking autoimmunity.The aim of this study was to identify potentially immunogenic synthetic peptides derived from HHV-6 U12 and U51 amino acid sequences and to find evidences of the possible involvement of these proteins in AIT development. 62 AIT patients positive for HHV-6 infection were enrolled in this study. 30 different synthetic peptides designed from HHV-6 U12 and U51 proteins’ amino acid sequences, as well as, recombinant human CCR1, CCR3 and CCR5 proteins were used for suspension multiplex immunological assay (SMIA) to detect specific IgG, and IgM antibodies.HHV-6 peptide specific IgG and IgM antibodies were found in patient’s samples, with higher signals for IgM antibodies, which is indicative of reactivation and active HHV-6 infection. As well recombinant CCR1 and CCR5 showed high signals on IgM antibodies which is indicating on the presence of potential auto-antibodies against human G protein-coupled receptors. No cross reactivity between HHV-6 peptide specific antibodies and human recombinant CCR1, CCR3 and CCR5 was found, however, the possibility of cross-reactive autoantibodies specific for structural epitopes cannot be excluded.
Variability of an early developmental cell population underlies stochastic laterality defects
Authors: Moreno-Ayala Roberto , Olivares-Chauvet Pedro , Schäfer Ronny , Junker Jan Philipp 
Published: July 2020

SummaryEmbryonic development seemingly proceeds with almost perfect precision. However, it is largely unknown how much underlying microscopic variability is compatible with normal development. Here, we quantified embryo-to-embryo variability in vertebrate development, by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub-population of the endoderm, the dorsal forerunner cells (which later form the left-right organizer), exhibits significantly more embryo-to-embryo variation than the rest of the endoderm. We found that, when incubated at elevated temperature, the frequency of left-right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells. Furthermore, we observed that these fluctuations have a large stochastic component among fish of the same genetic background. Hence, a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be associated with maternal effects in the specification of the dorsal forerunner cells.
Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut
Authors: Zhi Hui , Behnsen Judith , Aron Allegra , Subramanian Vivekanandan , Liu Janet Z. , Gerner Romana R. , Petras Daniel , Green Keith D. , Price Sarah L. , Camacho Jose , Hillman Hannah , Tjokrosurjo Joshua , Montaldo Nicola P. , Hoover Evelyn , Treacy-Abarca Sean , Gilston Benjamin A. , Skaar Eric P. , Chazin Walter J. , Garneau-Tsodikova Sylvie , Lawrenz Matthew B. , Perry Robert D. , Nuccio Sean-Paul , Dorrestein Pieter C. , Raffatellu Manuela 
Published: July 2020

ABSTRACTZinc is an essential cofactor for bacterial metabolism, and manyEnterobacteriaceaeexpress the zinc transporters ZnuABC and ZupT to acquire this metal in the host. Unexpectedly, the probiotic bacteriumEscherichia coliNissle 1917 exhibited appreciable growth in zinc-limited media even when these transporters were deleted. By utilizingin vitroandin vivostudies, as well as native spray metal infusion mass spectrometry and ion identity molecular networking, we discovered that Nissle utilizes yersiniabactin as a zincophore. Indeed, yersiniabactin enables Nissle to scavenge zinc in zinc-limited media, to resist calprotectin-mediated zinc sequestration, and to thrive in the inflamed gut. Moreover, we discovered that yersiniabactin’s affinity for iron or zinc changes in a pH-dependent manner, with higher affinity for zinc as the pH increased. Altogether, we demonstrate that siderophore metal affinity can be influenced by the local environment and reveal a mechanism of zinc acquisition available to many commensal and pathogenicEnterobacteriaceae.
Demographic history impacts stratification in polygenic scores
Authors: Zaidi Arslan A. , Mathieson Iain 
Published: July 2020

AbstractLarge genome-wide association studies (GWAS) have identified many loci exhibiting small but statistically significant associations with complex traits and disease risk. However, control of population stratification continues to be a limiting factor, particularly when calculating polygenic scores where subtle biases can cumulatively lead to large errors. We simulated GWAS under realistic models of demographic history to study the effect of residual stratification in large GWAS. We show that when population structure is recent, it cannot be fully corrected using principal components based on common variants—the standard approach—because common variants are uninformative about recent demographic history. Consequently, polygenic scores calculated from such GWAS results are biased in that they recapitulate non-genetic environmental structure. Principal components calculated from rare variants or identity-by-descent segments largely correct for this structure if environmental effects are smooth. However, even these corrections are not effective for local or batch effects. While sibling-based association tests are immune to stratification, the hybrid approach of ascertaining variants in a standard GWAS and then re-estimating effect sizes in siblings reduces but does not eliminate bias. Finally, we show that rare variant burden tests are relatively robust to stratification. Our results demonstrate that the effect of population stratification on GWAS and polygenic scores depends not only on the frequencies of tested variants and the distribution of environmental effects but also on the demographic history of the population.
Multiple Capsid Protein Binding Sites Mediate Selective Packaging of the Alphavirus Genomic RNA
Authors: Brown Rebecca S. , Anastasakis Dimitrios G. , Hafner Markus , Kielian Margaret 
Published: July 2020

