bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of gentamicin MICs by agar dilution and Etest for clinical isolates of Neisseria gonorrhoeae
Authors: Kularatne Ranmini , Kufa Tendesayi , Gumede Lindy , Maseko Venessa 
Published: May 2020

AbstractBackgroundIn South Africa, Neisseria gonorrhoeae (NG) is the predominant cause of male urethritis syndrome (MUS). The national MUS treatment guidelines recommend gentamicin as salvage therapy for ceftriaxone treatment failures. We ascertained and compared gentamicin MICs obtained by agar dilution and Etest for clinical isolates of NG.MethodsGentamicin MICs for NG culture isolates obtained from 272 MUS cases in 2017 were determined using agar dilution, as per CLSI agar dilution methods, and Etest® (bioMérieux, Marcy-l’Étoile, France). Previously published interpretive criteria were used: MIC ≤4 mg/L, susceptible (S); MIC 8–16 mg/L, intermediately resistant (IR); and MIC ≥32 mg/L, resistant (R). WHO 2008 NG reference strains were used as comparison standards.ResultsGentamicin agar dilution versus Etest MIC results (mg/L) were as follows: MIC50 = 16 versus 4; MIC90 = 16 versus 8; minimum MIC = 4 versus 1; and maximum MIC = 32 versus 16. Interpretive categories for agar dilution versus Etest were as follows: S, 4.4% versus 86.8%; IR, 86.0% versus 13.4%; and R, 9.6% versus 0%. The gentamicin MIC50 by agar dilution was significantly higher than by Etest (sign test P value &lt;0.001); overall MIC agreement was 7.4% [kappa statistic (κ) = −0.014 (95% CI −0.039 to 0.010)]. Correlation with expected MICs for WHO reference strains was consistently better with Etest than with agar dilution.ConclusionsThere was a significant discordance between NG gentamicin MICs by agar dilution versus Etest. NG gentamicin AST methodology must be standardized and interpretive criteria established to optimize the monitoring of susceptibility trends.
Dissemination of the blaCTX-M-15 gene among Enterobacteriaceae via outer membrane vesicles
Authors: Bielaszewska Martina , Daniel Ondřej , Karch Helge , Mellmann Alexander 
Published: May 2020

Abstract

Background
Bacterial outer membrane vesicles (OMVs) are an emerging source of antibiotic resistance transfer but their role in the spread of the blaCTX-M-15 gene encoding the most frequent CTX-M ESBL in Enterobacteriaceae is unknown.

Objectives
To determine the presence of blaCTX-M-15 and other antibiotic resistance genes in OMVs of the CTX-M-15-producing MDR Escherichia coli O104:H4 outbreak strain and the ability of these OMVs to spread these genes among Enterobacteriaceae under different conditions.

Methods
OMV-borne antibiotic resistance genes were detected by PCR; OMV-mediated transfer of blaCTX-M-15 and the associated blaTEM-1 was quantified under laboratory conditions, simulated intraintestinal conditions and under ciprofloxacin stress; resistance to antibiotics and the ESBL phenotype were determined by the CLSI disc diffusion methods and the presence of pESBL by plasmid profiling and Southern blot hybridization.

Results
E. coli O104:H4 OMVs carried blaCTX-M-15 and blaTEM-1 located on the pESBL plasmid, but not chromosomal antibiotic resistance genes. The OMVs transferred blaCTX-M-15, blaTEM-1 and the associated pESBL into Enterobacteriaceae of different species. The frequencies of the OMV-mediated transfer were significantly increased under simulated intraintestinal conditions and under ciprofloxacin stress when compared with laboratory conditions. The ‘vesiculants’ (i.e. recipients that received the blaCTX-M-15- and blaTEM-1-harbouring pESBL via OMVs) acquired resistance to cefotaxime, ceftazidime and cefpodoxime and expressed the ESBL phenotype. They were able to further spread pESBL and the blaCTX-M-15 and blaTEM-1 genes via OMVs.

