bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the MYCOPLASMA IST3 urogenital mycoplasma assay in an international multicentre trial
Authors: Boostrom Ian , Bala Yohan , Vasic Jelena Minic , Gluvakov Jelena , Chanard Emmanuel , Barratt Andrew H , Sands Kirsty , Portal Edward , Devigne Laurence , Jones Lucy C , Spiller Owen B 
Published: August 2021

Abstract

Objectives
To evaluate the accuracy, susceptibility and specificity of MYCOPLASMA IST3, the next generation of the most popular culture-based in vitro diagnostic device designed to detect, identify and test the susceptibility of urogenital mycoplasma infections.

Methods
MYCOPLASMA IST3 was evaluated against culture- and molecular-based gold standard methodologies to detect, identify, enumerate and determine antimicrobial resistance for Mycoplasma hominis and Ureaplasma species in 516 clinical samples collected across France, Serbia and the UK. Sample types included vulvovaginal/endocervical or urethral swabs (dry swab or eSwab®), semen and urine samples, which included blinded analysis following addition of a panel of 80 characterized control strains.

Results
Overall species identification was excellent for both Ureaplasma spp. (98.4% sensitivity, 99.7% specificity) and M. hominis (95.7% sensitivity, 100% specificity) relative to combined colony morphology on agar and quantitative PCR standards. Non-dilution-based bacterial load estimation by the assay was accurate between 83.7% (M. hominis) and 86.3% (Ureaplasma spp.) of the time (increased to 94.2% and 100%, respectively, if ±10-fold variance was allowed) relative to colonies counted on agar. Resistance accuracy for Ureaplasma spp. varied from gold standards for only 11/605 of individual tests (major error rate = 1.8%) and for 14/917 individual tests for M. hominis (major error rate = 1.5%).

Conclusions
The redesigned MYCOPLASMA IST3 assay eliminated previous shortcomings by providing independent accurate resistance screening of M. hominis and Ureaplasma species, even in mixed infections, with CLSI-compliant thresholds. Specificity, sensitivity and enumeration estimates correlated closely with the confirmatory methods.
Intrathoracic lipoma in the horizontal fissure of the right lung: a case report
Authors: Nakajima Eiji , Takahashi Hidenobu , Kajiwara Naohiro , Furukawa Kinya , Ishizumi Taichiro , Kataba Hiroaki , Okubo Mitsuru , Hirano Hiroshi , Ikeda Norihiko 
Published: August 2021

Abstract
Lipomas are benign tumors that originate from mesenchymal tissue, such as subcutaneous tissue. Intrathoracic lipomas are rare, and they can occur in the chest wall, mediastinum and bronchi. In the present case, the patient had an intrathoracic lipoma that was located in the horizontal fissure of the right lung. Retrospective review of chest radiographs taken at a previous health checkup confirmed that the tumor was growing. The patient had no symptoms, and computed tomography and magnetic resonance imaging suggested that the tumor was a hamartoma. The tumor was resected by video-assisted thoracic surgery, and was diagnosed by pathological analysis as an intrathoracic lipoma consisting of no atypical fats.
Three classes of hemoglobins are required for optimal vegetative and reproductive growth of Lotus japonicus: genetic and biochemical characterization of LjGlb2-1
Authors: Villar Irene , Rubio Maria C , Calvo-Begueria Laura , Pérez-Rontomé Carmen , Larrainzar Estibaliz , Wilson Michael T , Sandal Niels , Mur Luis A , Wang Longlong , Reeder Brandon , Duanmu Deqiang , Uchiumi Toshiki , Stougaard Jens , Becana Manuel 
Published: August 2021

