bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blood Bacterial Profiles Associated With Human Immunodeficiency Virus Infection and Immune Recovery
Authors: Serrano-Villar Sergio , Sanchez-Carrillo Sergio , Talavera-Rodríguez Alba , Lelouvier Benjamin , Gutiérrez Carolina , Vallejo Alejandro , Servant Florence , Bernadino José I , Estrada Vicente , Madrid Nadia , Gosalbes María José , Bisbal Otilia , de Lagarde María , Martínez-Sanz Javier , Ron Raquel , Herrera Sabina , Moreno Santiago , Ferrer Manuel 
Published: June 2020

Abstract
Human immunodeficiency virus (HIV) infection impairs mucosal immunity and leads to bacterial translocation, fueling chronic inflammation and disease progression. While this is well established, questions remain about the compositional profile of the translocated bacteria, and to what extent it is influenced by antiretroviral therapy (ART). Using 16S ribosomal DNA targeted sequencing and shotgun proteomics, we showed that HIV increases bacterial translocation from the gut to the blood. HIV increased alpha diversity in the blood, which was dominated by aerobic bacteria belonging to Micrococcaceae (Actinobacteria) and Pseudomonadaceae (Proteobacteria) families, and the number of circulating bacterial proteins was also increased. Forty-eight weeks of ART attenuated this phenomenon. We found that enrichment with Lactobacillales order, and depletion of Actinobacteria class and Moraxellaceae and Corynebacteriacae families, were significantly associated with greater immune recovery and correlated with several inflammatory markers. Our findings suggest that the molecular cross talk between the host and the translocated bacterial products could influence ART-mediated immune recovery.
The Practices of Evaluating Entitlements: Rethinking “Reputation” in International Politics
Authors: Sundaram Sasikumar S 
Published: June 2020

AbstractHow do reputations work in international politics? The dominant frameworks in international relations scholarship argue that reputation is subservient to real interest or past actions do not influence observers’ behavior in anarchy, and inconsistent reputational beliefs are irrational among policymakers who have miscalculated their interests. These substantialist accounts are problematic in the light of taking political practices seriously. I argue that reputations work within communities of practice through a tripartite process involving actor's entitlement claims, audiences’ relational evaluation of such claims, and the actor's performance to secure entitlements in issue-specific interactions. I illustrate the analytical usefulness of this conceptualization against conventional accounts by studying Brazil's multiple reputational concerns in the issue area of humanitarian crises in the post–Cold War period. The framework offered in the article has a wider relevance for examining how reputations work across states, for example, in India and China, and in different issue areas by foregrounding normative appraisals of each other by community members in distinct reputational games. It also sets the stage for further examination of the intersection of reputational practices upon other social capital such as status.
Microevolution of acquired colistin resistance in Enterobacteriaceae from ICU patients receiving selective decontamination of the digestive tract
Authors: Janssen Axel B , van Hout Denise , Bonten Marc J M , Willems Rob J L , van Schaik Willem 
Published: June 2020

Abstract

Background
Colistin is an antibiotic that targets the LPS molecules present in the membranes of Gram-negative bacteria. It is used as a last-resort drug to treat infections with MDR strains. Colistin is also used in selective decontamination of the digestive tract (SDD), a prophylactic therapy used in patients hospitalized in ICUs to selectively eradicate opportunistic pathogens in the oropharyngeal and gut microbiota.

Objectives
To unravel the mechanisms of acquired colistin resistance in Gram-negative opportunistic pathogens obtained from SDD-treated patients.

Results
Routine surveillance of 428 SDD-treated patients resulted in 13 strains with acquired colistin resistance (Escherichia coli, n = 9; Klebsiella aerogenes, n = 3; Enterobacter asburiae, n = 1) from 5 patients. Genome sequence analysis showed that these isolates represented multiple distinct colistin-resistant clones but that colistin-resistant strains within the same patient were clonally related. We identified previously described mechanisms that lead to colistin resistance, i.e. a G53 substitution in the response regulator PmrA/BasR and the acquisition of the mobile colistin resistance gene mcr-1.1, but we also observed novel variants of basR with an 18 bp deletion and a G19E substitution in the sensor histidine kinase BasS. We experimentally confirmed that these variants contribute to reduced colistin susceptibility. In a single patient, we observed that colistin resistance in a single E. coli clone evolved through two unique variants in basRS.