Conclusions
OMVs are efficient vehicles for dissemination of the blaCTX-M-15 gene among Enterobacteriaceae and may contribute to blaCTX-M-15 transfer in the human intestine.
Health, housing, and ‘direct threats’ during a pandemic
Authors: Wagner Jennifer K 
Published: May 2020

Abstract
The COVID-19 pandemic brought into stark relief the intimate nexus between health and housing. This extraordinary infectious disease outbreak combined with the astounding lack of a clear, coordinated, prompt, and effective public health response in the U.S. created conditions and introduced practical challenges that left many disoriented-not only health care providers but also housing providers. Innumerable issues are worth examination, such as implications of moratoria on evictions and foreclosures, force majeure contract clauses, insurability of pandemic-related damages and disruptions, holdover tenancies and delayed occupancies, and possible abatement of rent or homeowner/condominium association dues in light of closed common facilities (such as fitness areas) or reduced benefits to be enjoyed with residential property; however, this article focuses on fair housing law and the ``direct threat'' exemption; finds it unlikely that COVID-19 is a disability, likely that the ``direct threat'' defense is available, and both determinations to be case-specific inquiries dependent upon rapidly-changing scientific understanding of this disease. By highlighting adequate housing as a human right for which the government has primary responsibility for ensuring its achievement, this article underscores the importance of finding a holistic solution to public health and housing problems before the next public health emergency arises.
Ontario, Canada’s LTSP Experience: Forging Lasting Research Partnerships and the Adaptive Management Cycle in Action
Authors: Morris Dave M , Fleming Rob L , Hazlett Paul W 
Published: May 2020

Abstract
In this paper, we summarize Ontario’s Long-term Soil Productivity (LTSP) experience focusing on our efforts to forge lasting research partnerships, highlight the approaches we feel were effective in getting emerging science into forest policy within an adaptive management (AM) framework, and describe the future direction of Ontario’s LTSP program as new policy issues are emerging as part of the continuous AM cycle. Fourteen installations were established on nutrient-poor, conifer-dominated sites, considered to be the most sensitive to increased biomass removals. From 1993 to 1995, all sites were clearcut-harvested, with replicated (three reps per site) biomass removal treatments that included: stem only, full-tree, and full-tree + forest floor removal. Routine (every 5 years) measurements have been carried out to track changes in soil carbon and nutrient levels, as well as stand- and individual-tree growth and development metrics and foliar nutrition. The published results from Ontario’s LTSP program, in combination with the North American-wide LTSP synthesis outputs, have suggested that these nutrient-poor, conifer-dominated sites are less sensitive to biomass (nutrient) removals than previously thought. The evidence provided through peer-reviewed publications, conference and workshop presentations, and field tours was substantive and led to a review and revision of the full-tree logging direction within Ontario’s guidelines. We conclude with a set of recommendations (lessons learned) for the successful delivery of any new long-term, interdisciplinary research projects examining the sustainability of forest-management practices.
Replaced right hepatic artery arising from the gastroduodenal artery: a rare and challenging anatomical variant of the Whipple procedure
Authors: Pueyo-Périz Eva María , Sánchez-Velázquez Patricia , De Miguel Maite , Radosevic Aleksandar , Petrowsky Henrik , Burdío Fernando 
Published: May 2020

Abstract
Accurate assessment of the vascular anatomy is a prerequisite of any pancreatic resection, since an unnoticed arterial injury in the context of a complex resection such as Whipple procedure, can seriously jeopardize patient’s safety. This article aims to describe an infrequent anatomic variant of a replaced right hepatic artery originating directly from the gastroduodenal artery and its potential implications for duodenopancreatectomy, as the gastroduodenal artery is routinely divided. We present here two different cases of this arterial abnormality identified during a Whipple procedure and its implications in each different setting. Preoperative identification of anatomical variations is essential for proficient surgical planning. Nevertheless, when detected during surgery, an meticulous dissection of the hepatoduodenal ligament is required to identify all the vascular relations in order to avoid irreversible damage.
Emergency surgery in an elective setting: a case report detailing incidental diagnosis of a de Garengeot hernia
Authors: Brosnan Conor , Keogh Shane , Bolger Jarlath C , Farrell Kevin , Hannan Enda , Mulholland Doug , Butt Abeeda , Hill Arnold D K 
Published: May 2020

