bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative ‘omics analyses differentiateMycobacterium tuberculosisandMycobacterium bovisand reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli
Authors: Malone Kerri M. , Rue-Albrecht Kévin , Magee David A. , Conlon Kevin , Schubert Olga T. , Nalpas Nicolas C. , Browne John A. , Smyth Alicia , Gormley Eamonn , Aebersold Ruedi , MacHugh David E. , Gordon Stephen V. 
Published: November 2017

AbstractMembers of theMycobacterium tuberculosiscomplex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity, yet distinct host tropism. Notably, whileMycobacterium bovisis highly virulent and pathogenic for cattle, the human pathogenM. tuberculosisis attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strainsM. bovisAF2122/97 andM. tuberculosisH37Rv at both the global transcriptional and translational level via RNA-sequencing and SWATH mass spectrometry. Furthermore, a bovine alveolar macrophage infection time course model was employed to investigate the shared and divergent host transcriptomic response to infection withM. tuberculosisorM. bovis. Significant differential expression of virulence-associated pathways between the two bacilli was revealed, including the ESX-1 secretion system. A divergent transcriptional response was observed betweenM. tuberculosisandM. bovisinfection of bovine alveolar macrophages, in particular cytosolic DNA-sensing pathways at 48 hours post-infection, and highlights a distinct engagement ofM. boviswith the bovine innate immune system. The work presented here therefore provides a basis for the identification of host innate immune mechanisms subverted by virulent host-adapted mycobacteria to promote their survival during the early stages of infection.ImportanceTheMycobacterium tuberculosiscomplex (MTBC) includes the most important global pathogens for humans and animals, namelyMycobacterium tuberculosisandMycobacterium bovis,respectively. These two exemplar mycobacterial pathogens share a high degree of genetic identity, but the molecular basis for their distinct host preference is unknown. In this work we integrated transcriptomic and proteomic analyses of the pathogens to elucidate global quantitative differences between them at the mRNA and protein level. We then integrated this data with transcriptome analysis of the bovine macrophage response to infection with either pathogen. Increased expression of the ESX-1 virulence system inM. bovisappeared a key driver of an increased cytosolic nucleic acid sensing and interferon response in bovine macrophages infected withM. boviscompared toM. tuberculosis.Our work demonstrates the specificity of host-pathogen interaction and how the subtle interplay between mycobacterial phenotype and host response may underpin host specificity amongst MTBC members.
Zika: An ongoing threat to women and infants
Authors: Coimbra Beatriz Macedo , Coelho Flávio Codeço , Armstrong Margaret , Saraceni Valeria , Lemos Cristina 
Published: November 2017

AbstractRecent data from Rio de Janeiro shows a sharp drop in the number of notified cases of Zika in the summer of 2016-17, compared to the previous summer. This is probably due to herd immunity built up after the previous year's epidemic. There is still a much higher incidence among women than men, almost certainly due to sexual transmission. An unexpected feature of the new data is that there are proportionally far more cases in children under 15 months than in older age classes. By comparing the incidence for 2016-17 with that of 2015-16, we can deduce the proportion of reported cases for men and women, and also verify that the disparity of incidence between them is still present. Women and children still represent risk groups with regard to Zika infection, even during a non-epidemic season.
Conversion between parallel and antiparallel β-sheets in wild-type and Iowa mutant fibrils
Authors: Xi Wenhui , Hansmann Ulrich H.E. 
Published: November 2017

AbstractUsing a variant of Hamilton-Replica-Exchange we study for wild type and Iowa mutant Aβ40the conversion between fibrils with antiparallel β-sheets, and such with parallel β-sheets. We show that wild type and mutant form distinct salt bridges that in turn stabilize different fibril organizations. The conversion between the two fibril forms leads to the release of small aggregates that in the Iowa mutant may shift the equilibrium from fibrils to more toxic oligomers.
Fungal communities associated with the eastern larch beetle: diversity and variation within developmental stages
Authors: Durand Audrey-Anne , Buffet Jean-Philippe , Constant Philippe , Déziel Eric , Guertin Claude 
Published: November 2017