Conclusions
We show that prophylactic use of colistin during SDD can select for colistin resistance in species that are not intrinsically colistin resistant. This highlights the importance of continued surveillance for strains with acquired colistin resistance in patients treated with SDD.
Extensive antimicrobial resistance mobilization via multicopy plasmid encapsidation mediated by temperate phages
Authors: Rodríguez-Rubio Lorena , Serna Carlos , Ares-Arroyo Manuel , Matamoros Bosco R , Delgado-Blas Jose F , Montero Natalia , Bernabe-Balas Cristina , Wedel Emilia F , Mendez Irene S , Muniesa Maite , Gonzalez-Zorn Bruno 
Published: June 2020

AbstractObjectivesTo investigate the relevance of multicopy plasmids in antimicrobial resistance and assess their mobilization mediated by phage particlesMethodsSeveral databases with complete sequences of plasmids and annotated genes were analysed. The 16S methyltransferase gene armA conferring high-level aminoglycoside resistance was used as a marker in eight different plasmids, from different incompatibility groups, and with differing sizes and plasmid copy numbers. All plasmids were transformed into Escherichia coli bearing one of four different lysogenic phages. Upon induction, encapsidation of armA in phage particles was evaluated using qRT–PCR and Southern blotting.ResultsMulticopy plasmids carry a vast set of emerging clinically important antimicrobial resistance genes. However, 60% of these plasmids do not bear mobility (MOB) genes. When carried on these multicopy plasmids, mobilization of a marker gene armA into phage capsids was up to 10000 times more frequent than when it was encoded by a large plasmid with a low copy number.ConclusionsMulticopy plasmids and phages, two major mobile genetic elements (MGE) in bacteria, represent a novel high-efficiency transmission route of antimicrobial resistance genes that deserves further investigation.
High prevalence and risk factors of multiple antibiotic resistance in patients who fail first-line Helicobacter pylori therapy in southern China: a municipality-wide, multicentre, prospective cohort study
Authors: Lyu Tao , Cheung Ka Shing , Ni Li , Guo Jiaqi , Mu Pei , Li Yinpeng , Yang Qiu , Yu Xiqiu , Lyu Zhiwu , Wu Jianwei , Guo Haijian , Leung Wai K , Seto Wai-Kay 
Published: June 2020

Abstract

Background
We aimed to study the prevalence of secondary antibiotic resistance of Helicobacter pylori in southern China and its risk factors, particularly geographical and socio-economic factors.

Methods
This was a municipality-wide, multicentre, prospective cohort study involving five major hospitals. Patients aged ≥18 years who failed first-line bismuth-based quadruple anti-H. pylori therapy between September 2016 and February 2018 were recruited. Participants underwent upper gastrointestinal endoscopy with biopsy from the antrum and body for H. pylori culture and antimicrobial susceptibility testing for six antibiotics (clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline and furazolidone). Patients with failure of H. pylori culture were excluded. Participants completed a questionnaire profiling 22 potential risk factors of H. pylori infection and antibiotic resistance, including medical, social, household and birthplace factors.

Results
A total of 1113 patients failed first-line therapy, with successful H. pylori culture in 791 (71.1%) [male = 433 (54.7%); median age = 43 years]. Secondary resistance rates of dual antibiotics (clarithromycin + metronidazole and levofloxacin + metronidazole) and triple antibiotics (clarithromycin + levofloxacin + metronidazole) were 34.0%, 38.7% and 17.8%, respectively. Risk factors for clarithromycin + metronidazole resistance were history of ≥2 courses of H. pylori therapies [adjusted OR (aOR) = 1.71; 95% CI = 1.17–2.54], ≥3 household members (aOR = 2.00; 95% CI = 1.07–3.90) and family history of gastric cancer (aOR = 1.85; 95% CI = 1.18–2.85). Risk factors for levofloxacin + metronidazole resistance were age ≥40 years (aOR = 1.94; 95% CI = 1.37–2.75), lower gross domestic product per capita (aOR = 0.29; 95% CI = 0.10–0.80) and higher number of doctors/10 000 population (aOR = 1.59; 95% CI = 1.07–2.39). A higher human development index was of borderline significance (aOR = 2.79; 95% CI = 0.97–8.70).

