bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of the MALDIxin test for the rapid identification of colistin resistance in Klebsiella pneumoniae using MALDI-TOF MS
Authors: Dortet Laurent , Broda Agnieszka , Bernabeu Sandrine , Glupczynski Youri , Bogaerts Pierre , Bonnin Rémy , Naas Thierry , Filloux Alain , Larrouy-Maumus Gerald 
Published: September 2019

Abstract

Background
With the dissemination of carbapenemase producers, a revival of colistin was observed for the treatment of infections caused by MDR Gram-negatives. Unfortunately, the increasing usage of colistin led to the emergence of resistance. In Klebsiella pneumoniae, colistin resistance arises through addition of 4-amino-l-arabinose (l-Ara4N) or phosphoethanolamine (pEtN) to the native lipid A. The underlying mechanisms involve numerous chromosome-encoded genes or the plasmid-encoded pEtN transferase MCR. Currently, detection of colistin resistance is time-consuming since it still relies on MIC determination by broth microdilution. Recently, a rapid diagnostic test based on MALDI-TOF MS detection of modified lipid A was developed (the MALDIxin test) and tested on Escherichia coli and Acinetobacter baumannii.

Objectives
Optimize the MALDIxin test for the rapid detection of colistin resistance in K. pneumoniae.

Methods
This optimization consists of an additional mild-acid hydrolysis of 15 min in 1% acetic acid. The optimized method was tested on a collection of 81 clinical K. pneumoniae isolates, including 49 colistin-resistant isolates (45 with chromosome-encoded resistance, 3 with MCR-related resistance and 1 with both mechanisms).

Results
The optimized method allowed the rapid (&lt;30 min) identification of l-Ara4N- and pEtN-modified lipid A of K. pneumoniae, which are known to be the real triggers of polymyxin resistance. At the same time, it discriminates between chromosome-encoded and MCR-related polymyxin resistance.

Conclusions
The MALDIxin test has the potential to become an accurate tool for the rapid determination of colistin resistance in clinically relevant Gram-negative bacteria.
Integrase strand transfer inhibitor (INSTI)-resistance mutations for the surveillance of transmitted HIV-1 drug resistance
Authors: Tzou Philip L , Rhee Soo-Yon , Descamps Diane , Clutter Dana S , Hare Bradley , Mor Orna , Grude Maxime , Parkin Neil , Jordan Michael R , Bertagnolio Silvia , Schapiro Jonathan M , Harrigan P Richard , Geretti Anna Maria , Marcelin Anne-Geneviève , Shafer Robert W ,   on behalf of the WHO HIVResNet Working Groups
Published: September 2019

Abstract

Background
Integrase strand transfer inhibitors (INSTIs) are expected to be widely adopted globally, requiring surveillance of resistance emergence and transmission.

Objectives
We therefore sought to develop a standardized list of INSTI-resistance mutations suitable for the surveillance of transmitted INSTI resistance.

Methods
To characterize the suitability of the INSTI-resistance mutations for transmitted HIV-1 drug resistance (TDR) surveillance, we classified them according to their presence on published expert lists, conservation in INSTI-naive persons, frequency in INSTI-treated persons and contribution to reduced in vitro susceptibility. Mutation prevalences were determined using integrase sequences from 17302 INSTI-naive and 2450 INSTI-treated persons; 53.3% of the INSTI-naive sequences and 20.0% of INSTI-treated sequences were from non-B subtypes. Approximately 10% of sequences were from persons who received dolutegravir alone or a first-generation INSTI followed by dolutegravir.

Results
Fifty-nine previously recognized (or established) INSTI-resistance mutations were present on one or more of four published expert lists. They were classified into three main non-overlapping groups: 29 relatively common non-polymorphic mutations, occurring in five or more individuals and significantly selected by INSTI treatment; 8 polymorphic mutations; and 22 rare mutations. Among the 29 relatively common INSTI-selected mutations, 24 emerged as candidates for inclusion on a list of INSTI surveillance drug-resistance mutations: T66A/I/K, E92G/Q, G118R, F121Y, E138A/K/T, G140A/C/S, Y143C/H/R/S, S147G, Q148H/R/K, N155H, S230R and R263K.

