bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence of acute kidney injury (AKI) and its impact on patient outcomes among adult hospitalized patients with carbapenem-resistant Gram-negative infections who received targeted treatment with a newer β-lactam or β-lactam/β-lactamase inhibitor-, polymyxin- or aminoglycoside-containing regimen
Authors: Lodise Thomas P , Yucel Emre , Obi Engels N , Watanabe Alexandre H , Nathanson Brian H 
Published: November 2023

Abstract

Background
Limited comparative data exist on acute kidney injury (AKI) risk and AKI-associated outcomes in hospitalized patients with carbapenem-resistant Gram-negative infections (CR-GNIs) treated with a newer β-lactam/β-lactam-β-lactamase inhibitor (BL/BL-BLI)-, polymyxin (PB)- or aminoglycoside (AG)-containing regimen. This study quantified the risk of AKI and AKI-related outcomes among patients with CR-GNIs treated with a newer BL/BL-BLI-, PB- or AG-containing regimen.

Methods
A multicentre, retrospective, observational study was performed (2016–20). The study included adult hospitalized patients with (i) baseline estimated glomerular filtration rates ≥30 mL/min/1.73 m2; (ii) CR-GN pneumonia, complicated urinary tract infection or bloodstream infection; and (iii) receipt of newer BL/BL-BLI, PG or AG within 7 days of index CR-GN culture for ≥3 days. Outcomes included AKI, in-hospital mortality and hospital costs.

Results
The study included 750 patients and most (48%) received a newer BL/BL-BLI. The median (IQR) treatment duration was 8 (5–11), 5 (4–8) and 7 (4–8) days in the newer BL/BL-BLI group, AG group and PB group, respectively. The PB group had the highest adjusted AKI incidence (95% CI) (PB: 25.1% (15.6%–34.6%) versus AG: 8.9% (5.7%–12.2%) versus newer BL/BL-BLI: 11.9% (8.1%–15.7%); P = 0.001). Patients with AKI had significantly higher in-hospital mortality (AKI: 18.5% versus ‘No AKI’: 5.6%; P = 0.001) and mean hospital costs (AKI: $49 192 versus ‘No AKI’: $38,763; P = 0.043).

Conclusions
The AKI incidence was highest among PB patients and patients with AKI had worse outcomes. Healthcare systems should consider minimizing the use of antibiotics that augment AKI risk as a measure to improve outcomes in patients with CR-GNIs.
Enteropathogenic Escherichia coli is a predominant pathotype in healthy pigs in Hubei Province of China
Authors: Zhuo Wenxiao , Zhao Yang , Zhao Xianglin , Yao Zhiming , Qiu Xiuxiu , Huang Yaxue , Li Huaixia , Shen Jing , Zhu Zhihao , Li Tingting , Li Shaowen , Huang Qi , Zhou Rui 
Published: November 2023

Abstract

Aim
This study aims to investigate the prevalence of intestinal pathogenic Escherichia coli (InPEC) in healthy pig-related samples and evaluate the potential virulence of the InPEC strains.

Methods and results
A multiplex PCR method was established to identify different pathotypes of InPEC. A total of 800 rectal swab samples and 296 pork samples were collected from pig farms and slaughterhouses in Hubei province, China. From these samples, a total of 21 InPEC strains were isolated, including 19 enteropathogenic E. coli (EPEC) and 2 shiga toxin-producing E. coli (STEC) strains. By whole-genome sequencing and in silico typing, it was shown that the sequence types and serotypes were diverse among the strains. Antimicrobial susceptibility assays showed that 90.48% of the strains were multi-drug resistant. The virulence of the strains was first evaluated using the Galleria mellonella larvae model, which showed that most of the strains possessed medium to high pathogenicity. A moderately virulent EPEC isolate was further selected to characterize its pathogenicity using a mouse model, which suggested that it could cause significant diarrhea. Bioluminescence imaging (BLI) was then used to investigate the colonization dynamics of this EPEC isolate, which showed that the EPEC strain could colonize the mouse cecum for up to 5 days.
‘The collar never comes off’: A qualitative study of clergy professionalism
Authors: Beaty R Ryan , Biwa Valerie , Millender Lauren 
Published: November 2023

