bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coli O80 hybrid pathotype strains producing Shiga toxin and ESBL: molecular characterization and potential therapeutic options
Authors: Cointe Aurélie , Birgy André , Bridier-Nahmias Antoine , Mariani-Kurkdjian Patricia , Walewski Violaine , Lévy Corinne , Cohen Robert , Fach Patrick , Delannoy Sabine , Bidet Philippe , Bonacorsi Stéphane 
Published: November 2019

Abstract

Objectives
Enterohaemorrhagic Escherichia coli (EHEC) infections may be complicated by haemolytic uraemic syndrome (HUS). The emerging worldwide EHEC serogroup O80 has acquired a mosaic plasmid combining extraintestinal virulence and antibiotic resistance. This hybrid pathotype is associated with invasive infections that require antibiotic therapy, classically not recommended in EHEC infections, increasing the risk of HUS. We characterized two ESBL-producing O80 EHEC strains, which is an unusual resistance mechanism among EHECs, and determined the safest therapy to be used for invasive infections.

Methods
WGS of two strains isolated from the stools of an asymptomatic carrier and a patient with HUS was performed using Illumina and Nanopore technologies. Generated reads were combined to assemble genomes. We determined the safest therapy by comparing Shiga toxin (Stx) production by the two strains in the presence of several antibiotics.

Results
The strains were genetically close to the O80 EHEC clone, belonging to ST301 and harbouring stx2d, eae-ξ, ehxA and genes characteristic of the extraintestinal virulence plasmid pS88. Long-read sequencing identified the acquisition of an additional plasmid harbouring CTX-M-type genes (blaCTX-M-14 and blaCTX-M-1). Azithromycin decreased Stx production at subinhibitory concentrations, ciprofloxacin increased it and imipenem had no major effect. The combination of azithromycin and imipenem overall reduced Stx production.

Conclusions
Acquisition of an additional plasmid harbouring ESBL genes is a step towards increasing the risk of O80 EHEC dissemination and represents a serious public health concern. The combination of azithromycin and imipenem reduced Stx production and suggests that this combination could be tested in clinical trials.
Dynamics of the leaf endoplasmic reticulum modulate β-glucosidase-mediated stress-activated ABA production from its glucosyl ester
Authors: Han Yiping , Watanabe Shunsuke , Shimada Hiroshi , Sakamoto Atsushi 
Published: November 2019

AbstractThe phytohormone abscisic acid (ABA) is produced via a multistep de novo biosynthesis pathway or via single-step hydrolysis of inactive ABA-glucose ester (ABA-GE). The hydrolysis reaction is catalyzed by β-glucosidase (BG, or BGLU) isoforms localized to various organelles, where they become activated upon stress, but the mechanisms underlying this organelle-specific activation remain unclear. We investigated the relationship between the subcellular distribution and stress-induced activation of BGLU18 (BG1), an endoplasmic reticulum enzyme critical for abiotic stress responses, in Arabidopsis thaliana leaves. High BGLU18 levels were present in leaf petioles, primarily in endoplasmic reticulum bodies. These Brassicaceae-specific endoplasmic reticulum-derived organelles responded dynamically to abiotic stress, particularly drought-induced dehydration, by changing in number and size. Under stress, BGLU18 distribution shifted toward microsomes, which was accompanied by increasing BGLU18-mediated ABA-GE hydrolytic activity and ABA levels in leaf petioles. Under non-stress conditions, impaired endoplasmic reticulum body formation caused a microsomal shift of BGLU18 and increased its enzyme activity; however, ABA levels increased only under stress, probably because ABA-GE is supplied to the endoplasmic reticulum only under these conditions. Loss of BGLU18 delayed dehydration-induced ABA accumulation, suggesting that ABA-GE hydrolysis precedes the biosynthesis. We propose that dynamics of the endoplasmic reticulum modulate ABA homeostasis and abiotic stress responses by activating BGLU18-mediated ABA-GE hydrolysis.
Comparison of risk factors and outcomes of Candida auris candidemia with non-Candida auris candidemia: A retrospective study from Pakistan
Authors: Sayeed Muneeba Ahsan , Farooqi Joveria , Jabeen Kauser , Mahmood Syed Faisal 
Published: November 2019

