bluuebunny/crossref_metadata_2025_split huggingface dataset:
P26 Phenotypic and genotypic characterization of antimicrobial resistance in Clostridioides difficile in North Wales
Authors: Thomas R. , Coupe B. , Bull M. , Copsey S. , Morris T. , Perry M. , Morgan C. 
Published: February 2022

Abstract

Background
Clostridioides difficile poses a major infection control challenge and remains a huge burden to our healthcare system. The emergence of hypervirulent strains of C. difficile has highlighted the need for monitoring antimicrobial resistance (AMR) and continual epidemiological vigilance. Agar dilution is the current gold standard method for antimicrobial susceptibility testing of C. difficile and the method routinely utilized in the Public Health Wales (PHW) UK Anaerobe Reference Unit (UKARU) at the University Hospital of Wales, Cardiff. However, this method is laborious and time consuming. Meanwhile, the emergence of WGS introduces the possibility of acquiring rapid genotypic information in terms of AMR.

Methods
In this research project, isolates obtained from faecal samples submitted across the Betsi Cadwalader health board (BCUHB) that were either GDH or PCR positive were sequenced as part of the C. difficile Genomic Sequencing and Typing (DIGEST) pilot project performed at the PHW Pathogen Genomics Unit (PenGU) in Cardiff.

Results
Results highlights include the finding that 93% of the isolates analysed for the presence of AMR genes were found to have the cdeA gene associated with conferring resistance to fluoroquinolones such as ciprofloxacin. Other common genes observed included blaCDD-1 and blaCDD-2, associated with β-lactam resistance.

Conclusions
While further work must be done to link genotypic characterization with phenotype, this study provides a valuable insight into AMR mechanisms in C. difficile and may in future become an important tool providing early indication of shift in C. difficile epidemiology or the emergence of a new hypervirulent and MDR strain.
P29 A retrospective multi-centre review of antimicrobial usage in patients diagnosed with aspiration pneumonia
Authors: Ashtey Blend , Troise Oliver , Hughes Stephen 
Published: February 2022

Abstract

Background
Over-diagnosis of infective aspiration pneumonia is common in healthcare settings and represents a potential for misuse of antimicrobial therapy.

Methods
A retrospective analysis was undertaken of all hospitalized patients treated for aspiration pneumonia within a multicentre Acute NHS Trust (April–May 2021, London, UK). Data collected included: age, initial antibiotics prescribed, duration of therapy, relevant microbiology (sputum samples or blood cultures) and chest X-ray. Treatment response was analysed including body temperature after 24 h of antimicrobials, use of oxygen support after 48 h, any escalation of antimicrobial therapy and 30 day in-hospital mortality. The study was registered as service evaluation project.

Results
In total, 94 patients treated for aspiration pneumonia were included; median age 82 years (IQR 67–89). Co-amoxiclav monotherapy was the most frequently prescribed treatment (67/94); cephalosporins (8/94) and ciprofloxacin (4/94) were also commonly used. Duration (median) of treatment was 4.4 days (IQR 1–6.7); 32/94 patients received &lt;48 h. Radiological evidence of consolidation, O2 support at 48 h and fever at 24 h was present in 32/94, 25/94 and 12/94 patients, respectively. A microbiological diagnosis to confirm infection was present in 12/94. Consolidation [OR 2.36 (95% CI 1.04–10.25); P = 0.037] and O2 support at 48 h [OR 3.22 (95% CI 1.02–10.25); P = 0.044], but not fever at 24 h [OR 0.94 (95% CI 0.18–4.80)], were associated with treatment escalation. No association between O2 support/fever and total duration was evident. The 30 day in-hospital mortality was 17% (16/94).