ABSTRACTThe alphavirus capsid protein (Cp) selectively packages genomic RNA (gRNA) into the viral nucleocapsid to produce infectious virus. Using photoactivatable ribonucleoside crosslinking and an innovative biotinylated Cp retrieval method, we comprehensively defined binding sites for Semliki Forest virus (SFV) Cp on the gRNA. While data in infected cells demonstrated Cp binding to the proposed genome packaging signal (PS), mutagenesis experiments showed that PS was not required for production of infectious SFV or Chikungunya virus. Instead, we identified multiple novel Cp binding sites that were enriched on gRNA-specific regions and promoted infectious SFV production and gRNA packaging. Comparisons of binding sites in cytoplasmic vs. viral nucleocapsids demonstrated that budding caused discrete changes in Cp-gRNA interactions. Notably, Cp’s top binding site was maintained throughout virus assembly, and specifically bound and assembled with Cp into core-like particles in vitro. Together our data suggest a new model for selective alphavirus genome recognition and assembly.
SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB
Authors: Neufeldt Christopher J. , Cerikan Berati , Cortese Mirko , Frankish Jamie , Lee Ji-Young , Plociennikowska Agnieszka , Heigwer Florian , Joecks Sebastian , Burkart Sandy S. , Zander David Y. , Gendarme Mathieu , El Debs Bachir , Halama Niels , Merle Uta , Boutros Michael , Binder Marco , Bartenschlager Ralf 
Published: July 2020

AbstractSARS-CoV-2 is a novel virus that has rapidly spread, causing a global pandemic. In the majority of infected patients, SARS-CoV-2 leads to mild disease; however, in a significant proportion of infections, individuals develop severe symptoms that can lead to permanent lung damage or death. These severe cases are often associated with high levels of pro-inflammatory cytokines and low antiviral responses which can lead to systemic complications. We have evaluated transcriptional and cytokine secretion profiles from infected cell cultures and detected a distinct upregulation of inflammatory cytokines that parallels samples taken from infected patients. Building on these observations, we found a specific activation of NF-κB and a block of IRF3 nuclear translocation in SARS-CoV-2 infected cells. This NF-κB response is mediated by cGAS-STING activation and could be attenuated through STING targeting drugs. Our results show that SARS-CoV-2 curates a cGAS-STING mediated NF-κB driven inflammatory immune response in epithelial cells that likely contributes to inflammatory responses seen in patients and might be a target to suppress severe disease symptoms.
Biochemical characterization of recombinant UDP-sugar pyrophosphorylase and galactinol synthase fromBrachypodium distachyon
Authors: Minen Romina I. , Martínez María P. , Iglesias Alberto A. , Figueroa Carlos M. 
Published: July 2020

AbstractRaffinose (Raf) protects plant cells during seed desiccation and under different abiotic stress conditions. The biosynthesis of Raf starts with the production of UDP-galactose by UDP-sugar pyrophosphorylase (USPPase) and continues with the synthesis of galactinol by galactinol synthase (GolSase). Galactinol is then used by Raf synthase to produce Raf. In this work, we report the biochemical characterization of USPPase (BdiUSPPase) and GolSase 1 (BdiGolSase1) fromBrachypodium distachyon. The catalytic efficiency ofBdiUSPPase was similar with galactose 1-phosphate and glucose 1-phosphate, but 5-to 17-fold lower with other sugar 1-phosphates. The catalytic efficiency ofBdiGolSase1 with UDP-galactose was three orders of magnitude higher than with UDP-glucose. A structural model ofBdiGolSase1 allowed us to determine the residues putatively involved in the binding of substrates. Among these, we found that Cys261lies within the putative catalytic pocket.BdiGolSase1 was inactivated by oxidation with diamide and H2O2. The activity of the diamide-oxidized enzyme was recovered by reduction with dithiothreitol orE. colithioredoxin, suggesting thatBdiGolSase1 is redox-regulated.
An optimization-based deep belief network for the detection of phishing e-mails
Authors: M. Arshey , K. S. Angel Viji 
Published: July 2020