Abstract
Candida auris has emerged as a nosocomial multi-drug resistant pathogen. This study aimed to compare the risk factors and outcomes of C. auris candidemia patients with non-C. auris candidemia, at a single center in Pakistan. A retrospective study compared 38 C. auris with 101 non-C. auris (36 C. albicans, 38 C. tropicalis, and 27 C. parapsilosis) candidemia patients between September 2014 and March 2017 at the Aga Khan University Hospital, Pakistan. Demographics, clinical history, management and outcomes were studied. Prior history of surgery (adjusted odds ratio [aOR] 4.9, 95% confidence interval [CI]: 1.4–17.5), antifungals exposure (aOR 38.3, 95% CI: 4.1–356) and prior MDR bacteria isolation (aOR 5.09, 95% CI: 1.6–15.9) were associated with C. auris candidemia. On survival analysis both groups of patients had similar outcome in terms of mortality (62.6% vs. 52.54%, hazard ratio [HR] 1.45, 95% CI: 0.84–2.4, P-value = .17) and microbiological failure rates (42.3% vs. 32.2%, HR 0.65, 95% CI: 0.35–1.2, P-value = .17) however, C. auris patients had a higher mean hospital stay (36.32 days vs. 14.8 days, P-value = &lt;.001) and higher &gt;15-day in-hospital stay from positive culture (HR 2.68, 95% CI: 1.1–6.3, P-value = .025). Antifungal susceptibility was different, with C. auris more often resistant to voriconazole (29.6% vs. 0%) and amphotericin (3.7 vs. 0%); though no echinocandin resistance was detected in either group. As opposed to other Candida species, C. auris candidemia occurred after nosocomial exposure, and its source was most commonly an indwelling line. Although these patients had a higher in-hospital stay, but there was no excess mortality when compared to other Candida species.
FIESTA – disentangling stellar variability from exoplanets in the Fourier domain
Authors: Zhao J , Tinney C G 
Published: November 2019

ABSTRACT
We propose a new analysis methodology – FourIEr phase SpecTrum Analysis (FIESTA, or $\mathit {\Phi }$ESTA) – for the study of spectral line profile variability in Fourier space. The philosophy of $\mathit {\Phi }$ESTA is highlighted in its interpretation of a line deformation as various shifts of the composing Fourier modes. With this ability, $\mathit {\Phi }$ESTA excels in distinguishing the effects of a bulk shift in a line profile, from changes in a line profile shape. In other words, it can distinguish a radial velocity shift due to orbiting companions like planets, from an apparent radial velocity shift due to stellar variability (often referred to as ‘jitter’). Most importantly, it can quantify the radial velocity impact of stellar jitter on each epoch. Our simulations show that (compared to a model that does not account for stellar activity), $\mathit {\Phi }$ESTA can almost triple the fraction of planets recovered with orbital parameters measured to within 10 per cent of their input parameters, when extracting a 2 m s−1 amplitude planetary signal in the midst of ∼2 m s−1 amplitude starspot jitter for high signal-to-noise ratio (&gt;200 pixel−1) data. $\mathit {\Phi }$ESTA can also be used to identify stellar activity related periods in a periodogram analysis and classify relative amplitudes of stellar jitter and planetary signals, with examples for the analysis of HARPS data of the active star HD 224789 and the active planet-host star HD 103720. In the end, we demonstrate that $\mathit {\Phi }$ESTA’s framework is working as well as other activity indicators in correlating with stellar jitter.
Ultra-low-frequency waves in the ion foreshock of Mercury: a global hybrid modelling study
Authors: Jarvinen R , Alho M , Kallio E , Pulkkinen T I 
Published: November 2019