Abstract
In this study, we examine clergy use of verbal and nonverbal communicative behaviors of professionalism within the pastor–parishioner dyad. In doing so, we interviewed 21 clergy from disparate Christian denominations—The Episcopal Church, USA, and The Assemblies of God, and analyzed data via modified constant comparative analysis. Findings, conceptualized through Uhl-Bien’s Relational Leadership Theory (RLT), produced answers as to why clergy members employ professionalism-based behaviors, which behaviors they frequently employ, and the benefit of professionalism to the pastor–parishioner leadership dyad. Findings theoretically contribute (1) an introduction toward the development of a clergy framework of professionalism, (2) an expansion on the understanding of professionalism, (3) a mechanism of influence and control inside RLT—professionalism, and (4) demonstrates that co-construction within a leadership relationship is guided by underlying assumptions of power within the dyad. The authors conclude with pragmatic implications for all leaders.
Rho of Plants patterning: linking mathematical models and molecular diversity
Authors: Deinum Eva E , Jacobs Bas 
Published: November 2023

Abstract
ROPs (Rho of Plants) are plant specific small GTPases involved in many membrane patterning processes and play important roles in the establishment and communication of cell polarity. These small GTPases can produce a wide variety of patterns, ranging from a single cluster in tip-growing root hairs and pollen tubes to an oriented stripe pattern controlling protoxylem cell wall deposition. For an understanding of what controls these various patterns, models are indispensable. Consequently, many modelling studies on small GTPase patterning exist, often focusing on yeast or animal cells. Multiple patterns occurring in plants, however, require the stable co-existence of multiple active ROP clusters, which does not occur with the most common yeast/animal models. The possibility of such patterns critically depends on the precise model formulation. Additionally, different small GTPases are usually treated interchangeably in models, even though plants possess two types of ROPs with distinct molecular properties, one of which is unique to plants. Furthermore, the shape and even the type of ROP patterns may be affected by the cortical cytoskeleton, and cortex composition and anisotropy differ dramatically between plants and animals. Here, we review insights into ROP patterning from modelling efforts across kingdoms, as well as some outstanding questions arising from these models and recent experimental findings.
The combination of manogepix and itraconazole is synergistic and inhibits the growth of Madurella mycetomatis in vitro but not in vivo
Authors: Konings Mickey , Eadie Kimberly , Strepis Nikolaos , Nyuykonge Bertrand , Fahal Ahmed H , Verbon Annelies , van de Sande Wendy W J 
Published: November 2023

Abstract
Mycetoma is a neglected tropical disease commonly caused by the fungus Madurella mycetomatis. Standard treatment consists of extensive treatment with itraconazole in combination with surgical excision of the infected tissue, but has a low success rate. To improve treatment outcomes, novel treatment strategies are needed. Here, we determined the potential of manogepix, a novel antifungal agent that targets the GPI-anchor biosynthesis pathway by inhibition of the GWT1 enzyme. Manogepix was evaluated by determining the minimal inhibitory concentrations (MICs) according to the CLSI-based in vitro susceptibility assay for 22 M. mycetomatis strains and by in silico protein comparison of the target protein. The synergy between manogepix and itraconazole was determined using a checkerboard assay. The efficacy of clinically relevant dosages was assessed in an in vivo grain model in Galleria mellonella larvae. MICs for manogepix ranged from &lt;0.008 to &gt;8 mg/l and 16/22 M. mycetomatis strains had an MIC ≥4 mg/ml. Differences in MICs were not related to differences observed in the GWT1 protein sequence. For 70% of the tested isolates, synergism was found between manogepix and itraconazole in vitro. In vivo, enhanced survival was not observed upon admission of 8.6 mg/kg manogepix, nor in combination treatment with 5.7 mg/kg itraconazole. MICs of manogepix were high, but the in vitro antifungal activity of itraconazole was enhanced in combination therapy. However, no efficacy of manogepix was found in an in vivo grain model using clinically relevant dosages. Therefore, the therapeutic potential of manogepix in mycetoma caused by M. mycetomatis seems limited.
The large-scale velocity field from the Cosmicflows-4 data
Authors: Hoffman Yehuda , Valade Aurelien , Libeskind Noam I , Sorce Jenny G , Tully R Brent , Pfeifer Simon , Gottlöber Stefan , Pomarède Daniel 
Published: November 2023