Abstract
Legumes express two major types of hemoglobins, namely symbiotic (leghemoglobins) and non-symbiotic (phytoglobins), with the latter being categorized into three classes according to phylogeny and biochemistry. Using knockout mutants, we show that all three phytoglobin classes are required for optimal vegetative and reproductive development of Lotus japonicus. The mutants of two class 1 phytoglobins showed different phenotypes: Ljglb1-1 plants were smaller and had relatively more pods, whereas Ljglb1-2 plants had no distinctive vegetative phenotype and produced relatively fewer pods. Non-nodulated plants lacking LjGlb2-1 showed delayed growth and alterations in the leaf metabolome linked to amino acid processing, fermentative and respiratory pathways, and hormonal balance. The leaves of mutant plants accumulated salicylic acid and contained relatively less methyl jasmonic acid, suggesting crosstalk between LjGlb2-1 and the signaling pathways of both hormones. Based on the expression of LjGlb2-1 in leaves, the alterations of flowering and fruiting of nodulated Ljglb2-1 plants, the developmental and biochemical phenotypes of the mutant fed on ammonium nitrate, and the heme coordination and reactivity of the protein toward nitric oxide, we conclude that LjGlb2-1 is not a leghemoglobin but an unusual class 2 phytoglobin. For comparison, we have also characterized a close relative of LjGlb2-1 in Medicago truncatula, MtLb3, and conclude that this is an atypical leghemoglobin.
Family Involvement in the End-of-Life Decision-Making Process: Legal and Bioethical Analysis of Empirical Findings
Authors: Karako-Eyal Nili , Gilbar Roy 
Published: August 2021

Abstract
End-of-life decision making involves clinicians, patients, and relatives; yet, the law in Israel hardly recognises the role of relatives. This raises the question of the law’s impact in practice and, hence, whether it should be amended. This issue is examined on the basis of findings from a qualitative, interview-based study conducted in Israel among relatives of dying patients. The findings indicate that there are areas in which clinicians and relatives do not adhere to the law in the end-of-life decision-making process. For example, they do not always ascertain the patient's end-of-life preferences, which ignores a patient's right to autonomy and their right to make informed decisions. The apparent gaps between the actual conduct of clinicians and relatives on the one hand and the directives of the Israeli Dying Patient Act 2005 on the other, lead us to propose several changes to the Act.
Axisymmetric simulations of the convective overstability in protoplanetary discs
Authors: Teed Robert J , Latter Henrik N 
Published: August 2021

ABSTRACT
Protoplanetary discs at certain radii exhibit adverse radial entropy gradients that can drive oscillatory convection (‘convective overstability’; COS). The ensuing hydrodynamical activity may reshape the radial thermal structure of the disc while mixing solid material radially and vertically or, alternatively, concentrating it in vortical structures. We perform local axisymmetric simulations of the COS using the code snoopy, showing first how parasites halt the instability’s exponential growth, and secondly, the different saturation routes it takes subsequently. As the Reynolds and (pseudo-) Richardson numbers increase, the system moves successively from (i) a weakly non-linear state characterized by relatively ordered non-linear waves, to (ii) wave turbulence, and finally to (iii) the formation of intermittent and then persistent zonal flows. In three dimensions, we expect the latter flows to spawn vortices in the orbital plane. Given the very high Reynolds numbers in protoplanetary discs, the third regime should be the most prevalent. As a consequence, we argue that the COS is an important dynamical process in planet formation, especially near features such as dead zone edges, ice lines, gaps, and dust rings.
Signatures of hierarchical mergers in black hole spin and mass distribution
Authors: Tagawa Hiromichi , Haiman Zoltán , Bartos Imre , Kocsis Bence , Omukai Kazuyuki 
Published: August 2021