Conclusions
A set of 24 non-polymorphic INSTI-selected mutations is likely to be useful for quantifying INSTI-associated TDR. This list may require updating as more sequences become available from INSTI-experienced persons infected with HIV-1 non-subtype B viruses and/or receiving dolutegravir.
Conflicts of Interest in Inflammatory Bowel Disease Articles on UpToDate
Authors: Khan Rishad , Li Juana , Scaffidi Michael A , Gimpaya Nikko , Pivetta Bianca , Grover Samir C 
Published: September 2019

Abstract

Background
Financial conflicts of interest (FCOIs) are widespread in inflammatory bowel disease (IBD) and may be particularly important in point-of-care (POC) resources, such as UpToDate, that are used to aid clinical decision making. In this study, we determined the prevalence of industry payments from companies making biologic medications for IBD to contributors of UpToDate articles on IBD.

Methods
This cross-sectional analysis included UpToDate articles that mention the use of biologic medications for IBD. We collected the names of the contributors (authors and editors) and their disclosures on UpToDate. We then searched for their names on the Center for Medicare and Medicaid Open Payments database and compared the payment information from 2013 to 2018 with UpToDate's disclosures. We presented data per episode, which describes one instance of participation by one person in one article, regardless of whether that person contributed to multiple articles.

Results
We identified 23 articles on the treatment of Crohn's disease and ulcerative colitis that mentioned the use of biologic medications, with 86 total episodes. Sixty-two (72%) episodes involved FCOIs. The median payment associated with each episode was $$55 (interquartile range = $44 to $145,241). Contributors did not fully disclose FCOIs in 41 (48%) episodes. Deputy editors, who are required to be free of FCOIs, in general did not have substantial episodes involving FCOI.

Conclusions
We found that UpToDate articles on inflammatory bowel disease involve substantial FCOI, many of which are not disclosed. The presence of these FCOIs may hamper trust in the objectivity of treatment recommendations.
Genome survey and identification of polymorphic microsatellites provide genomic information and molecular markers for the red crab Charybdis feriatus (Linnaeus, 1758) (Decapoda: Brachyura: Portunidae)
Authors: Fang Shaobin , Wu Renxie , Shi Xi , Zhang Yin , Ikhwanuddin Mhd , Lu Jianxue , Xia Lianjun , Wu Qingyang , Ma Hongyu 
Published: September 2019

Abstract
We conducted a whole genome survey in the portunid crab Charybdis feriatus (Linnaeus, 1758) using Illumina sequencing platform and developed a set of polymorphic microsatellite loci. A total of 117.7 Gb of clean reads were generated, with 74× coverage of the estimated genome size of 1.4 Gb. The GC content, heterozygosity rate, and repeat sequence rate of the genome were estimated to be 40%, 1.1%, and 51%, respectively. A total of 3,779,209 microsatellites were identified from the genome. Sixty microsatellite loci were evaluated in a wild population of 40 individuals. As a result, 14 polymorphic microsatellite loci (23.3%) were obtained. The number of alleles (3 to 15), polymorphism information content (0.365 to 0.884), observed heterozygosity (0.050 to 0.975), and expected heterozygosity (0.450 to 0.907) per locus averaged 6.8, 0.652, 0.691, and 0.707, respectively. We show that the genome of C. feriatus has a high heterozygosity and repeat sequence rates, and provide a novel insight into the genome profile of marine crabs. The genetic markers developed in this study are potentially useful for studies on population dynamics and conservation genetics of C. feriatus and other species of brachyuran crabs.
Targeting accepted as a criterion to establish international jurisdiction in online EU trade mark infringement cases
Authors: Rosati Eleonora 
Published: September 2019

Abstract
Court of Justice of the European Union, AMS Neve Ltd and Others v Heritage Audio SL and Pedro Rodríguez Arribas, Case C-172/18, EU:C:2019:674, 5 September 2019 (‘AMS Neve’)
In its decision in AMS Neve, the Court of Justice of the European Union (CJEU) has adopted a dynamic reading of Article 97(5) of the EU Trade Mark Regulation 207/2009 (now Article 125(5) of Regulation 2017/1001) and clarified that—in the event of an infringement of an EU trade mark over the Internet—also the courts of the place at which the defendant’s activity is targeted have jurisdiction to hear the resulting action.
Historical Analysis: Editors’ Reflections on 50 Years of the Journal of Pediatric Psychology
Authors: Kazak Anne E , Roberts Michael C , Brown Ronald T , Holmbeck Grayson N , Koocher Gerald P , La Greca Annette M , Routh Donald , Willis Diane , Palermo Tonya M 
Published: September 2019

Abstract

Objective
This article provides an historical perspective on the Journal of Pediatric Psychology (JPP) on the occasion of its 50th anniversary.

