bluuebunny/crossref_metadata_2025_split huggingface dataset:
CHROMAgar™ LIN-R as an efficient screening tool to assess the prevalence of linezolid-resistant enterococci in German hospital patients—a multicentre study approach, 2021–2022
Authors: Bender Jennifer K , Baufeld Elsa , Becker Karsten , Claus Heike , Dudakova Anna , Dörre Achim , Fila Nikoletta , Fleige Carola , Hamprecht Axel , Hoffmann Armin , Hogardt Michael , Kaasch Achim J , Kola Axel , Kriebel Nancy , Layer-Nicolaou Franziska , Marschal Matthias , Molitor Ernst , Mutters Nico T , Liese Jan , Nelkenbrecher Claudia , Neumann Bernd , Rohde Holger , Steinmann Jörg , Sörensen Michael , Thelen Philipp , Weig Michael , Zautner Andreas E , Werner Guido 
Published: July 2023

Abstract

Background
In recent years, an increasing number of linezolid-resistant enterococci (LRE) was recognized at the German National Reference Centre (NRC) for Enterococci. National guidelines on infection prevention recommend screening for LRE in epidemiologically linked hospital settings without referring to a reliable and rapid diagnostic method. Since 2020, CHROMAgar™ provide a chromogenic linezolid screening agar, LIN-R, suitable to simultaneously screen for linezolid-resistant staphylococci and enterococci.

Objectives
To assess the applicability of CHROMAgar™ LIN-R in clinical settings for detecting LRE directly from patient material and to infer prevalence rates of LRE amongst German hospital patients.

Methods
During the 3-month trial period, clinical samples were plated on CHROMAgar™ LIN-R. Antimicrobial susceptibility testing was performed using VITEK2 or disc diffusion. At the NRC, linezolid resistance was determined by broth microdilution, multiplex-PCR for cfr/optrA/poxtA and by a restriction-based assay for 23S rDNA mutations.

Results
The 12 participating study sites used 13 963 CHROMAgar™ LIN-R plates during the study period. Of 442 presumptive LRE, 192 were confirmed by phenotypic methods. Of these, 161 were received by the NRC and 121 (75%) were verified as LRE. Most of LR-E. faecium 53/81 (65%) exhibited a 23S rRNA gene mutation as the sole resistance-mediating mechanism, whereas optrA constituted the dominant resistance trait in LR-E. faecalis [39/40 (98%)]. Prevalence of LRE across sites was estimated as 1% (ranging 0.18%–3.7% between sites).

Conclusions
CHROMAgar™ LIN-R represents a simple and efficient LRE screening tool in hospital settings. A high proportion of false-positive results demands validation of linezolid resistance by a reference method.
An artesunate pharmacometric model to explain therapeutic responses in falciparum malaria
Authors: Saralamba Sompob , Simpson Julie A , Choosri Noppon , White Lisa , Pan-Ngum Wirichada , Dondorp Arjen M , White Nicholas J 
Published: July 2023

Abstract

Background
The artemisinins are potent and widely used antimalarial drugs that are eliminated rapidly. A simple concentration–effect pharmacometric model does not explain why dosing more frequently than once daily fails to augment parasite clearance and improve therapeutic responses in vivo. Artemisinins can induce a temporary non-replicative or ‘dormant’ drug refractory state in Plasmodium falciparum malaria parasites which may explain recrudescences observed in clinical trials despite full drug susceptibility, but whether it explains the dosing–response relationship is uncertain.

Objectives
To propose a revised model of antimalarial pharmacodynamics that incorporates reversible asexual parasite injury and temporary drug refractoriness in order to explain the failure of frequent dosing to augment therapeutic efficacy in falciparum malaria.

Methods
The model was fitted using a Bayesian Markov Chain Monte Carlo approach with the parasite clearance data from 39 patients with uncomplicated falciparum malaria treated with artesunate from western Cambodia and 40 patients from northwestern Thailand reported previously.

Results
The revised model captured the dynamics of parasite clearance data. Its predictions are consistent with observed therapeutic responses.

Conclusions
A within-host pharmacometric model is proposed in which it is hypothesized that some malaria parasites enter a temporary drug refractory state after exposure to artemisinin antimalarials, which is followed by delayed parasite death or reactivation. The model fitted the observed sequential parasite density data from patients with acute P. falciparum malaria, and it supported reduced ring stage activity in artemisinin-resistant infections.
Sponge-derived fatty acids inhibit biofilm formation of MRSA and MSSA by down-regulating biofilm-related genes specific to each pathogen
Authors: Khan Neyaz A , Barthes Nicolas , McCormack Grace , O'Gara James P , Thomas Olivier P , Boyd Aoife 
Published: July 2023

Abstract

Aim
A promising approach for the development of next-generation antimicrobials is to shift their target from causing bacterial death to inhibiting virulence. Marine sponges are an excellent potential source of bioactive anti-virulence molecules (AVM). We screened fractions prepared from 26 samples of Irish coastal sponges for anti-biofilm activity against clinically relevant pathogens.