ABSTRACT
We study the solar wind interaction with Mercury using a global three-dimensional hybrid model. In the analysed simulation run, we find a well-developed, dynamic Hermean ion foreshock ahead of the quasi-parallel bow shock under upstream solar wind and interplanetary magnetic field (IMF) conditions corresponding to the orbital perihelion of the planet. A portion of the incident solar wind ion flux is scattered back upstream near the quasi-parallel bow shock including both major solar wind ion species, protons and alphas. The scattered particles form the Hermean suprathermal foreshock ion population. A significant part of the suprathermal population is backstreaming with a velocity component towards the Sun in the near-foreshock at the planetocentric distance of few planetary radii in the plane of the IMF. The ion foreshock is associated with large-scale, oblique fast magnetosonic waves in the ultra-low-frequency (ULF) range convecting downstream with the solar wind. The ULF wave period is about 5 s in the analysed upstream condition case at Mercury, which corresponds to the 30-s foreshock waves at Earth when scaled by the IMF magnitude.
Searching for gamma-ray emission from galaxy clusters at low redshift
Authors: Colavincenzo Manuel , Tan Xiuhui , Ammazzalorso Simone , Camera Stefano , Regis Marco , Xia Jun-Qing , Fornengo Nicolao 
Published: November 2019

ABSTRACT
We report the identification of a positive cross-correlation signal between the unresolved gamma-ray emission, measured by the Fermi Large Area Telescope, and four different galaxy cluster catalogues. The selected catalogues peak at low-redshift and span different frequency bands, including infrared, optical, and X-rays. The signal-to-noise ratio of the detected cross-correlation amounts to 3.5 in the most significant case. We investigate and comment about its possible origin, in terms of compact gamma-ray emission from AGNs inside clusters or diffuse emission from the intracluster medium. The analysis has been performed by introducing an accurate estimation of the cross-correlation power-spectrum covariance matrix, built with mock realizations of the gamma and galaxy cluster maps. Different methods to produce the mock realizations starting from the data maps have been investigated and compared, identifying suitable techniques which can be generalized to other cross-correlation studies.
Bifurcation in the history of Uranus and Neptune: the role of giant impacts
Authors: Reinhardt Christian , Chau Alice , Stadel Joachim , Helled Ravit 
Published: November 2019

ABSTRACT
Despite many similarities, there are significant observed differences between Uranus and Neptune: While Uranus is tilted and has a regular set of satellites, suggesting their accretion from a disc, Neptune’s moons are irregular and are captured objects. In addition, Neptune seems to have an internal heat source, while Uranus is in equilibrium with solar insulation. Finally, structure models based on gravity data suggest that Uranus is more centrally condensed than Neptune. We perform a large suite of high-resolution SPH simulations to investigate whether these differences can be explained by giant impacts. For Uranus, we find that an oblique impact can tilt its spin axis and eject enough material to create a disc where the regular satellites are formed. Some of the discs are massive and extended enough, and consist of enough rocky material to explain the formation of Uranus’ regular satellites. For Neptune, we investigate whether a head-on collision could mix the interior, and lead to an adiabatic temperature profile, which may explain its larger flux and higher moment of inertia value. We find that massive and dense projectiles can penetrate towards the centre and deposit mass and energy in the deep interior, leading to a less centrally concentrated interior for Neptune. We conclude that the dichotomy between the ice giants can be explained by violent impacts after their formation.
Point mutations in topoisomerase I alter the mutation spectrum in E. coli and impact the emergence of drug resistance genotypes
Authors: Bachar Amit , Itzhaki Elad , Gleizer Shmuel , Shamshoom Melina , Milo Ron , Antonovsky Niv 
Published: November 2019

Abstract
Identifying the molecular mechanisms that give rise to genetic variation is essential for the understanding of evolutionary processes. Previously, we have used adaptive laboratory evolution to enable biomass synthesis from CO2 in Escherichia coli. Genetic analysis of adapted clones from two independently evolving populations revealed distinct enrichment for insertion and deletion mutational events. Here, we follow these observations to show that mutations in the gene encoding for DNA topoisomerase I (topA) give rise to mutator phenotypes with characteristic mutational spectra. Using genetic assays and mutation accumulation lines, we find that point mutations in topA increase the rate of sequence deletion and duplication events. Interestingly, we observe that a single residue substitution (R168C) results in a high rate of head-to-tail (tandem) short sequence duplications, which are independent of existing sequence repeats. Finally, we show that the unique mutation spectrum of topA mutants enhances the emergence of antibiotic resistance in comparison to mismatch-repair (mutS) mutators, and leads to new resistance genotypes. Our findings highlight a potential link between the catalytic activity of topoisomerases and the fundamental question regarding the emergence of de novo tandem repeats, which are known modulators of bacterial evolution.
Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing
Authors: Liu Bin , Chen Siwei , Rose Anouk La , Chen Deng , Cao Fangyuan , Zwinderman Martijn , Kiemel Dominik , Aïssi Manon , Dekker Frank J , Haisma Hidde J 
Published: November 2019