ABSTRACT
The reconstruction of the large-scale velocity field from the grouped Cosmicflows-4 (CF4) database is presented. The lognormal bias of the inferred distances and velocities data is corrected by the Bias Gaussianization correction scheme, and the linear density and velocity fields are reconstructed by means of the Wiener filter and constrained realizations (CRs) algorithm. These tools are tested against a suite of random and constrained Cosmicflows-3-like mock data. The CF4 data consist of three main subsamples – the 6dFGS and the SDSS data – and the ‘others’. The individual contributions of the subsamples have been studied. The quantitative analysis of the velocity field is done mostly by the mean overdensity (ΔL(R)) and the bulk velocity (Vbulk(R)) profiles of the velocity field out to $300\, {{h^{-1}\, {\rm Mpc}}}$.
The Vbulk(R) and ΔL(R) profiles of the CF4 data without its 6dFGS component are consistent with the cosmic variance to within 1σ. The 6dFGS sample dominates the Vbulk (ΔL) profile beyond $\sim 120\, {{h^{-1}\, {\rm Mpc}}}$, and drives it to roughly a 3.4σ (−1.9σ) excess (deficiency) relative to the cosmic variance at $R\sim 250\ (190)\ \, {{h^{-1}\, {\rm Mpc}}}$. The excess in the amplitude of Vbulk is dominated by its Supergalactic X component, roughly in the direction of the Shapley Concentration. The amplitude and alignment of the inferred velocity field from the CF4 data are at $\sim (2{-}3)\, \sigma$ discrepancy with respect to the Lambda cold dark matter model. Namely, it is somewhat atypical but yet there is no compelling tension with the model.
Spatial distribution of NH2D in massive star-forming regions
Authors: Li Yuqiang , Wang Junzhi , Li Juan , Liu Shu , Yang Kai , Zheng Siqi , Lu Zhe 
Published: November 2023

ABSTRACT
To understand the relation between NH2D and its physical environment, we mapped ortho-NH2D $1_{11}^s-1_{01}^a$ at 85.9 GHz toward 24 Galactic late-stage massive star-forming regions with Institut de Radioastronomie Millim${\rm \acute{e}}$trique (IRAM) 30-m telescope. Ortho-NH2D $1_{11}^s-1_{01}^a$ was detected in 18 of 24 sources. Comparing with the distribution of H13CN 1-0 as a dense gas tracer and radio recombination line H42α, ortho-NH2D $1_{11}^s-1_{01}^a$ present complex and diverse spatial distribution in these targets. 11 of the 18 targets, present a different distribution between ortho-NH2D $1_{11}^s-1_{01}^a$ and H13CN 1-0, while no significant difference between these two lines can be found in other 7 sources, mainly due to limited spatial resolution and sensitivity. Moreover, with H42α tracing massive young stellar objects, ortho-NH2D $1_{11}^s-1_{01}^a$ seems to show a relatively weak emission near the massive young stellar objects.
Host galaxies of ultra-strong Mg ii absorbers at z ∼ 0.7
Authors: Guha Labanya K , Srianand Raghunathan , Petitjean Patrick 
Published: November 2023

ABSTRACT
We report spectroscopic identification of the host galaxies of 18 ultra-strong Mg ii systems (USMg ii) at 0.6 ≤ z ≤ 0.8. We created the largest sample by merging these with 20 host galaxies from our previous survey within 0.4 ≤ z ≤ 0.6. Using this sample, we confirm that the measured impact parameters ($\rm 6.3\leqslant D[kpc] \leqslant 120$ with a median of 19 kpc) are much larger than expected, and the USMg ii host galaxies do not follow the canonical $\rm {\it W}_{2796}-{\it D}$ anticorrelation. We show that the presence and significance of this anticorrelation may depend on the sample selection. The $\rm {\it W}_{2796}-{\it D}$ anticorrelation seen for the general Mg ii absorbers show a mild evolution at low $\rm W_{2796}$ end over the redshift range 0.4 ≤ z ≤ 1.5 with an increase of the impact parameters. Compared to the host galaxies of normal Mg ii absorbers, USMg ii host galaxies are brighter and more massive for a given impact parameter. While the USMg ii systems preferentially pick star-forming galaxies, they exhibit slightly lower ongoing star-forming rates compared to main sequence galaxies with the same stellar mass, suggesting a transition from star-forming to quiescent states. For a limiting magnitude of mr &lt; 23.6, at least 29 per cent of the USMg ii host galaxies are isolated, and the width of the Mg ii absorption in these cases may originate from gas flows (infall/outflow) in isolated haloes of massive star forming but not starbursting galaxies. We associate more than one galaxy with the absorber in $\ge 21~{{\ \rm per\ cent}}$ cases, where interactions may cause wide velocity spread.
The dominant mechanism(s) for populating the outskirts of star clusters with neutron star binaries
Authors: Leigh Nathan W C , Ye Claire S , Grondin Steffani M , Fragione Giacomo , Webb Jeremy J , Heinke Craig O 
Published: November 2023