ABSTRACT
Recent gravitational wave (GW) observations by LIGO/Virgo show evidence for hierarchical mergers, where the merging BHs are the remnants of previous BH merger events. These events may carry important clues about the astrophysical host environments of the GW sources. In this paper, we present the distributions of the effective spin parameter (χeff), the precession spin parameter (χp), and the chirp mass (mchirp) expected in hierarchical mergers. Under a wide range of assumptions, hierarchical mergers produce (i) a monotonic increase of the average of the typical total spin for merging binaries, which we characterize with $\scriptstyle{{\bar{\chi }}_\mathrm{typ}\equiv \overline{(\chi _\mathrm{eff}^2+\chi _\mathrm{p}^2)^{1/2}}}$, up to roughly the maximum mchirp among first-generation (1g) BHs, and (ii) a plateau at ${\bar{\chi }}_\mathrm{typ}\sim 0.6$ at higher mchirp. We suggest that the maximum mass and typical spin magnitudes for 1g BHs can be estimated from ${\bar{\chi }}_\mathrm{typ}$ as a function of mchirp. The GW data observed in LIGO/Virgo O1–O3a prefers an increase in ${\bar{\chi }}_\mathrm{typ}$ at low mchirp, which is consistent with the growth of the BH spin magnitude by hierarchical mergers at ∼2σ confidence. A Bayesian analysis using the χeff, χp, and mchirp distributions suggests that 1g BHs have the maximum mass of ∼15–$30\, {\rm M}_\odot$ if the majority of mergers are of high-generation BHs (not among 1g–1g BHs), which is consistent with mergers in active galactic nucleus discs and/or nuclear star clusters, while if mergers mainly originate from globular clusters, 1g BHs are favoured to have non-zero spin magnitudes of ∼0.3. We also forecast that signatures for hierarchical mergers in the ${\bar{\chi }}_\mathrm{typ}$ distribution can be confidently recovered once the number of GW events increases to ≳ O(100).
Baryonic dense matter in view of gravitational-wave observations
Authors: Thapa Vivek Baruah , Kumar Anil , Sinha Monika 
Published: August 2021

ABSTRACT
The detection of gravitational waves (GWs) from the merger of binary neutron star (NS) events (GW170817 and GW190425) and subsequent estimations of tidal deformability play a key role in constraining the behaviour of dense matter. In addition, massive NS candidates (∼2 M⊙) along with NICER mass–radius measurements also set sturdy constraints on the dense matter equation of state. Strict bounds from GWs and massive NS observations constrain the theoretical models of nuclear matter comportment at large density regimes. On the other hand, model parameters providing the highly dense matter response are bounded by nuclear saturation properties. This work analyses coupling parametrizations from two classes based on covariant density functional models: non-linear and density-dependent schemes. Considering these constraints together, we study possible models and parametrization schemes with the feasibility of exotic degrees of freedom in dense matter which go well with the astrophysical observations as well as the terrestrial laboratory experiments. We show that most parametrizations with non-linear schemes do not support the observations and experiments while density-dependent scheme goes well with both. Astrophysical observations are well explained if the inclusion of heavier non-strange baryons is considered as one fraction of the dense matter particle spectrum.
Surface brightness fluctuations to constrain secondary stellar populations: revealing very low-metallicity stars in massive galaxies
Authors: Rodríguez-Beltrán P , Vazdekis A , Cerviño M , Beasley M A 
Published: August 2021

ABSTRACT
The aim of this work is to explore the potential of surface brightness fluctuations (SBF) for studying composite stellar populations (CSP). To do so, we have computed the standard (mean) and SBF spectra with E-MILES stellar population synthesis code. We have created a set of models composed by different mass fractions of two single stellar populations, as a first approximation of a CSP scenario. With these models we present an ensemble of SBF colour–colour diagnostic diagrams that reveal different secondary populations depending on the bands used. For this work we focus on those colours capable of unveiling small fractions of metal-poor components in elliptical galaxies, which are dominated by old metal-rich stellar populations. We fit a set of synthetic models and a selection of nearby elliptical galaxies to our CSP models using both mean and SBF colours. We find that the results are highly improved and return small secondary components when mean and SBF values are applied simultaneously, instead of employing them separately or as a constraint. Finally, we explore the possibility of tracking chemical enrichment histories by including in the analysis a variety of SBF colours. For this purpose we present an example where, with two different SBF colour–colour diagrams, we untangle a small contribution of a young solar population and an old metal-poor component from an old solar principal population. The results we have found are promising, but limited by the available data. We highlight the urgent need for new, better, and more consistent SBF observations.
Constraints on warm dark matter from UV luminosity functions of high-z galaxies with Bayesian model comparison
Authors: Rudakovskyi Anton , Mesinger Andrei , Savchenko Denys , Gillet Nicolas 
Published: August 2021