AbstractWe present a case of acute appendicitis within an incarcerated femoral hernia. This is a rare complication of the phenomenon eponymously known as a ‘De Garengeot Hernia’, which describes a vermiform appendix in an incarcerated femoral hernia sac. Our case is somewhat unique in the manner by which the affected patient had presented. Attending hospital for an unrelated elective surgery, an incarcerated hernia was diagnosed at time of admission. Thorough assessment in advance of the procedure and decisive action led to a satisfactory outcome. This may be the first case in literature reporting a ‘De Garengeot Hernia’ presenting in such a fashion.
Troubling the Tragic Paradigm: Genre and Epigraph in Thomas Hardy’s Tess of the d’Urbervilles
Authors: Rimmer Mary 
Published: May 2020

Abstract
The rarely discussed epigraph to Thomas Hardy’s Tess of the d’Urbervilles – ‘Poor wounded name! My bosom as a bed | Shall lodge thee’ – at first seems an odd choice. Tess is usually read as a tragedy; the epigraph’s source, Shakespeare’s The Two Gentlemen of Verona, is a comedy. The speaker of these lines in the play is a woman, the ‘wounded name’ a man’s, and the immediate context one of erotic playfulness as Julia tears up Proteus’s love letter and then tenderly gathers up the fragments. Yet the apparent mismatch works, because it gestures towards both the generic instability of Two Gentlemen, and the novel’s own unstable genre. Hardy recurrently raises the question of how Tess Durbeyfield’s story should be read. Tess’s ‘fall’ is at different times and for different people a fatal blot on her prospects, a venial error, and material for an amusing or satirical story. Novel and heroine hover between genres; generic interpretations are complicated by gender and class. Early reviewers who refused to read Tess as a tragedy may seem wrong-headed and puritanical in hindsight, but they were in some ways more alive to the novel’s generic slippages than many later readers. Hardy at once invokes and unsettles generic models, in his choice of epigraph and throughout the book.
Ribosome profiling in plants: what is not lost in translation?
Authors: Kage Udaykumar , Powell Jonathan J , Gardiner Donald M , Kazan Kemal 
Published: May 2020

Abstract
Translation is a highly dynamic cellular process whereby genetic information residing in an mRNA molecule is converted into a protein that in turn executes specific functions. However, pre-synthesized mRNA levels do not always correlate with corresponding protein levels, suggesting that translational control plays an essential role in gene regulation. A better understanding of how gene expression is regulated during translation will enable the discovery of new genes and mechanisms that control important traits in plants. Therefore, in recent years, several methods have been developed to analyse the translatome; that is, all mRNAs being actively translated at a given time, tissue, and/or developmental stage. Ribosome profiling or ribo-seq is one such technology revolutionizing our ability to analyse the translatome and in turn understand translational control of gene expression. Ribo-seq involves isolating mRNA–ribosome complexes, treating them with a RNase, and then identifying ribosome-protected mRNA regions by deep sequencing. Here, we briefly review recent ribosome profiling studies that revealed new insights into plant biology. Manipulation of novel genes identified using ribosome profiling could prove useful for increasing yield through improved biotic and abiotic stress tolerance.
Variability in the chloroplast area lining the intercellular airspace and cell walls drives mesophyll conductance in gymnosperms
Authors: Veromann-Jürgenson Linda-Liisa , Brodribb Timothy J , Niinemets Ülo , Tosens Tiina 
Published: May 2020

Abstract
The photosynthetic efficiency of plants in different environments is controlled by stomata, hydraulics, biochemistry, and mesophyll conductance (gm). Recently, gm was demonstrated to be the key limitation of photosynthesis in gymnosperms. Values of gm across gymnosperms varied over 20-fold, but this variation was poorly explained by robust structure-bound integrated traits such as leaf dry mass per area. Understanding how the component structural traits control gm is central for identifying the determinants of variability in gm across plant functional and phylogenetic groups. Here, we investigated the structural traits responsible for gm in 65 diverse gymnosperms. Although the integrated morphological traits, shape, and anatomical characteristics varied widely across species, the distinguishing features of all gymnosperms were thick mesophyll cell walls and low chloroplast area exposed to intercellular airspace (Sc/S) compared with angiosperms. Sc/S and cell wall thickness were the fundamental traits driving variations in gm across gymnosperm species. Chloroplast thickness was the strongest limitation of gm among liquid-phase components. The variation in leaf dry mass per area was not correlated with the key ultrastructural traits determining gm. Thus, given the absence of correlating integrated easy-to-measure traits, detailed knowledge of underlying component traits controlling gm across plant taxa is necessary to understand the photosynthetic limitations across ecosystems.
Objects of Choice
Authors: Schwarz Wolfgang 
Published: May 2020