Methods
Former and current editors of JPP participated in a symposium at the 2019 Society of Pediatric Psychology Annual Conference (SPPAC), each highlighting prominent types of articles published during their terms, the influence of these papers over time, and their reflections on the next 50 years of the journal. Their presentations were summarized and integrated for this article. Additional data on editorial teams, special issues, and publication metrics over time are included.

Results
The data demonstrate changes over time in the growth, scope, and impact of JPP. The article also shows the consistency in areas of emphasis over time. Anticipated topics for the future were quite consistent across editors and included increased use of technology, broader attention to teams and approaches, and methodological advances as the field will continue to grow.

Conclusions
This article provides an unusual collaboration among editors of JPP, providing an historical perspective on the journal’s growth over time and anticipation of continued impact into the future.
Formula size games for modal logic and μ-calculus
Authors: T Hella Lauri , S Vilander Miikka 
Published: September 2019

AbstractWe propose a new version of formula size game for modal logic. The game characterizes the equivalence of pointed Kripke models up to formulas of given numbers of modal operators and binary connectives. Our game is similar to the well-known Adler–Immerman game. However, due to a crucial difference in the definition of positions of the game, its winning condition is simpler, and the second player does not have a trivial optimal strategy. Thus, unlike the Adler–Immerman game, our game is a genuine two-person game. We illustrate the use of the game by proving a non-elementary succinctness gap between bisimulation invariant first-order logic $\textrm{FO}$ and (basic) modal logic $\textrm{ML}$. We also present a version of the game for the modal $\mu $-calculus $\textrm{L}_\mu $ and show that $\textrm{FO}$ is also non-elementarily more succinct than $\textrm{L}_\mu $.
The influence of inclinations on the dynamical stability of multi-planet systems
Authors: Wang Ying , Zhou Ji-lin , Liu Fu-yao , Sun Wei , Liu Hui-Gen , Yang Ming 
Published: September 2019

ABSTRACT
A type of compactly spaced and comparably sized multi-exoplanet system similar to TRAPPIST-1 has been discovered recently. The stability of these systems is an important issue, requiring further study. We examined how the initial inclinations influence the stability of multi-planet systems and derived an empirical formula describing the dependence of the instability time-scale on planetary mass, space separation and initial inclination. We find the following. (i) If space separations between planets are greater than 12RH (mutual Hill radius), coplanar multi-planet systems with 10−6 ≤ μ ≤ 10−3 (reduced planetary mass μ = m/M*) will remain stable within 1010Tin (the innermost orbital period). (ii) If initial inclinations of planets are smaller than 10° and space separations are greater than 10RH, multi-planet systems consisting of ≥5 planets with μ ≥ 10−5 will remain stable within 1010Tin. (iii) Initial inclinations in [0°, 10°] have inconsequential effects on the instability time-scales of massive multi-planet systems (μ ≥ 10−5), because eccentricities (excited during evolution) dominate the stability of these systems. (iv) If the initial inclinations are large enough (≥10°), sharp increases of instability time-scales in groups with 10−3 ≥ μ ≥ 10−5 will be moderated. This article presents a comprehensive study of the influence of inclination on the stability of multi-planet systems and discusses critical space separations for a multi-planet system becoming unstable.
Observing AGN feedback with CO intensity mapping
Authors: Breysse Patrick C , Alexandroff Rachael M 
Published: September 2019

ABSTRACTCurrent models of galaxy formation require star formation in high-mass galaxies to be limited by poorly understood mechanisms of quasar feedback. Feedback processes can be studied by examining the molecular gas content of AGN hosts through the CO rotational ladder, but the complexity of these observations means that current data are limited to only extremely CO-bright objects. Upcoming CO intensity mapping experiments offer an opportunity for a less biased probe of quasar feedback. By correlating intensity maps with spectroscopic AGN surveys, we can obtain a measurement of the mean CO luminosity of a large population of quasars simultaneously. We show that experiments like COMAP, CCAT-prime, and CONCERTO have enough sensitivity to detect this cross-correlation if existing AGN observations are representative of the whole population, and to place interesting upper limits if they are not. Future surveys will be able to increase the precision of these measurements by orders of magnitude, allowing detailed studies of quasar properties across a wide range of cosmic history.
Photometry and spectroscopy of massive stars observed during K2 Campaign 8
Authors: Eidam Jéssica M , Andrade Laerte , Emilio Marcelo , Rabello-Soares M Cristina , Pereira Alan W , Janot-Pacheco Eduardo , Armstrong James D 
Published: September 2019