Abstract
Despite the rapid development of CRISPR/Cas9-mediated gene editing technology, the gene editing potential of CRISPR/Cas9 is hampered by low efficiency, especially for clinical applications. One of the major challenges is that chromatin compaction inevitably limits the Cas9 protein access to the target DNA. However, chromatin compaction is precisely regulated by histone acetylation and deacetylation. To overcome these challenges, we have comprehensively assessed the impacts of histone modifiers such as HDAC (1–9) inhibitors and HAT (p300/CBP, Tip60 and MOZ) inhibitors, on CRISPR/Cas9 mediated gene editing efficiency. Our findings demonstrate that attenuation of HDAC1, HDAC2 activity, but not other HDACs, enhances CRISPR/Cas9-mediated gene knockout frequencies by NHEJ as well as gene knock-in by HDR. Conversely, inhibition of HDAC3 decreases gene editing frequencies. Furthermore, our study showed that attenuation of HDAC1, HDAC2 activity leads to an open chromatin state, facilitates Cas9 access and binding to the targeted DNA and increases the gene editing frequencies. This approach can be applied to other nucleases, such as ZFN and TALEN.
Adenosine-Induced Cardiac Arrest for Transvenous Embolization of Midbrain Arteriovenous Malformation
Authors: Lim Jaims , Shallwani Hussain , Vakharia Kunal , Siddiqui Adnan H 
Published: November 2019

Abstract

BACKGROUND AND IMPORTANCE
Few studies describe the use of adenosine-induced cardiac systole for treatment of cerebrovascular pathologies. We describe a midbrain arteriovenous malformation (AVM) treated with transvenous embolization using adenosine-induced asystole to achieve transient systemic hypotension with the purpose of furthering discussion on the technique and operative considerations for adenosine use in endovascular AVM treatments.

CLINICAL PRESENTATION
A 29-yr-old man presented with sudden onset of severe bilateral headache, blurred vision, and numbness on the right side of his face and tongue. Noncontrast head computed tomography revealed fourth ventricle hemorrhage. Diagnostic cerebral angiography revealed a high-flow midbrain AVM with a posterior wall perforator from the basilar artery terminus and a draining vein into the straight sinus. Transarterial AVM embolization was successful. The patient was discharged with no residual neurological deficits but returned 1 wk later with slurred speech and left-sided dysmetria. Repeat angiography revealed partial AVM filling. Attempts at transarterial embolization were unsuccessful. Thus, transvenous AVM embolization with adenosine-induced cardiac asystole and systemic hypotension was performed. A total of 60 mg of adenosine was administered, followed by 2 additional doses of 60 and 40 mg; and complete cardiac asystole with a mean arterial pressure of 40 mmHg was maintained, resulting in successful embolization of the AVM. No residual filling was visualized on postembolization arterial angiography runs. The patient was neurologically stable and discharged on postoperative day 2.

CONCLUSION
With appropriate and safe dosing, adenosine-induced asystole and systemic hypotension may be a feasible, safe option to reduce flow and assist endovascular transvenous embolization of high-flow AVMs.
Early China and the Quest for Mastery
Authors: Stalnaker Aaron 
Published: November 2019

AbstractThis chapter introduces early Chinese history, texts, and thought sufficiently to make the rest of the work intelligible to nonspecialists, and positions this study in relation to current debates in Chinese philosophy and the study of early China. The main argument is that we should stop seeing “China” as an inverted mirror image of the West, and let go of the enduring myth of Chinese and specifically Confucian authoritarianism. The chapter criticizes extreme versions of Confucian role ethics put forward by Ames and Rosemont, in favor of a Confucian relational self that possesses a conditioned form of autonomy, as advocated by Wong.
Social Democratic Capitalism and the Good Society
Authors: Kenworthy Lane 
Published: November 2019