Conclusions
Aspiration pneumonia has high in-hospital mortality and often necessitates antibacterial treatment. The true incidence of bacterial pneumonia is unclear, and many patients may benefit from early cessation of antibacterial treatment.
P31 Gut colonization of carbapenem-resistant Enterobacteriaceae among patients with haematological malignancies in National Cancer Institute, Sri Lanka
Authors: Suranadee Y. W. S. , Dissanayake Y. , Dissanayake B. M. B. T. , Jyalatharachchi H. R. , Gamage S. , Gunasekara S. P. 
Published: February 2022

Abstract

Background
Carbapenem-resistant Enterobacteriaceae (CRE) are the most critical group of MDR bacteria that pose a threat to human health especially affecting patients with haematological malignancies. Knowledge on the prevalence of CRE colonization of the gut will help healthcare providers to be vigilant in-patient management. However, there are no local studies exploring the gut colonizing CRE among patients with haematological malignancies. Hence, this study aimed to determine the prevalence of CRE genes in colonizing CRE isolates in patients with haematological malignancies and evaluate their antibiotic susceptibility pattern.

Methods
Rectal swab samples collected from patients with haematological malignancies were screened with selective chromogenic agar for CRE. Species identification and ABST of CRE isolates were done using VITEK® 2 system. blaKPC, blaNDM and blaOXA−48 genes were identified using an in-house conventional multiplex PCR, with previously described method and primers.

Results
A total of 264 adult patients with haematological malignancies were included in the study. Prevalence of gut colonization of CRE was 35.2% (93/264). A total of 119 CRE isolates from 93 study subjects were further studied. Klebsiella pneumoniae was the predominant carbapenemase producer [68/119 (57%)] among the isolates. Sixty-one (51.2%) isolates harboured blaNDM, 48 (40.3%) blaOXA−48 and 12 (10%) blaKPC. Three isolates (2.5%) were shown to harbour all three genes and 24 (20%) two genes. Twenty (16.8%) of isolates tested negative for all three genes.

Conclusions
A relatively high prevalence of CRE gene occurrence and co-occurrence was detected in the study population. This indicates a potential challenge to infection prevention and control in the institute as colonization with CRE carries a threat to endogenous infection and cross transfer.

Limitations
In-house conventional PCR method was used to identify CRE genes. Twenty isolates that were negative for all tested genes need to be studied further.
Development of optimal water distribution system design and operation approach considering hydraulic and water quality criteria in many-objective optimization framework
Authors: Choi Young Hwan 
Published: February 2022

Abstract
Water distribution systems (WDSs) are major infrastructure, and it needs to consider economic, hydraulic stability, and water quality safety to optimal design and operation of WDSs. However, the previous studies related to WDS design and operation were focused on each field (i.e. design: optimal pipe diameter, pump sizing, and valve location; operation: optimal pump scheduling, etc.) even though the WDS design and operation have a correlation. Therefore, to achieve economic feasibility, hydraulic stability, and water quality safety under WDS design and operation process, this study develops an optimal WDS design and operation approach considering hydraulic and water quality criteria in the many-objective optimization framework. To consider design and operation, this study applies three objective functions to minimize the total design and operation cost (i.e. the pipe cost, pump construction, and pump operation cost), maximize system robustness, and minimize the amount of chlorine requisition simultaneously under the hydraulic and quality constraints. The proposed optimal WDS design and operation model was applied to the two-stage optimization procedures. The first process determined the optimal pipe diameter set. The second process determined the optimal pump construction and scheduling considering three objective functions such as the total pump cost, the system robustness, and the quantity of the required residual chlorine for determining optimally the available number of pumps, capacity, and scheduling. For the optimization, the self-adaptive multi-objective harmony search is used and a famous benchmark network for the optimal design and pump operation of WDSs is applied to verify the proposed approach. This study can provide a new perspective on WDS design and operation technique considering the essential design factors to the water utility.
Inhibition of retinoid X receptor improved the morphology, localization of desmosomal proteins
and paracellular permeability in three-dimensional cultures of mouse keratinocytes
Authors: Ishikawa Shoko , Nikaido Misaki , Otani Takahito , Ogata Kayoko , Iida Hiroshi , Inai Yuko , Tamaoki Sachio , Inai Tetsuichiro 
Published: February 2022