ABSTRACTWe report in this paper spectroscopic and photometric analysis of eight massive stars observed during Campaign 8 of the Kepler/K2 mission from 2016 January to March. Spectroscopic data were obtained on these stars at OPD/LNA, Brazil, and their stellar parameters determined using sme. Periodic analyses of the light curves were performed through cleanest and period04 algorithms. Mass, luminosity, and radius of our stars were estimated employing cesam + posc grids. Three of our stars show significant periodicity. K2 ID 220679442 and K2 ID 220532854 have periods linked to the stellar rotation. K2 ID 220532854 has prominent silicon lines (Si ii 4128–4131 Å), a characteristic presented in the peculiar class of Ap magnetic main-sequence stars. However, in our spectral analysis, this object was found to be an evolved, luminous giant star. K2 ID 220466722 was revealed to be a δ Scuti variable, and 40 individual frequencies were determined for this star. No significant periodicity was found in the light curves for the remaining stars analysed in this work, besides the instrumental one.
Neutron star binary orbits in their host potential: effect on early r-process enrichment
Authors: Bonetti Matteo , Perego Albino , Dotti Massimo , Cescutti Gabriele 
Published: September 2019

ABSTRACT
Coalescing neutron star binary (NSB) systems are primary candidates for r-process enrichment of galaxies. The recent detection of r-process elements in ultrafaint dwarf (UFD) galaxies and the abundances measured in classical dwarfs challenges the NSB merger scenario both in terms of coalescence time-scales and merger locations. In this paper, we focus on the dynamics of NSBs in the gravitational potentials of different types of host galaxies and on its impact on the subsequent galactic enrichment. We find that, for a ∼t−1 delay time distribution, even when receiving a low kick (∼10 km s−1) from the second supernova explosion, in shallow dwarf galaxy potentials NSBs tend to merge with a large off-set from the host galaxy. This results in a significant geometrical dilution of the amount of produced r-process elements that fall back and pollute the host galaxy gas reservoir. The combination of dilution and small number statistics produces a large scatter in the expected r-process enrichment within a single UFD or classical dwarf galaxy. Comparison between our results and observed europium abundances reveals a tension that even a systematic choice of optimistic parameters in our models cannot release. Such a discrepancy could point to the need of additional r-process production sites that suffer less severe dilution or to a population of extremely fast merging binaries.
stroopwafel: simulating rare outcomes from astrophysical populations, with application to gravitational-wave sources
Authors: Broekgaarden Floor S , Justham Stephen , de Mink Selma E , Gair Jonathan , Mandel Ilya , Stevenson Simon , Barrett Jim W , Vigna-Gómez Alejandro , Neijssel Coenraad J 
Published: September 2019

ABSTRACT
Gravitational-wave observations of double compact object (DCO) mergers are providing new insights into the physics of massive stars and the evolution of binary systems. Making the most of expected near-future observations for understanding stellar physics will rely on comparisons with binary population synthesis models. However, the vast majority of simulated binaries never produce DCOs, which makes calculating such populations computationally inefficient. We present an importance sampling algorithm, stroopwafel, that improves the computational efficiency of population studies of rare events, by focusing the simulation around regions of the initial parameter space found to produce outputs of interest. We implement the algorithm in the binary population synthesis code compas, and compare the efficiency of our implementation to the standard method of Monte Carlo sampling from the birth probability distributions. stroopwafel finds ∼25–200 times more DCO mergers than the standard sampling method with the same simulation size, and so speeds up simulations by up to two orders of magnitude. Finding more DCO mergers automatically maps the parameter space with far higher resolution than when using the traditional sampling. This increase in efficiency also leads to a decrease of a factor of ∼3–10 in statistical sampling uncertainty for the predictions from the simulations. This is particularly notable for the distribution functions of observable quantities such as the black hole and neutron star chirp mass distribution, including in the tails of the distribution functions where predictions using standard sampling can be dominated by sampling noise.
Simple interpolation functions for the galaxy-wide stellar initial mass function and its effects in early-type galaxies
Authors: Dabringhausen J 
Published: September 2019