ABSTRACT
It has been argued that heavy binaries composed of neutron stars (NSs) and millisecond pulsars (MSPs) can end up in the outskirts of star clusters via an interaction with a massive black hole (BH) binary expelling them from the core. We argue here, however, that this mechanism will rarely account for such observed objects. Only for primary masses ≲100 M⊙ and a narrow range of orbital separations should a BH–BH binary be both dynamically hard and produce a sufficiently low recoil velocity to retain the NS binary in the cluster. Hence, BH binaries are in general likely to eject NSs from clusters. We explore several alternative mechanisms that would cause NS/MSP binaries to be observed in the outskirts of their host clusters after a Hubble time. The most likely mechanism is a three-body interaction involving the NS/MSP binary and a normal star. We compare to Monte Carlo simulations of cluster evolution for the globular clusters NGC 6752 and 47 Tuc, and show that the models not only confirm that normal three-body interactions involving all stellar-mass objects are the dominant mechanism for putting NS/MSP binaries into the cluster outskirts, but also reproduce the observed NS/MSP binary radial distributions without needing to invoke the presence of a massive BH binary. Higher central densities and an episode of core collapse can broaden the radial distributions of NSs/MSPs and NS/MSP binaries due to three-body interactions, making these clusters more likely to host NSs in the cluster outskirts.
On the plerionic rectangular supernova remnants of static progenitors
Authors: Meyer D M-A , Meliani Z , Velázquez P F , Pohl M , Torres D F 
Published: November 2023

ABSTRACT
Pulsar wind nebulae are a possible final stage of the circumstellar evolution of massive stars, where a fast-rotating, magnetized neutron star produces a powerful wind that interacts with the supernova ejecta. The shape of these so-called plerionic supernova remnants is influenced by the distribution of circumstellar matter at the time of the explosion, itself impacted by the magnetic field of the ambient medium, responsible for the expansion of the circumstellar bubble of the progenitor star. To understand the effects of magnetization on the circumstellar medium and resulting pulsar nebulae, we conduct 2D magnetohydrodynamic simulations. Our models explore the impact of the interstellar medium’s (ISM) magnetic field on the morphology of a supernova remnant and pulsar wind nebula that develop in the circumstellar medium of massive star progenitor in the warm phase of the Milky Way’s ISM. Our simulations reveal that the jet-like structures formed on both sides perpendicularly to the equatorial plane of the pulsar, creating complex radio synthetic synchrotron emissions. This morphology is characterized by a rectangular-like remnant, which is typical of the circumstellar medium of massive stars in a magnetized medium, along with the appearance of a spinning top structure within the projected rectangle. We suggest that this mechanism may be partially responsible for the complex morphologies observed in pulsar wind nebulae that do not conform to the typical torus/jet or bow shock/tail shapes observed in most cases.
On the core-collapse supernova explanation for LAMOST J1010 + 2358
Authors: Jeena S K , Banerjee Projjwal , Heger Alexander 
Published: November 2023