AbstractBacterial and fungal communities associated with bark beetles, especially some Dendroctonus species, mediate challenging aspects of the subcortical habitat for their hosts. Filamentous fungi and yeasts are important in various metabolic processes of certain bark beetles, with involvement in nutrition, protection and detoxification of plant defense compounds. The eastern larch beetle, Dendroctonus simplex, is recognized as a serious forest pest in the upper part of North America. Although D. simplex is well studied, the fungal communities and their ecological role remain to be investigated. Here, using 18S rRNA gene pyrosequencing, we provide a comprehensive overview of the yeasts and filamentous fungi associated with the eastern larch beetle and compare fungal communities between different developmental stages and microenvironments. Fungal mycobiome associated with the galleries was also investigated. Our study has unveiled an unexpected fungal diversity associated with the developmental stages. Significant differences in species richness between the developmental stages were determined. Yeasts were found to be predominant in the adult and larval stages, whereas filamentous fungi were most prevalent in the pupae. Our results indicate a possible implication of yeasts in the eastern larch beetle nutrition.
Dynamics of the upper airway microbiome in the pathogenesis of asthma-associated persistent wheeze in preschool children
Authors: Teo Shu Mei , Tang Howard HF , Mok Danny , Judd Louise M , Watts Stephen C , Pham Kym , Holt Barbara J. , Kusel Merci , Serralha Michael , Troy Niamh , Bochkov Yury A , Grindle Kristine , Lemanske Robert F , Johnston Sebastian L , Gern James E , Sly Peter D , Holt Patrick G , Holt Kathryn E , Inouye Michael 
Published: November 2017

ABSTRACTRepeated cycles of infection-associated lower airway inflammation drives the pathogenesis of persistent wheezing disease in children. Tracking these events across a birth cohort during their first five years, we demonstrate that >80% of infectious events indeed involve viral pathogens, but are accompanied by a shift in the nasopharyngeal microbiome (NPM) towards dominance by a small range of pathogenic bacterial genera. Unexpectedly, this change in NPM frequently precedes the appearance of viral pathogens and acute symptoms. In non-sensitized children these events are associated only with “transient wheeze” that resolves after age three. In contrast, in children developing early allergic sensitization, they are associated with ensuing development of persistent wheeze, which is the hallmark of the asthma phenotype. This suggests underlying pathogenic interactions between allergic sensitization and antibacterial mechanisms.
Within host selection for faster replicating bacterial symbionts
Authors: Chrostek Ewa , Teixeira Luis 
Published: November 2017

AbstractWolbachiais a widespread, intracellular symbiont of arthropods, able to induce reproductive distortions and antiviral protection in insects.Wolbachiacan also be pathogenic, as is the case withwMelPop, a virulent variant of the endosymbiont ofDrosophila melanogaster. An extensive genomic amplification of the 20kb region encompassing eightWolbachiagenes, called Octomom, is responsible forwMelPop virulence. The Octomom copy number inwMelPop can be highly variable between individualD. melanogasterflies, even when comparing siblings arising from a single female. Moreover, Octomom copy number can change rapidly between generations. These data suggest an intra-host variability in Octomom copy number betweenWolbachiacells. SincewMelPopWolbachiawith different Octomom copy numbers grow at different rates, we hypothesized that selection could act on this intra-host variability. Here we tested if total Octomom copy number changes during the lifespan of individualDrosophilahosts, revealing selection for differentWolbachiapopulations. We performed a time course analysis of Octomom amplification in flies whose mothers were controlled for Octomom copy number. We show that despite the Octomom copy number being relatively stable it increases slightly throughoutD. melanogasteradult life. This indicates that there is selection acting on the intra-host variation in the Octomom copy number over the lifespan of individual hosts. This within host selection for faster replicating bacterial symbionts may be in conflict with between host selection against highly pathogenicWolbachia.
iterative Random Forests to discover predictive and stable high-order interactions
Authors: Basu Sumanta , Kumbier Karl , Brown James B. , Yu Bin 
Published: November 2017

AbstractGenomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interactin vivoas components of larger molecular machines. Understanding how these high-order interactions drive gene expression presents a substantial statistical challenge. Building on Random Forests (RF), Random Intersection Trees (RITs), and through extensive, biologically inspired simulations, we developed the iterative Random Forest algorithm (iRF). iRF trains a feature-weighted ensemble of decision trees to detect stable, high-order interactions with same order of computational cost as RF. We demonstrate the utility of iRF for high-order interaction discovery in two prediction problems: enhancer activity in the earlyDrosophilaembryo and alternative splicing of primary transcripts in human derived cell lines. InDrosophila, among the 20 pairwise transcription factor interactions iRF identifies as stable (returned in more than half of bootstrap replicates), 80% have been previously reported as physical interactions. Moreover, novel third-order interactions, e.g. between Zelda (Zld), Giant (Gt), and Twist (Twi), suggest high-order relationships that are candidates for follow-up experiments. In human-derived cells, iRF re-discovered a central role of H3K36me3 in chromatin-mediated splicing regulation, and identified novel 5th and 6th order interactions, indicative of multi-valent nucleosomes with specific roles in splicing regulation. By decoupling the order of interactions from the computational cost of identification, iRF opens new avenues of inquiry into the molecular mechanisms underlying genome biology.
Attomol-level quantification of chemically modified ribonucleosides enabled by capillary porous graphitic carbon columns in nano LC-MS
Authors: Sarin L. Peter , Kienast Sandra D. , Leufken Johannes , Ross Robert L. , Limbach Patrick A. , Fufezan Christian , Drexler Hannes C. A. , Leidel Sebastian A. 
Published: November 2017

ABSTRACTPost-transcriptional chemical modifications of (t)RNA molecules are crucial in fundamental biological processes, such as translation. Despite their biological importance and accumulating evidence linking them to various human diseases, technical challenges have limited the development of methods for reliable detection and accurate quantification of these modifications. Here, we present a sensitive capillary nanoflow liquid chromatography mass spectrometry (nLC-MS) pipeline for quantitative high-resolution analysis of ribonucleoside modifications from complex biological samples. We evaluated two porous graphitic carbon (PGC) materials as stationary phases for reversed-phase separation of ribonucleosides and found that both PGC matrices have excellent retention and separation characteristics, as well as the capability to separate structural isomers. Using PGC matrices in nLC-MS yielded excellent signal-to-noise ratios in a detection range spanning up to six orders of magnitude, allowing for the analysis of individual ribonucleosides down to attomol concentrations. Furthermore, normalizing the obtained signal intensities to a stable isotope labeled spike-in enabled direct comparison of ribonucleoside levels between different samples. In conclusion, capillary PGC columns coupled to nLC-MS constitute a powerful and sensitive tool for quantitative analysis of chemically modified ribonucleosides in complex biological samples. This setup will be invaluable for further unraveling the intriguing and multifaceted biological roles of RNA modifications.
Identification of key pathways and metabolic fingerprints of longevity in C. elegans
Authors: Gao Arwen W. , Smith Reuben L. , van Weeghel Michel , Kamble Rashmi , Houtkooper Riekelt H. 
Published: November 2017