Conclusions
The rates of secondary resistance of H. pylori to multiple antibiotics were high in southern China. Certain population-level risk factors were associated with levofloxacin + metronidazole resistance.
A Fast GC-MS-Based Method for Efficacy Assessment of Natural Anti-Oxidants for Inhibiting Lipid Oxidation
Authors: Janssen Hans-Gerd , Gah Carmen , Steenbergen Herrald , Rosing Ed , Spraul Martin 
Published: June 2020

Abstract

Background
For health reasons it is preferred to prepare food products with edible fats and oils that are high in unsaturated fatty acids. Unfortunately, these unsaturated acids are susceptible to lipid oxidation and the addition of natural antioxidants, e.g., rosemary extracts, etc. is needed.

Objective
To assess the efficacy of natural oxidation inhibition strategies, fast, yet realistic, and objective methods are needed to study oxidation inhibition.

Methods
A model system consisting of salt and sunflower oil is proposed as a model for dry soups and sauces. Hexanal formation is studied using fast GC-MS as a quantitative indicator for lipid oxidation.

Results
A fast GC-MS method using a short, 6-m 150 µm inner-diameter column was developed that allowed elution of hexanal within approximately 20 s, with a total run time of 2 min. The GC method has quantification limits below 1 ppm and is hence much more sensitive than the human nose.

Conclusions
The new accelerated method with hexanal read-out was successfully applied in a study to identify spices and herbs mixtures that can act as natural inhibitors of lipid oxidation. The fast GC-MS method is extremely stable and allowed the analysis of thousands of samples with very little maintenance.

Highlights
With the right mixture of spices and herbs, lipid oxidation can be delayed more than 100 times as compared to non-stabilized systems.
A maxillary ameloblastic fibrosarcoma tumor: a rare case report from Syria
Authors: Soltany Amjad , Asaad Ghazal , Daher Rami , Dayoub Mouhannad , Khalil Ali , Alshehabi Zuheir 
Published: June 2020

Abstract
Ameloblastic fibrosarcoma (AFS) is a rare, aggressive malignant odontogenic tumor. AFS is seen most frequently in second and third decades of life. We are reporting a case of a low grade AFS in a 21-year-old male complaining of a painless swelling in the right side of the maxilla. The patient was treated with surgical excision followed by radiotherapy, which is considered the most effective approach for most of soft tissue sarcomas. AFS has a high-reported recurrence rate (up to 37%); therefore, long-term surveillance for recurrence is crucial.
Thinking with Ferrar Papers 1422: A c. 1681 Verse Miscellany
Authors: Smyth Adam 
Published: June 2020

Abstract
This article explores a late seventeenth-century manuscript verse miscellany held amongst the Ferrar Papers in Magdalene College, Cambridge, not previously discussed by critics. By attending to both the specific features of this manuscript miscellany (including poems by John Dryden, Katherine Philips. and others), and the larger Ferrar archive, the article considers broader questions about how to read and interpret manuscript miscellanies.
A Newly Discovered Edition of the English Palmerin D'oliva
Authors: Sánchez-Martí Jordi 
Published: June 2020

Abstract
This note examines the fragments of the English Palmerin d'Oliva discovered in the library of Christ Church, Oxford, in 2017. First, it briefly discusses the course the Castilian Palmerín de Olivia followed on the Continent until it crossed to England, where Anthony Munday's translation appeared in 1588. After explaining how the fragments were located, their placement, nature and contents are described. The text in the Christ Church fragments is collated with the other editions of the English Palmerin d'Oliva. The ESTC conjecturally states that the newly discovered edition was printed c. 1600 by Thomas Creede and Bernard Alsop. This article, however, argues that the available textual, typographical and bibliographical evidence suggests that this edition must have been printed c. 1609 by Creede, without the participation of Alsop. Finally, note is taken of the presence on the pages of the handwriting of Henry Aldrich, the seventeenth-century dean of Christ Church.
Quantifying Suspiciousness within correlated data sets
Authors: Lemos Pablo , Köhlinger Fabian , Handley Will , Joachimi Benjamin , Whiteway Lorne , Lahav Ofer 
Published: June 2020