ABSTRACT
The number density of small dark matter (DM) haloes hosting faint high-redshift galaxies is sensitive to the DM free-streaming properties. However, constraining these DM properties is complicated by degeneracies with the uncertain baryonic physics governing star formation. In this work, we use a flexible astrophysical model and a Bayesian inference framework to analyse ultraviolet (UV) luminosity functions (LFs) at z = 6–8. We vary the complexity of the astrophysical galaxy model (single versus double power law for the stellar – halo mass relation) as well as the matter power spectrum [cold DM versus thermal relic warm DM (WDM)], comparing their Bayesian evidences. Adopting a conservatively wide prior range for the WDM particle mass, we show that the UV LFs at z = 6–8 only weakly favour cold DM over WDM. We find that particle masses of ≲ 2 keV are rejected at a 95 per cent credible level in all models that have a WDM-like power spectrum cutoff. This bound should increase to ∼2.5 keV with the James Webb Space Telescope (JWST).
Conversions between gas-phase metallicities in MaNGA
Authors: Scudder Jillian M , Ellison Sara L , El Meddah El Idrissi Loubna , Poetrodjojo Henry 
Published: August 2021

ABSTRACT
We present polynomial conversions between each of 11 different strong line gas-phase metallicity calibrations, each based on ∼1.1 million star-forming spaxels in the public Sloan Digital Sky Survey (SDSS) Data Release 15 (DR15) Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey. For this sample, which is ∼20 times larger than previous works, we present fifth-order polynomial fits for each of 110 possible calibration conversions, for both Small Magellanic Cloud-type and Milky Way-type dust corrections. The typical 2σ scatter around our polynomial fits is 0.1 dex; we present the range over which the metallicities are valid. Conversions between metallicities which rely on the same set of line ratios, or a heavily shared set of emission lines, have reduced scatter in their conversions relative to those conversions with little overlap in required emission lines. Calibration conversions with less consistent sets of emission lines also have increased galaxy-to-galaxy variability, and this variability can account for up to 35 per cent of the total scatter. We also compare our conversions to previous work with the single fibre SDSS DR7 spectra along with higher spatial resolution data from the TYPHOON Integral Field Spectroscopy survey, resulting in comparison samples with spatial resolutions from several kpc down to ∼100 pc. Our metallicity conversions, obtained with the large sample of MaNGA, are robust against the influence of diffuse ionized gas, redshift, effective radius, and spatial blurring, and are therefore consistent across both integrated spectra and the high-resolution integral field spectroscopy data.
Characterization of the hidden break in giant clam 28S ribosomal RNA
Authors: Tan Keana , Conaco Cecilia 
Published: August 2021

ABSTRACT
The molluscan 28S ribosomal RNA (rRNA) naturally cleaves into two fragments of similar size as 18S rRNA. This phenomenon, known as the hidden break, has been described in many other protostome species. Here, we characterize the 28S rRNA hidden break region in seven giant clam species, Tridacna gigas, T. derasa, T. maxima, T. noae, T. crocea, Hippopus hippopus and H. porcellanus. We confirm that the break consistently occurs in giant clams and is observed in all tissues and developmental stages. The region of the giant clam 28S rRNA break is located at a position homologous to the well-characterized 28S rRNA break in insects. High AU content and a stem–loop secondary structure in the region may contribute to fragmentation of the 28S rRNA molecule. An awareness of the existence of the hidden break in molluscs, such as the giant clams, which are emerging systems for understanding how environmental change affects life in the ocean, will facilitate progress of RNA sequencing-based analyses that currently rely on standard RNA profiles as a measure of sample integrity.
The Polycomb protein RING1B enables estrogen-mediated gene expression by promoting enhancer–promoter interaction and R-loop formation
Authors: Zhang Yusheng , Liu Tong , Yuan Fenghua , Garcia-Martinez Liliana , Lee Kyutae D , Stransky Stephanie , Sidoli Simone , Verdun Ramiro E , Zhang Yanbin , Wang Zheng , Morey Lluis 
Published: August 2021