AbstractImpaired insulin/IGF-1 signaling (IIS) pathway and caloric restriction (CR) are two well-established interventions to prolong lifespan in worm C. elegans. However, a cross comparison of these longevity pathways using a multi-omics integration approach is lacking. In this study, we aimed to identify key pathways and metabolite fingerprints of longevity that are shared between IIS and CR worm models using a multi-omics integration approach. We generated transcriptomics and metabolomics data from two long-lived mutant worm strains, i.e. daf-2 (impaired IIS pathway) and eat-2 (CR model) and compared them with the N2 strain. Transcriptional profiling identified shared longevity signatures between the two strains, such as an upregulation of lipid storage and defense responses and downregulation of macromolecule synthesis and developmental processes. The shared longevity signatures revealed by metabolomics profiling included an increase in the levels of glycerol-3P, ademine, xanthine, and AMP, and a decrease in the levels of the amino acid pool, the C18:0 and C17:1 fatty acids. After we integrated transcriptomics and metabolomics data based on the annotations in KEGG, our results highlighted a downregulation of pyrimidine metabolism and upregulation of purine metabolism as a commonality between the two longevity mechanisms. Overall, our findings point towards the existence of shared metabolic pathways that are likely important for lifespan extension and provide novel insights into potential regulators and metabolic fingerprints for longevity.
Microstructure and corrosion behaviour of precipitation hardened and thermo-mechanical treated high strength Al-12Zn-3Mg-2.5Cu alloy
Authors: Ravikumar V.V. , Kumaran S. 
Published: November 2017

Purpose
The purpose of this paper is to study the corrosion behaviour of Al-12Zn-3Mg-2.5Cu alloy by cast, precipitation hardening and non-isothermal step rolling cum cold/cryo rolling (−80 and −196°C) in 3.5 per cent NaCl solution.

Design/methodology/approach
Aluminium alloy with high alloying concentration (Zn: 12 per cent, Mg: 3 per cent, Cu: 2.5 per cent) was prepared by squeeze casting method with controlled process parameters. The cast alloy was solution treated at 450°C for 24 h and aged at 120°C with varying time intervals. Initially, the alloy also underwent non-isothermal step rolling from 6 mm to 3 mm at 400-100°C at the step of 100ºC with 15% reduction in thickness. Non-isothermal rolled alloy (3 mm thickness) was the starting material for further rolling at three different temperatures, such as room temperature, −80 and −190°C with 85 per cent reduction. Microstructural evolution during precipitation and thermo-mechanical processing was studied with the help of optical microscopy and electron microscopy. A potentio-dynamic polarization study was performed to evaluate the corrosion behaviour of Al-12Zn-3Mg-2.5Cu alloy processed in different conditions in 3.5 per cent NaCl solution.

Findings
There is a distinct evidence that the alloy exhibits varying corrosion resistance by changing its structural features. In fact, the alloy with ultra-fine grained structure exhibits good corrosion resistance than that of alloy in cast. This is attributed to a greater grain boundary region with high dislocation density, and plastic strain adversely affects the corrosion resistance.

Originality/value
The results obtained by this investigation help in understanding the effect of precipitation hardening and non-isothermal step rolling cum cold/cryo rolling (−80 and −196°C) on corrosion behaviour.
Investigation on the effect of nano-ceria on the epoxy coatings for corrosion protection of mild steel in natural seawater
Authors: Xavier Joseph Raj 
Published: November 2017

Purpose
This paper aims to investigate the effect of introducing nano-ceria (CeO2) particles to the epoxy coatings on mild steel in natural seawater.

Design/methodology/approach
The epoxy–ceria nanoparticles were coated with mild steel using a wire-wound draw-down bar method. The effects of ceria nanoparticles on the corrosion resistance of epoxy-coated samples were analyzed using scanning electrochemical microscopy (SECM) and electrochemical impedance spectroscopy (EIS).

Findings
Localized measurements such as oxygen consumption and iron dissolution were observed using SECM in natural seawater in the epoxy-coated sample. The increase in film resistance (Rf) and charge transfer resistance (Rct) values by the addition of nano-ceria particles in the epoxy coating was measured from EIS measurements after wet and dry cyclic corrosion test. Scanning electron microscope (SEM)/energy dispersive X-ray spectroscope (EDX) analysis showed that complex oxides of nano-ceria were enriched in corrosion products at a scratched area of the coated mild steel after corrosion testing. Focused ion beam-transmission electron microscope (FIB-TEM) analysis confirmed the presence of the nanoscale oxide layers of ceria in the rust of the steel.