Methods and results
Fifteen fractions from eight sponge species inhibited biofilm of methicillin-susceptible Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA), and/or Listeria monocytogenes without causing growth inhibition. Gas chromatograph/mass spectroscopy analyses of Mycale contarenii fractions revealed the presence of myristic acid and oleic acid. These fatty acids repressed transcription of the fibronectin-binding protein fnbA and fnbB genes and the polysaccharide intercellular adhesin icaADBC operon, which are required for MRSA and MSSA biofilm formation, respectively.

Conclusions
This study illustrates the potential of AVM from Irish coastal sponges to specifically target bacterial virulence phenotypes, in this case, repression of biofilm formation via decreased transcription of biofilm-associated genes in MSSA and MRSA.
Streptomycesbiostimulants: an effective sustainable approach to reduce inorganic N input and maintain high yield of wheat crop in different soil types
Authors: Youseif Sameh H , El-Megeed Fayrouz H Abd , Salous Mousa S , Mohamed Akram H 
Published: July 2023

AbstractAimsThis study aimed to isolate and characterize endophytic plant growth-promoting (PGP) actinomycetes from the wild medicinal plant Zygophyllum album.Methods and resultsEight actinomycetes were isolated, identified, and screened for their PGP activities to improve the growth and production of wheat plants under low N-inputs. Based on 16S rRNA analysis, the isolated actinobacteria showed high diversity and had multiple in vitro PGP attributes. In pot experiments, Streptomyces sp. NGB-Act4 and NGB-Act6 demonstrated the highest significant PGP activities to enhance the growth of wheat plants under reduced N-inputs. Under various field conditions (high-fertility clay soils and low-fertility sandy soils), in combination with 50% N-dose, the two streptomycetes showed significant increases in grain N% and grain yield of the wheat crop compared with the 50% N-fertilized treatment. Irrespective of soil type, wheat plants inoculated with strain NGB-Act4 produced grain yield and grain N% significantly greater than or comparable to the full N-dose treatment.ConclusionsThis is the first field report on the successful use of endophytic streptomycetes as an effective strategy to improve wheat yield and reduce the use of synthetic N fertilizers.
Satisfaction With Participation in the First STEPS Behavioral Intervention: Experiences of Parents of Young Children With Newly Diagnosed Type 1 Diabetes
Authors: Baudino Marissa N , Inverso Hailey , Wang Christine , Tully Carrie , Levy Wendy , Clary Lauren , Gallagher Katherine A , Monaghan Maureen , Streisand Randi , Hilliard Marisa E 
Published: July 2023

Abstract

Objective
Parents of young children with new-onset type 1 diabetes (T1D) often experience significant distress and struggle with T1D management during a challenging developmental stage. The First STEPS (Study of Type 1 in Early childhood and Parenting Support) trial evaluated a stepped-care behavioral intervention comprising increasingly intensive intervention steps (peer parent coach, cognitive-behavioral counseling, consultations with diabetes educator and psychologist) based on need. The intervention improved parental depressive symptoms compared to usual care. Subsequently, we examined parent satisfaction with the intervention to guide potential implementation and refinement for future trials.

Methods
Participants were 157 parents of young children newly diagnosed with T1D. At 9 months post randomization, n = 153 completed satisfaction questionnaires and n = 17 completed qualitative interviews. Satisfaction ratings about trial procedures and each intervention step were summarized. We used thematic analysis with the interview transcripts to generate themes related to participants’ experiences in the trial overall and intervention specifically. We explored differences in themes between participants who did versus did not respond to the intervention and among those who experienced different intervention steps.

Results
Most participants in both arms rated study participation and methods positively (&gt;95%), and those completing interviews described high satisfaction with study procedures overall, retention incentives, and contact with study staff. Intervention participants’ satisfaction ratings were high across steps. Two qualitative themes reflected satisfaction with the intervention enhancing self-efficacy and social support.