ABSTRACT
The galaxy-wide stellar initial mass function (IGIMF) of a galaxy is thought to depend on its star formation rate (SFR). Using a catalogue of observational properties of early-type galaxies (ETGs) and a relation that correlates the formation time-scales of ETGs with their stellar masses, the dependencies of the IGIMF on the SFR are translated into dependencies on more intuitive parameters like present-day luminosities in different passbands. It is found that up to a luminosity of approximately 109 L⊙ (quite independent of the considered passband), the total masses of the stellar populations of ETGs are slightly lower than expected from the canonical stellar initial mass function (IMF). However, the actual mass of the stellar populations of the most luminous ETGs may be up to two times higher than expected from a simple stellar population model with the canonical IMF. The variation of the IGIMF with the mass of ETGs is presented here also as convenient functions of the luminosity in various passbands.
Tentative detection of the circumgalactic medium of the isolated low-mass dwarf galaxy WLM
Authors: Zheng Yong , Putman Mary E , Emerick Andrew , McQuinn Kristen B W , Werk Jessica K , Lockman Felix J , Oppenheimer Benjamin D , Fox Andrew J , Kirby Evan N , Burchett Joseph N 
Published: September 2019

ABSTRACT
We report a tentative detection of the circumgalactic medium (CGM) of Wolf–Lundmark–Melotte (WLM), an isolated, low-mass (logM*/M⊙ ≈ 7.6), dwarf irregular galaxy in the Local Group (LG). We analyse an HST/COS archival spectrum of a quasar sightline (PHL2525), which is 45 kpc (0.5 virial radius) from WLM and close to the Magellanic Stream (MS). Along this sightline, two ion absorbers are detected in Si ii, Si iii, Si iv, C ii, and C iv at velocities of ∼−220 km s−1 (Component v-220) and ∼−150 km s−1 (Component v-150). To identify their origins, we study the position–velocity alignment of the components with WLM and the nearby MS. Near the magellanic longitude of PHL2525, the MS-related neutral and ionized gas moves at ≲−190 km s−1, suggesting an MS origin for Component v-220, but not for Component v-150. Because PHL2525 passes near WLM and Component v-150 is close to WLM’s systemic velocity (∼−132 km s−1), it is likely that Component v-150 arises from the galaxy’s CGM. This results in a total Si mass in WLM’s CGM of $M_{\rm Si}^{\rm CGM}\sim (0.2-1.0)\times 10^5~\mathrm{M}_\odot$ using assumption from other COS dwarf studies. Comparing $M_{\rm Si}^{\rm CGM}$ to the total Si mass synthesized in WLM over its lifetime (∼1.3 × 105 M⊙), we find ∼3 per cent is locked in stars, ∼6 per cent in the ISM, ∼15–77 per cent in the CGM, and the rest (∼14–76 per cent) is likely lost beyond the virial radius. Our finding resonates with other COS dwarf galaxy studies and theoretical predictions that low-mass galaxies can easily lose metals into their CGM due to stellar feedback and shallow gravitational potential.
Role of cosmic-ray streaming and turbulent damping in driving galactic winds
Authors: Holguin F , Ruszkowski M , Lazarian A , Farber R , Yang H-Y K 
Published: September 2019

ABSTRACT
Large-scale galactic winds driven by stellar feedback are one phenomenon that influences the dynamical and chemical evolution of a galaxy, redistributing material throughout the circumgalatic medium. Non-thermal feedback from galactic cosmic rays (CRs) – high-energy charged particles accelerated in supernovae and young stars – can impact the efficiency of wind driving. The streaming instability limits the speed at which they can escape. However, in the presence of turbulence, the streaming instability is subject to suppression that depends on the magnetization of turbulence given by its Alfvén Mach number. While previous simulations that relied on a simplified model of CR transport have shown that super-Alfvénic streaming of CRs enhances galactic winds, in this paper we take into account a realistic model of streaming suppression. We perform three-dimensional magnetohydrodynamic simulations of a section of a galactic disc and find that turbulent damping dependent on local magnetization of turbulent interstellar medium (ISM) leads to more spatially extended gas and CR distributions compared to the earlier streaming calculations, and that scale heights of these distributions increase for stronger turbulence. Our results indicate that the star formation rate increases with the level of turbulence in the ISM. We also find that the instantaneous wind mass loading is sensitive to local streaming physics with the mass loading dropping significantly as the strength of turbulence increases.