Research limitations/implications
The tip current at −0.70 V for the epoxy–CeO2-coated sample decreased rapidly because of cathodic reduction of the dissolved oxygen. The increase in film resistance (Rf) and charge transfer resistance (Rct) values by the addition of nano-ceria particles in the epoxy coating were measured from EIS measurements after wet and dry cyclic corrosion test.

Practical implications
The presence of complex oxide layers of nano-ceria layers protects the coated steel from rusting.

Social implications
The use of this nano-ceria for corrosion protection is environment-friendly.

Originality/value
The results of this study indicated the significant effect of nano-ceria particles on the protective performance and corrosion resistance of the epoxy coating on mild steel. The dissolution of Fe2+ was lower in the epoxy–ceria nanoparticle-coated mild steel than that of the epoxy-coated mild steel resulting in a lower anodic current of steel. The increase in film resistance and the charge transfer resistance showed that the nano-ceria particles and the formation of complex oxides provide better barrier protection to the coating metal surfaces.
Experimental and DFT studies of 1-methylimidazolium trinitrophenoxide as modifier for corrosion inhibition of SDS for mild steel in hydrochloric acid
Authors: Yousefi Ali , Aslanzadeh Saeed Amir , Akbari Jafar 
Published: November 2017

Purpose
The purpose of this paper is to investigate the surface properties, particle sizes and corrosion inhibition performance of sodium dodecyl sulfate (SDS) in the presence of imidazolium-based ionic liquid as an additive. Up to now, different properties of alone surfactants and ionic liquids have been studied. However, few studies have been devoted to mixed ionic liquid and surfactant. The significance and novelty of this research is the investigation of 1-methylimidazolium trinitrophenoxide ([MIm][TNP]) as ionic liquid effects on SDS corrosion behavior.

Design/methodology/approach
The inhibition effect of [MIm][TNP], SDS and their mixtures on mild steel surface in 2 M hydrochloric acid (HCl) solution was examined by electrochemical impedance spectroscopy, potentiodynamic polarization (PDP), scanning electron microscopy (SEM), atomic force microscopy and quantum chemical calculations as well as dynamic light scattering (DLS) and surface tension measurements to discuss surface properties of studied solutions.

Findings
Based on the results, ionic liquid/SDS mixtures significantly indicated better inhibition properties than pure surfactant solution. PDP curves indicated that the studied compounds act as mixed-type of inhibitors. The critical micelle concentration, surface properties and particle sizes were investigated from the surface tension measurements and DLS results.

Originality/value
Adsorption of the inhibitors on the steel surface obeyed the Villamil adsorption model. SEM was used for surface analysis and verified the inhibition efficiency of mixed IL/SDS system. Quantum chemical calculations were performed using density functional theory, and a good relationship between experimental and theoretical data has been obtained.
A brief history of food retail
Authors: Stanton John L. 
Published: November 2017

Purpose
The purpose of this paper is to provide a historic perspective on the supermarket industry that has changed from the small Mom and Pop stores to major supermarket chains.

Design/methodology/approach
This study is a review of secondary information from trade literature, popular new media and academic publications.

Findings
The changes in supermarkets and food stores followed the trends in how consumers have changed and developed. As consumers around the world continue to change, so will food retailers.

Research limitations/implications
The author could have included more on the development in underdeveloped countries.

Practical implications
This paper has practical implication in that to understand that food retailers must continue to follow consumer and technology changes if they want to grow and prosper. To quote Winston Churchill, “The farther backward you can look, the farther forward you are likely to see.”

Social implications
Supermarkets must be responsive to consumer changes and as consumer become more demanding for convenience so must supermarkets must continue to provide it or disappear.

Originality/value
This study is original to the extent that it brought together the different eras in supermarket. The actual changes have been well known.