Conclusions
High satisfaction suggests implementing a stepped-care behavioral intervention as part of routine clinical care following T1D diagnosis would be well received.
The MillenniumTNG Project: inferring cosmology from galaxy clustering with accelerated N-body scaling and subhalo abundance matching
Authors: Contreras Sergio , Angulo Raul E , Springel Volker , White Simon D M , Hadzhiyska Boryana , Hernquist Lars , Pakmor Rüdiger , Kannan Rahul , Hernández-Aguayo César , Barrera Monica , Ferlito Fulvio , Delgado Ana Maria , Bose Sownak , Frenk Carlos 
Published: July 2023

ABSTRACT
We introduce a novel technique for constraining cosmological parameters and galaxy assembly bias using non-linear redshift-space clustering of galaxies. We scale cosmological N-body simulations and insert galaxies with the SubHalo Abundance Matching extended (SHAMe) empirical model to generate over 175 000 clustering measurements spanning all relevant cosmological and SHAMe parameter values. We then build an emulator capable of reproducing the projected galaxy correlation function at the monopole, quadrupole, and hexadecapole level for separations between $0.1\, h^{-1}\, {\rm Mpc}$ and $25\, h^{-1}\, {\rm Mpc}$. We test this approach by using the emulator and Monte Carlo Markov Chain (MCMC) inference to jointly estimate cosmology and assembly bias parameters both for the MTNG740 hydrodynamic simulation and for a semi-analytical model (SAM) galaxy formation built on the MTNG740-DM dark matter-only simulation, obtaining unbiased results for all cosmological parameters. For instance, for MTNG740 and a galaxy number density of $n\sim 0.01 h^{3}\, {\rm Mpc}^{-3}$, we obtain $\sigma _{8}=0.799^{+0.039}_{-0.044}$ and $\Omega _\mathrm{M}h^2= 0.138^{+ 0.025}_{- 0.018}$ (which are within 0.4 and 0.2σ of the MTNG cosmology). For fixed Hubble parameter (h), the constraint becomes $\Omega _\mathrm{M}h^2= 0.137^{+ 0.011}_{- 0.012}$. Our method performs similarly well for the SAM and for other tested sample densities. We almost always recover the true amount of galaxy assembly bias within 1σ. The best constraints are obtained when scales smaller than $2\, h^{-1}\, {\rm Mpc}$ are included, as well as when at least the projected correlation function and the monopole are incorporated. These methods offer a powerful way to constrain cosmological parameters using galaxy surveys.
Star formation and molecular gas properties of post-starburst galaxies
Authors: Baron Dalya , Netzer Hagai , French K Decker , Lutz Dieter , Davies Richard I , Prochaska J Xavier 
Published: July 2023

ABSTRACT
Post-starburst galaxies are believed to be in a rapid transition between major merger starbursts and quiescent ellipticals. Their optical spectrum is dominated by A-type stars, suggesting a starburst that was quenched recently. While optical observations suggest little ongoing star formation, some have been shown to host significant molecular gas reservoirs. This led to the suggestion that gas depletion is not required to end the starburst, and that star formation is suppressed by other processes. We present NOEMA CO(1−0) observations of 15 post-starburst galaxies with emission lines consistent with active galactic nucleus (AGN) photoionization. We collect post-starburst candidates with molecular gas measurements from the literature, with some classified as classical E + A, while others with line ratios consistent with AGN and/or shock ionization. Using far-infrared observations, we show that systems that were reported to host exceptionally large molecular gas reservoirs host in fact obscured star formation, with some systems showing star formation rates comparable to ULIRGs. Among E + A galaxies with molecular gas measurements, 7 out of 26 (26 per cent) host obscured starbursts. Using far-infrared observations, post-starburst candidates show similar SFR–$M_{\mathrm{H_2}}$ and Kennicutt–Schmidt relations to those observed in star-forming and starburst galaxies. In particular, there is no need to hypothesize star formation quenching by processes other than the consumption of molecular gas by star formation. The combination of optical, far-infrared, and CO observations indicates that some regions within these galaxies have been recently quenched, while others are still forming stars in highly obscured regions. All this calls into question the traditional interpretation of such galaxies.
Planetary nebulae and supernova remnants in NGC 4214 from the SIGNALS survey
Authors: Vicens-Mouret Sébastien , Drissen Laurent , Robert Carmelle , Rousseau-Nepton Laurie , Martin René Pierre , Amram Philippe 
Published: July 2023