Abstract
Rational agents are supposed to maximize expected utility. But what are the options from which they choose? I outline some constraints on an adequate representation of an agent’s options. The options should, for example, contain no information of which the agent is unsure. But they should be sufficiently rich to distinguish all available acts from one another. These demands often come into conflict, so that there seems to be no adequate representation of the options at all. After reviewing existing proposals for how to construe decision-theoretic options and finding them all wanting, I suggest that our model of rational agents should include a special domain of ‘virtual’ option propositions to serve as formal objects of deliberation and choice.
Instability of non-Keplerian warped discs
Authors: Doğan S , Nixon C J 
Published: May 2020

ABSTRACT
Many accretion discs are thought to be warped. Recent hydrodynamical simulations show that (i) discs can break into distinct planes when the amplitude of an imposed warp is sufficiently high and the viscosity sufficiently low, and that (ii) discs can tear up into discrete rings when an initially planar disc is subject to a forced precession. Previously, we investigated the local stability of isolated, Keplerian, warped discs in order to understand the physics causing an accretion disc to break into distinct planes, finding that antidiffusion of the warp amplitude is the underlying cause. Here, we explore the behaviour of this instability in disc regions where the rotation profile deviates from Keplerian. We find that at small warp amplitudes non-Keplerian rotation can stabilize the disc by increasing the critical warp amplitude for instability, while at large warp amplitudes non-Keplerian rotation can lead to an increased growth rate for discs that are unstable. Tidal effects on discs in binary systems are typically weak enough such that the disc remains close to Keplerian rotation. However, the inner regions of discs around black holes are strongly affected, with the smallest radius at which the disc can break into discrete planes being a function of the black hole spin. We suggest that interpreting observed frequencies in the power spectra of light curves from accreting compact objects as nodal and apsidal precession of discrete orbits requires an instability that can break the disc into discrete rings such as the one explored here.
The impact of AGN feedback on the 1D power spectra from the Ly α forest using the Horizon-AGN suite of simulations
Authors: Chabanier Solène , Bournaud Frédéric , Dubois Yohan , Palanque-Delabrouille Nathalie , Yèche Christophe , Armengaud Eric , Peirani Sébastien , Beckmann Ricarda 
Published: May 2020

ABSTRACT
The Lyman-α forest is a powerful probe for cosmology, but it is also strongly impacted by galaxy evolution and baryonic processes such as active galactic nucleus (AGN) feedback, which can redistribute mass and energy on large scales. We constrain the signatures of AGN feedback on the 1D power spectrum of the Lyman-α forest using a series of eight hydro-cosmological simulations performed with the adaptive mesh refinement code ramses. This series starts from the Horizon-AGN simulation and varies the subgrid parameters for AGN feeding, feedback, and stochasticity. These simulations cover the whole plausible range of feedback and feeding parameters according to the resulting galaxy properties. AGNs globally suppress the Lyman-α power at all scales. On large scales, the energy injection and ionization dominate over the supply of gas mass from AGN-driven galactic winds, thus suppressing power. On small scales, faster cooling of denser gas mitigates the suppression. This effect increases with decreasing redshift. We provide lower and upper limits of this signature at nine redshifts between z = 4.25 and 2.0, making it possible to account for it at post-processing stage in future work given that running simulations without AGN feedback can save considerable amounts of computing resources. Ignoring AGN feedback in cosmological inference analyses leads to strong biases with 2 per cent shift on σ8 and 1 per cent shift on ns, which represents twice the standards deviation of the current constraints on ns.
Electrostatic charging of permanently shadowed craters on the Moon
Authors: Mishra S K , Bhardwaj Anil 
Published: May 2020