Abstract
Retinoic acid (RA) plays an important role in epithelial homeostasis and influences the morphology, proliferation, differentiation and permeability of epithelial cells. Mouse keratinocytes, K38, reconstituted non-keratinized stratified epithelium in three-dimensional (3D) cultures with serum, which contains retinol (a source of RA), but the morphology was different from in vivo epithelium. The formed epithelium was thick, with loosened cell–cell contacts. Here, we investigated whether the inhibition of RA receptor (RAR)/retinoid X receptor (RXR)-mediated signaling by an RXR antagonist, HX 531, improved K38 3D cultures in terms of morphology and intercellular junctions. The epithelium formed by 0.5 μM HX531 was thin, and the intercellular space was narrowed because of the restoration of the layer-specific distribution of desmoglein (DSG)-1, DSG3 and plakoglobin (PG). Moreover, the levels of desmosomal proteins and tight junction proteins, including DSG1, DSG2, DSG3, PG, claudin (CLDN)-1 and CLDN4 increased, but the adherens junction protein, E-cadherin, did not show any change. Furthermore, CLDN1 was recruited to occludin-positive cell–cell contacts in the superficial cells and transepithelial electrical resistance was increased. Therefore, K38 3D cultures treated with 0.5 μM HX531 provides a useful in vitro model to study intercellular junctions in the non-keratinized epithelium.
Relational Work and its Pitfalls: Nonprofits’ Participation in Government-Sponsored Voluntary Accreditation
Authors: Luo Wei , Zheng Wenjuan , Long Yan 
Published: February 2022

AbstractAround the world, voluntary programs are an increasingly prevalent regulatory instrument in governing nonprofit organizations. But accounts of mechanisms driving nonprofits’ participation in those programs are underdeveloped. This article combines and expands insights from voluntary regulation and institutional work theories to examine the impact of government’s informal relational work on nonprofits’ regulatory participation. Drawing on interviews and survey data from a random sample of 203 nonprofits in Shenzhen, China, the authors study the country’s pioneering government-sponsored voluntary accreditation program and its varying receptions among nonprofits. The empirical analysis shows that politically embedded nonprofits, those with closer organizational connections with the local government, are more likely to participate in accreditation. Since government agencies rely on existing regulatory networks to conduct relational work at both organizational and personal levels to persuade or cajole nonprofits to participate, they tend to direct their recruitment efforts towards more politically embedded nonprofits. However, these targeted recruitment practices may generate reactions much more complicated than the dichotomy of acceptance versus resistance, which ultimately facilitates some nonprofits seeking accreditation while deterring others.
Local Group timing argument and virial theorem mass estimators from cosmological simulations
Authors: Hartl Odelia V , Strigari Louis E 
Published: February 2022

ABSTRACT
We identify Local Group (LG) analogues in the IllustrisTNG cosmological simulation, and use these to study two-mass estimators for the LG: One based on the timing argument (TA) and one based on the virial theorem (VT). Including updated measurements of the Milky Way-M31 tangential velocity and the cosmological constant, we show that the TA mass estimator slightly overestimates the true median LG-mass, though the ratio of the TA to the true mass is consistent at the approximate 90 per cent c.l.. These are in broad agreement with previous results using dark matter-only simulations. We show that the VT estimator better estimates the true LG-mass, though there is a larger scatter in the virial mass to true mass ratio relative to the corresponding ratio for the TA. We attribute the broader scatter in the VT estimator to several factors, including the predominantly radial orbits for LG satellite galaxies, which differs from the VT assumption of isotropic orbits. With the systematic uncertainties we derive, the updated measurements of the LG mass at 90 per cent c.l. are $4.75_{-2.41}^{+2.22} \times 10^{12}$ M⊙ from the TA and $2.0_{-1.5}^{+2.1} \times 10^{12}$ M⊙ from the VT. We consider the LMC’s effect on the TA and VT LG mass estimates, and do not find exact LMC–MW–M31 analogues in the Illustris simulations. However, in LG simulations with satellite companions as massive as the LMC, we find that the effect on the TA and VT estimators is small, though we need further studies on a larger sample of LMC–MW–M31 systems to confirm these results.
The spiral density-wave structure of the Milky Way in the 3-kpc-scale solar neighbourhood: line-of-sight velocities of 252 young open clusters
Authors: Griv Evgeny , Gedalin Michael , Jiang Ing-Guey 
Published: February 2022