PurposePhishing is a serious cybersecurity problem, which is widely available through multimedia, such as e-mail and Short Messaging Service (SMS) to collect the personal information of the individual. However, the rapid growth of the unsolicited and unwanted information needs to be addressed, raising the necessity of the technology to develop any effective anti-phishing methods.Design/methodology/approachThe primary intention of this research is to design and develop an approach for preventing phishing by proposing an optimization algorithm. The proposed approach involves four steps, namely preprocessing, feature extraction, feature selection and classification, for dealing with phishing e-mails. Initially, the input data set is subjected to the preprocessing, which removes stop words and stemming in the data and the preprocessed output is given to the feature extraction process. By extracting keyword frequency from the preprocessed, the important words are selected as the features. Then, the feature selection process is carried out using the Bhattacharya distance such that only the significant features that can aid the classification are selected. Using the selected features, the classification is done using the deep belief network (DBN) that is trained using the proposed fractional-earthworm optimization algorithm (EWA). The proposed fractional-EWA is designed by the integration of EWA and fractional calculus to determine the weights in the DBN optimally.FindingsThe accuracy of the methods, naive Bayes (NB), DBN, neural network (NN), EWA-DBN and fractional EWA-DBN is 0.5333, 0.5455, 0.5556, 0.5714 and 0.8571, respectively. The sensitivity of the methods, NB, DBN, NN, EWA-DBN and fractional EWA-DBN is 0.4558, 0.5631, 0.7035, 0.7045 and 0.8182, respectively. Likewise, the specificity of the methods, NB, DBN, NN, EWA-DBN and fractional EWA-DBN is 0.5052, 0.5631, 0.7028, 0.7040 and 0.8800, respectively. It is clear from the comparative table that the proposed method acquired the maximal accuracy, sensitivity and specificity compared with the existing methods.Originality/valueThe e-mail phishing detection is performed in this paper using the optimization-based deep learning networks. The e-mails include a number of unwanted messages that are to be detected in order to avoid the storage issues. The importance of the method is that the inclusion of the historical data in the detection process enhances the accuracy of detection.
A variational approach for novel solitary solutions of FitzHugh–Nagumo equation arising in the nonlinear reaction–diffusion equation
Authors: Khan Yasir 
Published: July 2020

PurposeIn the nonlinear model of reaction–diffusion, the Fitzhugh–Nagumo equation plays a very significant role. This paper aims to generate innovative solitary solutions of the Fitzhugh–Nagumo equation through the use of variational formulation.Design/methodology/approachThe partial differential equation of Fitzhugh–Nagumo is modified by the appropriate wave transforms into a dimensionless nonlinear ordinary differential equation, which is solved by a semi-inverse variational method.FindingsThis paper uses a variational approach to the Fitzhugh–Nagumo equation developing new solitary solutions. The condition for the continuation of new solitary solutions has been met. In addition, this paper sets out the Fitzhugh–Nagumo equation fractal model and its variational principle. The findings of the solitary solutions have shown that the suggested method is very reliable and efficient. The suggested algorithm is very effective and is almost ideal for use in such problems.Originality/valueThe Fitzhugh–Nagumo equation is an important nonlinear equation for reaction–diffusion and is typically used for modeling nerve impulses transmission. The Fitzhugh–Nagumo equation is reduced to the real Newell–Whitehead equation if β = −1. This study provides researchers with an extremely useful source of information in this area.
Robust optimization model for sustainable supply chain for production and distribution of polyethylene pipe
Authors: Valizadeh Jaber , Sadeh Ehsan , Amini Sabegh Zainolabedin , Hafezalkotob Ashkan 
Published: July 2020

Purpose
In this study, the authors consider the key decisions in the design of the green closed-loop supply chain (CSLC) network. These decisions include considering the optimal location of suppliers, production facilities, distribution, customers, recycling centers and disposal of non-recyclable goods. In the proposed model, the level of technology used in recycling and production centers is taken into account. Moreover, in this paper is the environmental impacts of production and distribution of products based on the eco-indicator 99 are considered.

Design/methodology/approach
In this study, the author consider the key decisions in the design of the green CLSC network. These decisions include considering the optimal location of suppliers, production facilities, distribution, customers, recycling centers and disposal of non-recyclable goods. In the proposed model, the level of technology used in recycling and production centers is taken into account. Moreover, the environmental impacts of production and distribution of products based on the eco-indicator 99 are considered.

Findings
The results indicate that the results obtained from the colonial competition algorithm have higher quality than the genetic algorithm. This quality of results includes relative percentage deviation and computational time of the algorithm and it is shown that the computational time of the colonial competition algorithm is significantly lower than the computational time of the genetic algorithm. Furthermore, the limit test and sensitivity analysis results show that the proposed model has sufficient accuracy.