ABSTRACT
Using datacubes from the imaging Fourier transform spectrometer SITELLE at the Canada–France–Hawaii Telescope as part of the star formation, ionized gas, and nebular abundances legacy survey, we identify 15 new planetary nebulae (PNe) as well as five new supernova remnants (SNRs) in the outer parts of the nearby dwarf starburst galaxy NGC 4214. These data also allow us to study the morphology and kinematics of all 18 known SNRs in this galaxy. We highlight the use of a $\xi = \sigma \frac{\rm {[S{\small \,II}]}}{\rm {H\alpha }}$ diagnostic diagram (σ being the velocity dispersion) to separate SNRs from H ii regions and its advantage compared to classical BPT or Sabbadin diagrams. We provide the emission-line flux ([O iii] λ5007, H α, and H β) and radial velocities of all new PNe candidates, as well as those of 12 of the 17 PNe previously discovered in the central part of the galaxy with Hubble Space Telescope (HST) data. Finally, we use the [O iii] emission-line luminosity function of the PNe sample to establish a new velocity-independent distance for NGC 4214: $D = 3.23^{+0.18}_{-0.25}$ Mpc.
Discovery of a magnetar candidate X-ray pulsar in the Large Magellanic Cloud
Authors: Imbrogno M , Israel G L , Rodríguez Castillo G A , Buckley D A H , Coti Zelati F , Rea N , Monageng I M , Casella P , Stella L , Haberl F , Esposito P , Tombesi F , De Luca A , Tiengo A 
Published: July 2023

ABSTRACT
During a systematic search for new X-ray pulsators in the XMM–Newton archive, we discovered a high amplitude ($PF\simeq 86~{{\ \rm per\ cent}}$) periodic ($P\simeq 7.25\, \mathrm{s}$) modulation in the X-ray flux of 4XMM J045626.3–694723 (J0456 hereafter), a previously unclassified source in the Large Magellanic Cloud (LMC). The period of the modulation is strongly suggestive of a spinning neutron star (NS). The source was detected only during one out of six observations in 2018–2022. Based on an absorbed power-law spectral model with photon slope of Γ ≃ 1.9, we derive a 0.3–10 keV luminosity of $L_\mathrm{X}\simeq 2.7\times 10^{34}\, \mathrm{erg}\, \mathrm{s}^{-1}$ for a distance of 50 kpc. The X-ray properties of J0456 are at variance with those of variable LMC X-ray pulsars hosted in high-mass X-ray binary systems with a Be-star companion. Based on Southern African Large Telescope (SALT) spectroscopic observations of the only optical object that matches the X-ray uncertainty region, we cannot completely rule out that J0456 is an NS accreting from a late-type (G8-K3) star, an as-yet-unobserved binary evolutionary outcome in the Magellanic Clouds (MCs). We show that the source properties are in better agreement with those of magnetars. J0456 may thus be the second known magnetar in the LMC after SGR 0526–66.
The MillenniumTNG Project: refining the one-halo model of red and blue galaxies at different redshifts
Authors: Hadzhiyska Boryana , Hernquist Lars , Eisenstein Daniel , Delgado Ana Maria , Bose Sownak , Kannan Rahul , Pakmor Rüdiger , Springel Volker , Contreras Sergio , Barrera Monica , Ferlito Fulvio , Hernández-Aguayo César , White Simon D M , Frenk Carlos 
Published: July 2023

ABSTRACT
Luminous red galaxies (LRGs) and blue star-forming emission-line galaxies (ELGs) are key tracers of large-scale structure used by cosmological surveys. Theoretical predictions for such data are often done via simplistic models for the galaxy–halo connection. In this work, we use the large, high-fidelity hydrodynamical simulation of the MillenniumTNG project (MTNG) to inform a new phenomenological approach for obtaining an accurate and flexible galaxy-halo model on small scales. Our aim is to study LRGs and ELGs at two distinct epochs, z = 1 and z = 0, and recover their clustering down to very small scales, $r \sim 0.1 \ h^{-1}\, {\rm Mpc}$, i.e. the one-halo regime, while a companion paper extends this to a two-halo model for larger distances. The occupation statistics of ELGs in MTNG inform us that (1) the satellite occupations exhibit a slightly super-Poisson distribution, contrary to commonly made assumptions, and (2) that haloes containing at least one ELG satellite are twice as likely to host a central ELG. We propose simple recipes for modelling these effects, each of which calls for the addition of a single free parameter to simpler halo occupation models. To construct a reliable satellite population model, we explore the LRG and ELG satellite radial and velocity distributions and compare them with those of subhaloes and particles in the simulation. We find that ELGs are anisotropically distributed within haloes, which together with our occupation results provides strong evidence for cooperative galaxy formation (manifesting itself as one-halo galaxy conformity); i.e. galaxies with similar properties form in close proximity to each other. Our refined galaxy-halo model represents a useful improvement of commonly used analysis tools and thus can be of help to increase the constraining power of large-scale structure surveys.
CircKDM5B sponges miR-128 to regulate porcine blastocyst development by modulating trophectoderm barrier function
Authors: Gao Di , Wang Xin , Yan Ye-Lian , Li Chao , Tan Yong-Peng , Liu Qiu-Chen , Zhang Meng-Ya , Zhang Jian V , Sun Qing-Yuan , Cao Zu-Bing , Zhang Yun-Hai 
Published: July 2023