ABSTRACT
Following Lin and Shu, the spiral structure in the Milky Way disc is considered as an oscillating density-wave pattern. As such, regular enhancements in density are relatedly linked to systematic variations in velocity of young stars and stellar clusters, and interstellar gas. We explain measured line-of-sight velocities of 252 open clusters with ages &lt;100 Myr of Tarricq et al. in the 3-kpc-scale solar neighbourhood in terms of a density wave. New estimates of the parameters of solar peculiar motion and Galactic differential rotation corrected for the effects of small-amplitude density waves, the radial and tangential components of systematic motion of clusters due to the spiral arms as well as the geometrical and dynamical parameters of the waves are suggested.
quokka: a code for two-moment AMR radiation hydrodynamics on GPUs
Authors: Wibking Benjamin D , Krumholz Mark R 
Published: February 2022

ABSTRACT
We present quokka, a new subcycling-in-time, block-structured adaptive mesh refinement (AMR) radiation hydrodynamics (RHD) code optimized for graphics processing units (GPUs). quokka solves the equations of HD with the piecewise parabolic method (PPM) in a method-of-lines formulation, and handles radiative transfer via the variable Eddington tensor (VET) radiation moment equations with a local closure. We use the amrex library to handle the AM management. In order to maximize GPU performance, we combine explicit-in-time evolution of the radiation moment equations with the reduced speed-of-light approximation. We show results for a wide range of test problems for HD, radiation, and coupled RHD. On uniform grids in 3D on a single GPU, our code achieves &gt;250 million hydrodynamic updates per second and almost 40 million radiation hydrodynamic updates per second. For RHD problems on uniform grids in 3D, our code scales from 4 to 256 GPUs with an efficiency of 76 per cent. The code is publicly released under an open-source license on GitHub.
Long term radio and X-ray evolution of the magnetar Swift J1818.0-1607
Authors: Rajwade K M , Stappers B W , Lyne A G , Shaw B , Mickaliger M B , Liu K , Kramer M , Desvignes G , Karuppusamy R , Enoto T , Güver T , Hu Chin-Ping , Surnis M P 
Published: February 2022

ABSTRACT
We report on the the long term monitoring campaign of the seemingly youngest magnetar Swift J1818.0–1607 at radio and X-ray wavelengths over a span of one year. We obtained a coherent timing solution for the magnetar over the same time span. The frequency derivative of the magnetar shows systematic variation with the values oscillating about a mean value of −1.37 × 10−11 Hz s−1. The magnitude of the variation in the frequency derivative reduces with time before converging on the mean value. This corresponds to a characteristic age of ∼ 860 years, 2–4 times more than previously estimated. We were able to identify four states in the spin-frequency derivative that were quantified by the amount of modulation about the mean value and the transition between these states seem to be correlated with the change in the radio emission of the magnetar while no correlation is seen in the average radio profile variability on a shorter time-scale (days). The 0.5–12 keV X-ray flux shows a monotonic decrease that can be attributed to thermal emission from a hot spot on the surface of the neutron star that is reducing in size. Such decrease is consistent with what is seen in other magnetars. The potential correlation between the radio emission mode and the behaviour of the spin-down rate hints to a global change in the magnetopshere of the magnetar akin to the correlation seen in a subset of mode-changing radio pulsars and suggests a physical link between the two sub-populations.
The early afterglow of GRB 190829A
Authors: Dichiara S , Troja E , Lipunov V , Ricci R , Oates S R , Butler N R , Liuzzo E , Ryan G , O’Connor B , Cenko S B , Cosentino R G , Lien A Y , Gorbovskoy E , Tyurina N , Balanutsa P , Vlasenko D , Gorbunov I , Podesta R , Podesta F , Rebolo R , Serra M , Buckley D A H 
Published: February 2022