Originality/value
Solid modeling of the green supply chain of the closed loop using the solid optimized method by Bertsimas and Sim. Development of models that considered environmental impacts to the closed loop supply chain. Considering the impact of the technology type in the manufacture of products and the recycling of waste that will reduce emissions of environmental pollutants. Another innovation of the model is the multi-cycle modeling of the closed loop of supply chain by considering the uncertainty and the fixed and variable cost of transport.
It's about time
Authors: Wofford Larry 
Published: July 2020

PurposeTime is a critical element of commercial real estate (CRE) and has received only cursory attention. This paper identifies and describes the interactions between time, change and CRE. It leads to important implications and possible changes in professional practice, teaching and research.Design/methodology/approachThe research design involves identifying and synthesising research in a disparate discipline into a coherent portrayal of time, change and CRE. Using the CRE environment as a foundation, a more comprehensive, multi-disciplinary approach is developed to highlight the temporal issues within CRE.FindingsThe extreme levels of complexity, dynamism and uncertainty characterising current CRE environments affect the interaction of time, change and CRE. In response, CRE has become increasingly specialised in property types and time segments. The paper identifies four issues for CRE: the role of CRE as an integrator of different layers of civilisation with different clock speeds, the need for a temporal mindset recognising finite and infinite games, the need for temporal ambidexterity and the use of strategic foresight and scenarios. The very definition of CRE as an industry is questioned.Research limitations/implicationsNeed for essential empirical work as well as additional work for implications.Practical implicationsCRE faces disruption from many sources, and this paper considers how to incorporate time and change into analysis of the CRE market environment. It identifies specific ways CRE can understand and avoid disruption. Further, areas of teaching and research are highlighted.Social implicationsReal estate assets are substantial, long-lived assets with important consequences for society. This paper advances the analysis of such assets.Originality/valueAreas of concentration in CRE and academia needing attention are identified. The areas have generally not been considered prior to this paper.
Competitive advantage from marketing the SDGs: a luxury perspective
Authors: Hepner Judith , Chandon Jean-Louis , Bakardzhieva Damyana 
Published: July 2020

PurposeShall luxury firms promote their sustainable development goals (SDGs)? What are the risks and the competitive advantages? Some answers from sustainability-oriented luxury buyers are provided.Design/methodology/approachQuantitative and qualitative analysis from an online survey of 315 luxury buyers in 28 countries.FindingsSustainability-oriented luxury buyers want branding strategies aligned with the SDGs and rank SDGs in order of importance for the luxury industry. However, they are unable to rank consistently most brands based on their sustainability efforts. The Stella McCartney brand is a clear exception to the general findings: sustainability-oriented luxury buyers rank Stella the most sustainable luxury brand by a vast margin, show willingness to purchase more from this brand, recommend it and are ready to pay a premium.Research limitations/implicationsThe paper uses partial ranking of 20 luxury brands because in pretests, luxury buyers found it difficult to provide a complete ranking of the sustainability efforts of all the brands. Further research in more cultural or geographical contexts is needed.Originality/valueThe research empirically provides an example of a successful marketing strategy leveraging the SDGs to meet sustainability-oriented luxury buyers with targeted actions and messaging to gain competitive advantage.
European bird declines: Do we need to rethink approaches to the management of abundant generalist predators?
Authors: McMahon Barry J. , Doyle Susan , Gray Aimée , Kelly Seán B. A. , Redpath Steve M. 
Published: July 2020

Abstract

Bird species are declining across Europe. Current European policy, that is, the Birds and Habitats Directives, focus on habitat management as a way of halting the declines. This paper explores the role of predation in causing bird population declines and asks if we need to reconsider our approach to the management of generalist predators.

We analysed bird population trends and distribution changes across Europe, Britain and Ireland, reflecting an increasing gradient of generalist predator abundance (principally red fox Vulpes vulpes and species of the family Corvidae). We tested if ground‐nesting bird species, considered more vulnerable to predation, were in greater decline compared to other nesting strategies. We also compared Annex I designated species to non‐designated species as a proxy for habitat management.

We found that across Europe, 74% of ground‐nesting bird species were in decline, compared to 41% of other species. This was especially evident in Britain, where the pattern was 66% compared to 31%, and in Ireland, 71% compared to 20%. Ground‐nesting species were significantly more likely to be declining than other species.

These patterns are consistent with the idea that population declines are at least partially related to the increased abundance of generalist predators. In Britain, ground‐nesting species were less likely to be in decline if covered by Annex I designation. However, in Europe and Ireland, Annex I status did not mitigate the effect of nesting strategy.

Policy implications. Current legislation is clearly insufficient to prevent widespread declines in ground‐nesting birds, and this is the case across Europe, in Britain and Ireland. Ignoring the role of generalist predators in modern landscapes may lead to further declines and losses. We urgently need large‐scale experiments to establish causality in the impact of generalist predators on ground‐nesting birds in different landscapes. If we value our ground‐nesting bird species, consideration needs to be given to the control of widespread generalist predators, at least until landscapes are restored.