ABSTRACTWe propose a principled Bayesian method for quantifying tension between correlated data sets with wide uninformative parameter priors. This is achieved by extending the Suspiciousness statistic, which is insensitive to priors. Our method uses global summary statistics, and as such it can be used as a diagnostic for internal consistency. We show how our approach can be combined with methods that use parameter space and data space to identify the existing internal discrepancies. As an example, we use it to test the internal consistency of the KiDS-450 data in four photometric redshift bins, and to recover controlled internal discrepancies in simulated KiDS data. We propose this as a diagnostic of internal consistency for present and future cosmological surveys, and as a tension metric for data sets that have non-negligible correlation, such as Large Synoptic Spectroscopic Survey and Euclid.
K-CLASH: Strangulation and ram pressure stripping in galaxy cluster members at 0.3 &lt; z &lt; 0.6
Authors: Vaughan Sam P , Tiley Alfred L , Davies Roger L , Prichard Laura J , Croom Scott M , Bureau Martin , Stott John P , Bunker Andrew , Cappellari Michele , Ansarinejad Behzad , Jarvis Matt J 
Published: June 2020

ABSTRACT
Galaxy clusters have long been theorized to quench the star formation of their members. This study uses integral-field unit observations from the K-band MultiObject Spectrograph (KMOS) – Cluster Lensing And Supernova survey with Hubble (CLASH) survey (K-CLASH) to search for evidence of quenching in massive galaxy clusters at redshifts 0.3 &lt; z &lt; 0.6. We first construct mass-matched samples of exclusively star-forming cluster and field galaxies, then investigate the spatial extent of their H α emission and study their interstellar medium conditions using emission line ratios. The average ratio of H α half-light radius to optical half-light radius ($r_{\mathrm{e}, {\rm {H}\,\alpha }}/r_{\mathrm{e}, R_{\mathrm{c} } }$) for all galaxies is 1.14 ± 0.06, showing that star formation is taking place throughout stellar discs at these redshifts. However, on average, cluster galaxies have a smaller $r_{\mathrm{e}, {\rm {H}\alpha }}/r_{\mathrm{e}, R_{\mathrm{c} } }$ ratio than field galaxies: 〈$r_{\mathrm{e}, {\rm {H}\alpha }}/r_{\mathrm{e}, R_{\mathrm{c} } }$〉 = 0.96 ± 0.09 compared to 1.22 ± 0.08 (smaller at a 98 per cent credibility level). These values are uncorrected for the wavelength difference between H α emission and Rc-band stellar light but implementing such a correction only reinforces our results. We also show that whilst the cluster and field samples follow indistinguishable mass–metallicity (MZ) relations, the residuals around the MZ relation of cluster members correlate with cluster-centric distance; galaxies residing closer to the cluster centre tend to have enhanced metallicities (significant at the 2.6σ level). Finally, in contrast to previous studies, we find no significant differences in electron number density between the cluster and field galaxies. We use simple chemical evolution models to conclude that the effects of disc strangulation and ram-pressure stripping can quantitatively explain our observations.
Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju
Authors: Tovo Anna , Menzel Peter , Krogh Anders , Cosentino Lagomarsino Marco , Suweis Samir 
Published: June 2020

Abstract
Characterizing species diversity and composition of bacteria hosted by biota is revolutionizing our understanding of the role of symbiotic interactions in ecosystems. Determining microbiomes diversity implies the assignment of individual reads to taxa by comparison to reference databases. Although computational methods aimed at identifying the microbe(s) taxa are available, it is well known that inferences using different methods can vary widely depending on various biases. In this study, we first apply and compare different bioinformatics methods based on 16S ribosomal RNA gene and shotgun sequencing to three mock communities of bacteria, of which the compositions are known. We show that none of these methods can infer both the true number of taxa and their abundances. We thus propose a novel approach, named Core-Kaiju, which combines the power of shotgun metagenomics data with a more focused marker gene classification method similar to 16S, but based on emergent statistics of core protein domain families. We thus test the proposed method on various mock communities and we show that Core-Kaiju reliably predicts both number of taxa and abundances. Finally, we apply our method on human gut samples, showing how Core-Kaiju may give more accurate ecological characterization and a fresh view on real microbiomes.
Anti-MDA5 autoantibodies associated with juvenile dermatomyositis constitute a distinct phenotype in North America
Authors: Mamyrova Gulnara , Kishi Takayuki , Shi Min , Targoff Ira N , Huber Adam M , Curiel Rodolfo V , Miller Frederick W , Rider Lisa G ,   for the Childhood Myositis Heterogeneity Collaborative Study Group
Published: June 2020