ABSTRACT
GRB 190829A at z = 0.0785 is the fourth closest long GRB ever detected by the Neil Gehrels Swift observatory, and the third confirmed case with a very high-energy component. We present our multiwavelength analysis of this rare event, focusing on its early stages of evolution, and including data from Swift, the MASTER global network of optical telescopes, ALMA, and ATCA. We report sensitive limits on the linear polarization of the optical emission, disfavouring models of off-axis jets to explain the delayed afterglow peak. The study of the multiwavelength light curves and broad-band spectra supports a model with at least two emission components: a bright reverse shock emission, visible at early times in the optical and X-rays and, later, in the radio band; and a forward shock component dominating at later times and lower radio frequencies. A combined study of the prompt and afterglow properties shows many similarities with cosmological long GRBs, suggesting that GRB 190829A is an example of classical GRBs in the nearby universe.
The vertical structure of debris discs and the impact of gas
Authors: Olofsson Johan , Thébault Philippe , Kral Quentin , Bayo Amelia , Boccaletti Anthony , Godoy Nicolás , Henning Thomas , van Holstein Rob G , Maucó Karina , Milli Julien , Montesinos Matías , Rein Hanno , Sefilian Antranik A 
Published: February 2022

ABSTRACT
The vertical structure of debris discs provides clues about their dynamical evolution and the collision rate of the unseen planetesimals. Thanks to the ever-increasing angular resolution of contemporary instruments and facilities, we are beginning to constrain the scale height of a handful of debris discs, either at near-infrared or millimeter wavelengths. None the less, this is often done for individual targets only. We present here the geometric modeling of eight discs close to edge-on, all observed with the same instrument (SPHERE) and using the same mode (dual-beam polarimetric imaging). Motivated by the presence of CO gas in two out of the eight discs, we then investigate the impact that gas can have on the scale height by performing N-body simulations including gas drag and collisions. We show that gas can quickly alter the dynamics of particles (both in the radial and vertical directions), otherwise governed by gravity and radiation pressure. We find that, in the presence of gas, particles smaller than a few tens of microns can efficiently settle toward the midplane at the same time as they migrate outward beyond the birth ring. For second generation gas (Mgas ≤ 0.1 M⊕), the vertical settling should be best observed in scattered light images compared to observations at millimeter wavelengths. But if the gas has a primordial origin (Mgas ≥ 1 M⊕), the disc will appear very flat both at near-infrared and sub-mm wavelengths. Finally, far beyond the birth ring, our results suggest that the surface brightness profile can be as shallow as ∼−2.25.
Galaxy classification: a deep learning approach for classifying Sloan Digital Sky Survey images
Authors: Gharat Sarvesh , Dandawate Yogesh 
Published: February 2022

ABSTRACTIn recent decades, large-scale sky surveys such as Sloan Digital Sky Survey (SDSS) have resulted in generation of tremendous amount of data. The classification of this enormous amount of data by astronomers is time consuming. To simplify this process, in 2007 a volunteer-based citizen science project called ‘Galaxy Zoo’ was introduced, which has reduced the time for classification by a good extent. However, in this modern era of deep learning, automating this classification task is highly beneficial as it reduces the time for classification. For the last few years, many algorithms have been proposed which happen to do a phenomenal job in classifying galaxies into multiple classes. But all these algorithms tend to classify galaxies into less than six classes. However, after considering the minute information which we know about galaxies, it is necessary to classify galaxies into more than eight classes. In this study, a neural network model is proposed so as to classify SDSS data into 10 classes from an extended Hubble Tuning Fork. Great care is given to disc edge and disc face galaxies, distinguishing between a variety of substructures and minute features which are associated with each class. The proposed model consists of convolution layers to extract features making this method fully automatic. The achieved test accuracy is 84.73 per cent which happens to be promising after considering such minute details in classes. Along with convolution layers, the proposed model has three more layers responsible for classification, which makes the algorithm consume less time.