Abstract
Abstract: To this point in history, the most successful societies have been those that feature capitalism, a democratic political system, good elementary and secondary (K–12) schooling, a big welfare state, public services that are conducive to employment, and moderate regulation of product and labor markets. I call this set of policies and institutions “social democratic capitalism.” Social democratic capitalism improves living standards for the least well-off, enhances economic security, and very likely boosts equality of opportunity. It does so without sacrificing the many other things we want in a good society, from liberty to economic growth to health to happiness and much more.
Islamic Law and International Law
Authors: Powell Emilia Justyna 
Published: November 2019

Abstract
This chapter explores in considerable detail differences and similarities between the Islamic legal tradition and international law. It discusses in detail the historical interaction between these legal traditions, their co-evolution, and the academic conversations on this topic. The chapter also addresses the Islamic milieu’s contributions to international law, and sources of Islamic law including the Quran, sunna, judicial consensus, and analogical reasoning. It talks about the role of religion in international law. Mapping the specific characteristics of Islamic law and international law offers a glimpse of the contrasting and similar paradigms, spirit, and operation of law. This chapter identifies three points of convergence: law of scholars, customary law, and rule of law; as well as three points of departure: relation between law and religion, sources of law, and religious features in the courtroom (religious affiliation and gender of judges, holy oaths).
Divine Women, Femmes, and Whores
Authors: Hedenborg White Manon 
Published: November 2019

Abstract
The chapter presents the frameworks utilized within the study to analyze the construction of femininities. Beginning with an overview of how feminist theorists have approached the complex of femininity, I contend that femininity has remained undertheorized in academic research, frequently associated with lack, artifice, subordination, and restriction. Building on the work of scholars working within queer and poststructuralist feminist paradigms—including Luce Irigaray, Judith Butler, Mimi Schippers, and Rosi Braidotti—I assert that any social system contains multiple femininities, which relate to each other as well as to masculinity. Moreover, femininities are neither exclusively oriented toward heterosexuality nor do they exist in any given relationship to (female) biology. Throughout the discussion, I also engage with feminist theorization of feminine sexuality, allying myself with sex-radical theorists who have argued that an analysis of feminine sexuality must account for mechanisms of both oppression and resistance.
The Scarlet Goddess and the Wine of Her Fornications
Authors: Hedenborg White Manon 
Published: November 2019

Abstract
Beginning with an overview of feminine stereotypes in fin-de-siècle culture, the chapter introduces Aleister Crowley and his concepts of Babalon and the related figure of the Scarlet Woman. An unconventional figure and founder of the religion Thelema, Crowley led an openly bisexual life and advocated free sexuality. In 1909, Crowley experimented with Enochian magic in the Algerian desert with his lover and disciple Victor B. Neuburg, beholding a series of visions, including one featuring a great goddess. Based on a positive reinterpretation of the Whore of Babylon (Rev. 17), Crowley linked this goddess—called Babalon—to the initiatory ordeal of crossing the Abyss, when the seeker must annihilate their ego to become one with all. I argue that Crowley’s articulation of Babalon built on the fin-de-siècle trope of the femme fatale, which he reinterpreted as a soteriological ideal, thus challenging notions of feminine sexual modesty and bourgeois, masculine rationality.
Feminist Difference
Authors: Hedenborg White Manon 
Published: November 2019

Abstract
This chapter analyzes how contemporary esotericists conceptualize Babalon as a challenge to hegemonic perceptions of femininity. As highlighted in previous chapters, the 1990s onward has witnessed increasing gender-critical awareness in the esoteric milieu. Present-day esotericists connect Babalon to assertiveness, liberated sexuality, sexual aggression, and dominance, thus presenting her as a symbol that runs counter to normative ideas about femininity as nurturing, maternal, soft, and family-oriented. The chapter also explores how the Babalon discourse intersects with critiques of historical Western esotericism and Thelema as well as how esotericists today address perceived sexism in the writings of Crowley and other male occultists. A number of esoteric writers and practitioners posit Babalon as the epitome of the empowered woman magician. While some of these interpretations emphasize the link between femininity and biology, others stress femininity as something more flexible in ways that acknowledge genderqueer and transgendered experience.