Abstract

Objective
Myositis-specific autoantibodies have defined distinct phenotypes of patients with juvenile myositis (JIIM). We assessed the frequency and clinical significance of anti-melanoma differentiation-associated gene 5 (MDA5) autoantibody-associated JIIM in a North American registry.

Methods
Retrospective examination of the characteristics of 35 JIIM patients with anti-MDA5 autoantibodies was performed, and differences from other myositis-specific autoantibody groups were evaluated.

Results
Anti-MDA5 autoantibodies were present in 35/453 (7.7%) of JIIM patients and associated with older age at diagnosis, and lower serum creatine kinase and aldolase levels. Patients with anti-MDA5 autoantibodies had more frequent weight loss, adenopathy, arthritis, interstitial lung disease (ILD), and less frequent falling compared with anti-transcriptional intermediary factor 1 (TIF1), anti-nuclear matrix protein 2 (NXP2) and myositis-specific autoantibody/myositis-associated autoantibody-negative patients. They had a different season of diagnosis and less frequent mechanic’s hands and ILD compared with those with anti-synthetase autoantibodies. Anti-MDA5 patients received fewer medications compared with anti-TIF1, and corticosteroid treatment was shorter compared with anti-TIF1 and anti-nuclear matrix protein 2 autoantibody groups. The frequency of remission was higher in anti-MDA5 than anti-synthetase autoantibody-positive JIIM. In multivariable analyses, weight loss, arthritis and arthralgia were most strongly associated with anti-MDA5 autoantibody-positive JIIM.

Conclusion
Anti-MDA5 JIIM is a distinct subset, with frequent arthritis, weight loss, adenopathy and less severe myositis, and is also associated with ILD. Anti-MDA5 is distinguished from anti-synthetase autoantibody-positive JIIM by less frequent ILD, lower creatine kinase levels and differing seasons of diagnosis. Anti-MDA5 has comparable outcomes, but with the ability to discontinue steroids more rapidly and less frequent flares compared with anti-TIF1 autoantibodies, and more frequent remission compared with anti-synthetase JIIM patients.
Trustee decision-making: the substratum fallacy and the exercise of discretionary powers
Authors: Machell John 
Published: June 2020

Abstract
The Court of Appeal for Bermuda (Clarke P, Smellie JA and Subair Williams JA) recently handed down judgment in Grand View Private Trust Company Limited v Wong 20 April 2020, overturning the decision by Kawaley AJ at first instance and rejecting his use of the so-called substratum principle to limit the scope of widely drawn powers. The trust and wealth management industry should breath a collective sigh of relief. The industry is able to sell modern discretionary trusts to wealthy clients precisely because of their flexibility and the extent of the powers they contain, particularly discretionary powers of amendment, powers to add and remove beneficiaries and powers to distribute and resettle assets. The decision at first instance threatened to undermine that flexibility and to hamper the way in which trustees operate trusts of this kind. It is suggested that the Court of Appeal was right to reject the argument based on the supposed substratum rule. The argument gives inappropriate and independent life to what (if it is useful at all in this context) should only be a conclusionary metaphor; the argument involves what philosophers might describe as “unjustified reification”, or what the rest of us may think of as the tail wagging the dog. Use of the substratum metaphor risks distraction from the true task, that is, the proper construction of the words used in the relevant instrument in the light of the admissible factual matrix. The purpose of this article is to examine the Court of Appeal’s decision in Grand View, and tentatively to offer some thoughts on the analytical framework within which the validity of the exercise of powers is assessed.