ABSTRACT
Low-metallicity very massive stars with an initial mass of ∼140–$260\, \mathrm{M}_\odot$ are expected to end their lives as pair-instability supernovae (PISNe). The abundance pattern resulting from a PISN differs drastically from regular core-collapse supernova (CCSN) models and is expected to be seen in very metal-poor (VMP) stars of [Fe/H] ≲ −2. Despite the routine discovery of many VMP stars, the unique abundance pattern expected from PISNe has not been unambiguously detected. The recently discovered VMP star LAMOST J1010 + 2358, however, shows a peculiar abundance pattern that is remarkably well fit by a PISN, indicating the potential first discovery of a bonafide star born from gas polluted by a PISN. In this paper, we study the detailed nucleosynthesis in a large set of models of CCSN of Pop III and Pop II star of metallicity [Fe/H] = −3 with masses ranging from 12 to $30\, \mathrm{M}_\odot$. We find that the observed abundance pattern in LAMOST J1010 + 2358 can be fit at least equally well by CCSN models of ∼12–$14\, \mathrm{M}_\odot$ that undergo negligible fallback following the explosion. The best-fitting CCSN models provide a fit that is even marginally better than the best-fitting PISN model. We conclude the measured abundance pattern in LAMOST J1010 + 2358 could have originated from a CCSN and therefore cannot be unambiguously identified with a PISN given the set of elements measured in it to date. We identify key elements that need to be measured in future detections in stars like LAMOST J1010 + 2358 that can differentiate between CCSN and PISN origin.
Correlation structure in flux-density calibrator models
Authors: Molteno Timothy C A 
Published: November 2023

ABSTRACT
Astronomical radio-interferometric imaging typically uses published observations of standard flux-calibrator sources to calibrate the spectral response of the instrument. The spectra of standard flux-calibrator sources are usually provided as polynomial models of flux-density as a function of frequency. In this paper we show that there is significant covariance in these polynomial coefficients, and that failing to take this into account leads to significantly larger variance when sampling from the polynomial models. This paper presents polynomial models of calibrator sources that include the covariance structure of the coefficients which are computed using Markov Chain Monte Carlo sampling. In addition a data-free inference technique is presented that can be used to estimate the covariance structure from a simple polynomial model when access to the original data is not available. This data-free technique is compared with estimates of covariance calculated from original observation data. The data-free technique is shown to provide reasonable agreement with covariances calculated from source data. A python package is described that implements this inference, and a catalogue of common flux-calibrator models including covariance is provided. We suggest that when polynomial models of flux-calibrators are used as priors in a Bayesian context, then taking this correlation structure into account will lead to significantly reduced posterior variance.
OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem
Authors: Altenhoff Adrian M , Warwick Vesztrocy Alex , Bernard Charles , Train Clement-Marie , Nicheperovich Alina , Prieto Baños Silvia , Julca Irene , Moi David , Nevers Yannis , Majidian Sina , Dessimoz Christophe , Glover Natasha M 
Published: November 2023

Abstract
In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes. We also introduce a revamped Local Synteny Viewer to compare genomic neighborhoods across both extant and ancestral genomes. Hierarchical Orthologous Groups (HOGs) are now annotated with Gene Ontology annotations, and users can easily perform extant or ancestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome quality assessment, OMAMO for model organism selection and Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthology analysis and comparative genomics. OMA is accessible at https://omabrowser.org.
Decoding complexity in biomolecular recognition of DNA i-motifs with microarrays
Authors: Yazdani Kamyar , Seshadri Srinath , Tillo Desiree , Yang Mo , Sibley Christopher D , Vinson Charles , Schneekloth John S 
Published: November 2023

Abstract
DNA i-motifs (iMs) are non-canonical C-rich secondary structures implicated in numerous cellular processes. Though iMs exist throughout the genome, our understanding of iM recognition by proteins or small molecules is limited to a few examples. We designed a DNA microarray containing 10976 genomic iM sequences to examine the binding profiles of four iM-binding proteins, mitoxantrone and the iMab antibody. iMab microarray screens demonstrated that pH 6.5, 5% BSA buffer was optimal, and fluorescence was correlated with iM C-tract length. hnRNP K broadly recognizes diverse iM sequences, favoring 3–5 cytosine repeats flanked by thymine-rich loops of 1–3 nucleotides. Array binding mirrored public ChIP-Seq datasets, in which 35% of well-bound array iMs are enriched in hnRNP K peaks. In contrast, other reported iM-binding proteins had weaker binding or preferred G-quadruplex (G4) sequences instead. Mitoxantrone broadly binds both shorter iMs and G4s, consistent with an intercalation mechanism. These results suggest that hnRNP K may play a role in iM-mediated regulation of gene expression in vivo, whereas hnRNP A1 and ASF/SF2 are possibly more selective in their binding preferences. This powerful approach represents the most comprehensive investigation of how biomolecules selectively recognize genomic iMs to date.