ABSTRACT
An open question of the electrostatic charge development on the lunar surface in the electron-rich region within the permanently shadowed craters (PSCs) is addressed. We propose that the fine dust grains on the crater surface may act as efficient field emission centres generating electrons via quantum field tunnelling. This return current may be sufficient to establish a steady-state dynamical equilibrium for the surface-plasma system. This leads to the crater surface attaining a finite electric potential. Our analysis illustrates that the PSC having ∼100 nm dust, covering 1 per cent of the surface area within the electron-rich region, may acquire a negative potential of few hundred volts in the steady-state condition.
eIF4G has intrinsic G-quadruplex binding activity that is required for tiRNA function
Authors: Lyons Shawn M , Kharel Prakash , Akiyama Yasutoshi , Ojha Sandeep , Dave Dhwani , Tsvetkov Vladimir , Merrick William , Ivanov Pavel , Anderson Paul 
Published: May 2020

AbstractAs cells encounter adverse environmental conditions, such as hypoxia, oxidative stress or nutrient deprivation, they trigger stress response pathways to protect themselves until transient stresses have passed. Inhibition of translation is a key component of such cellular stress responses and mounting evidence has revealed the importance of a class of tRNA-derived small RNAs called tiRNAs in this process. The most potent of these small RNAs are those with the capability of assembling into tetrameric G-quadruplex (G4) structures. However, the mechanism by which these small RNAs inhibit translation has yet to be elucidated. Here we show that eIF4G, the major scaffolding protein in the translation initiation complex, directly binds G4s and this activity is required for tiRNA-mediated translation repression. Targeting of eIF4G results in an impairment of 40S ribosome scanning on mRNAs leading to the formation of eIF2α-independent stress granules. Our data reveals the mechanism by which tiRNAs inhibit translation and demonstrates novel activity for eIF4G in the regulation of translation.
Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters
Authors: Ni Weiya , Perez Andrew A , Schreiner Shannon , Nicolet Charles M , Farnham Peggy J 
Published: May 2020

Abstract
Our study focuses on a family of ubiquitously expressed human C2H2 zinc finger proteins comprised of ZFX, ZFY and ZNF711. Although their protein structure suggests that ZFX, ZFY and ZNF711 are transcriptional regulators, the mechanisms by which they influence transcription have not yet been elucidated. We used CRISPR-mediated deletion to create bi-allelic knockouts of ZFX and/or ZNF711 in female HEK293T cells (which naturally lack ZFY). We found that loss of either ZFX or ZNF711 reduced cell growth and that the double knockout cells have major defects in proliferation. RNA-seq analysis revealed that thousands of genes showed altered expression in the double knockout clones, suggesting that these TFs are critical regulators of the transcriptome. To gain insight into how these TFs regulate transcription, we created mutant ZFX proteins and analyzed them for DNA binding and transactivation capability. We found that zinc fingers 11–13 are necessary and sufficient for DNA binding and, in combination with the N terminal region, constitute a functional transactivator. Our functional analyses of the ZFX family provides important new insights into transcriptional regulation in human cells by members of the large, but under-studied family of C2H2 zinc finger proteins.
Transcriptome Analysis of Low- and High-Sucrose Pear Cultivars Identifies Key Regulators of Sucrose Biosynthesis in Fruits
Authors: Lü Jiahong , Tao Xin , Yao Gaifang , Zhang Shaoling , Zhang Huping 
Published: May 2020

Abstract
Sucrose accumulation is one of the important factors that determine fruit enlargement and quality. Evaluation of the sugar profile of 105 pear cultivars revealed low-sucrose and high-sucrose (HS) types of pear fruits. To better understand the molecular mechanisms governing the sucrose content of pear fruits, this study performed transcriptome analysis during fruit development using low-sucrose ‘Korla’ fragrant pear and HS ‘Hosui’ pear, and a coexpression module uniquely associated with the control of high-sucrose accumulation was identified by weighted gene coexpression network analysis. These results suggested that there are seven candidate genes encoding key enzymes (fructokinase, glucose-6-phosphate isomerase, sucrose phosphate synthase and sucrose synthase) involved in sucrose biosynthesis and several transcription factors (TFs) whose expression patterns correlate with those of genes associated with sucrose biosynthesis. This correlation was confirmed by linear regression analysis between predicted gene expression and sucrose content in different pear cultivars during fruit development. This study provides insight into the molecular mechanism underlying differences in sucrose content across pear cultivars and presents candidate structural genes and TFs that could play important roles in regulating carbohydrate partitioning and sucrose accumulation.