Abstract
Circular RNAs (circRNAs), which exert critical functions in the regulation of transcriptional and post-transcriptional gene expression, are found in mammalian cells but their functions in mammalian preimplantation embryo development remain poorly understood. Here, we showed that circKDM5B mediated miRNA-128 (miR-128) to regulate porcine early embryo development. We screened circRNAs potentially expressed in porcine embryos through an integrated analysis of sequencing data from mouse and human embryos, as well as porcine oocytes. An authentic circRNA originating from histone demethylase KDM5B (referred to as circKDM5B) was abundantly expressed in porcine embryos. Functional studies revealed that circKDM5B knockdown not only significantly reduced blastocyst formation but also decreased the number of total cells and trophectoderm (TE) cells. Moreover, the knockdown of circKDM5B resulted in the disturbance of tight junction assembly and impaired paracellular sealing within the TE epithelium. Mechanistically, miR-128 inhibitor injection could rescue the early development of circKDM5B knockdown embryos. Taken together, the findings revealed that circKDM5B functions as a miR-128 sponge, thereby facilitating early embryonic development in pigs through the modulation of gene expression linked to tight junction assembly.
Action-at-a-distance mutations induced by 8-oxo-7,8-dihydroguanine are dependent on APOBEC3
Authors: Fukushima Ruriko , Suzuki Tetsuya , Kobayakawa Akari , Kamiya Hiroyuki 
Published: July 2023

Abstract
DNA oxidation is a serious threat to genome integrity and is involved in mutations and cancer initiation. The G base is most frequently damaged, and 8-oxo-7,8-dihydroguanine (GO, 8-hydroxyguanine) is one of the predominant damaged bases. In human cells, GO causes a G:C→T:A transversion mutation at the modified site, and also induces untargeted substitution mutations at the G bases of 5ʹ-GpA-3ʹ dinucleotides (action-at-a-distance mutations). The 5ʹ-GpA-3ʹ sequences are complementary to the 5ʹ-TpC-3ʹ sequences, the preferred substrates for apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) cytosine deaminases, and thus their contribution to mutagenesis has been considered. In this study, APOBEC3B, the most abundant APOBEC3 protein in human U2OS cells, was knocked down in human U2OS cells, and a GO-shuttle plasmid was then transfected into the cells. The action-at-a-distance mutations were reduced to ~25% by the knockdown, indicating that GO-induced action-at-a-distance mutations are highly dependent on APOBEC3B in this cell line.
Different SWI/SNF complexes coordinately promote R-loop- and RAD52-dependent transcription-coupled homologous recombination
Authors: Davó-Martínez Carlota , Helfricht Angela , Ribeiro-Silva Cristina , Raams Anja , Tresini Maria , Uruci Sidrit , van Cappellen Wiggert A , Taneja Nitika , Demmers Jeroen A A , Pines Alex , Theil Arjan F , Vermeulen Wim , Lans Hannes 
Published: July 2023

Abstract
The SWI/SNF family of ATP-dependent chromatin remodeling complexes is implicated in multiple DNA damage response mechanisms and frequently mutated in cancer. The BAF, PBAF and ncBAF complexes are three major types of SWI/SNF complexes that are functionally distinguished by their exclusive subunits. Accumulating evidence suggests that double-strand breaks (DSBs) in transcriptionally active DNA are preferentially repaired by a dedicated homologous recombination pathway. We show that different BAF, PBAF and ncBAF subunits promote homologous recombination and are rapidly recruited to DSBs in a transcription-dependent manner. The PBAF and ncBAF complexes promote RNA polymerase II eviction near DNA damage to rapidly initiate transcriptional silencing, while the BAF complex helps to maintain this transcriptional silencing. Furthermore, ARID1A-containing BAF complexes promote RNaseH1 and RAD52 recruitment to facilitate R-loop resolution and DNA repair. Our results highlight how multiple SWI/SNF complexes perform different functions to enable DNA repair in the context of actively transcribed genes.