Abstract
Polycomb complexes have traditionally been prescribed roles as transcriptional repressors, though increasing evidence demonstrate they can also activate gene expression. However, the mechanisms underlying positive gene regulation mediated by Polycomb proteins are poorly understood. Here, we show that RING1B, a core component of Polycomb Repressive Complex 1, regulates enhancer–promoter interaction of the bona fide estrogen-activated GREB1 gene. Systematic characterization of RNA:DNA hybrid formation (R-loops), nascent transcription and RNA Pol II activity upon estrogen administration revealed a key role of RING1B in gene activation by regulating R-loop formation and RNA Pol II elongation. We also found that the estrogen receptor alpha (ERα) and RNA are both necessary for full RING1B recruitment to estrogen-activated genes. Notably, RING1B recruitment was mostly unaffected upon RNA Pol II depletion. Our findings delineate the functional interplay between RING1B, RNA and ERα to safeguard chromatin architecture perturbations required for estrogen-mediated gene regulation and highlight the crosstalk between steroid hormones and Polycomb proteins to regulate oncogenic programs.
Charcot–Marie–Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response
Authors: Mendonsa Samantha , von Kuegelgen Nicolai , Bujanic Lucija , Chekulaeva Marina 
Published: August 2021

Abstract
Toxic gain-of-function mutations in aminoacyl-tRNA synthetases cause a degeneration of peripheral motor and sensory axons, known as Charcot–Marie–Tooth (CMT) disease. While these mutations do not disrupt overall aminoacylation activity, they interfere with translation via an unknown mechanism. Here, we dissect the mechanism of function of CMT mutant glycyl-tRNA synthetase (CMT-GARS), using high-resolution ribosome profiling and reporter assays. We find that CMT-GARS mutants deplete the pool of glycyl-tRNAGly available for translation and inhibit the first stage of elongation, the accommodation of glycyl-tRNA into the ribosomal A-site, which causes ribosomes to pause at glycine codons. Moreover, ribosome pausing activates a secondary repression mechanism at the level of translation initiation, by inducing the phosphorylation of the alpha subunit of eIF2 and the integrated stress response. Thus, CMT-GARS mutant triggers translational repression via two interconnected mechanisms, affecting both elongation and initiation of translation.
HbA1c and beyond
Authors: Rossing Peter 
Published: August 2021

Abstract
The Kidney Disease: Improving Global Outcomes (KDIGO) Clinical Practice Guideline on Diabetes Management in Chronic Kidney Disease from 2020 comes at an opportune time when progress in diabetes technology and therapeutics offers new options to manage the large population of patients with diabetes and chronic kidney disease (CKD) at high risk of poor health outcomes. Management of haemoglobin A1c is important in diabetes, but an enlarging base of evidence from large clinical trials has demonstrated important new treatments offering organ protection and not just glucose management, such as sodium–glucose cotransporter 2 inhibitors and glucagon-like peptide-1 receptor agonists. It is the ambition that the guideline can help to optimize the clinical care of people with diabetes and CKD by integrating new options with existing management strategies based on high-quality evidence. Here, the focus has been on comprehensive care of patients with diabetes and CKD, glycaemic monitoring and targets, antihyperglycaemic therapies in patients with diabetes and CKD, and new developments since the guideline was published offering new opportunities and a wider target population for the new interventions.
Use of Electronic Cigarettes as a Predictor of Cannabis Experimentation: A Longitudinal Study Among German Youth
Authors: Seidel Ann-Kathrin , Morgenstern Matthis , Galimov Artur , Pedersen Anya , Isensee Barbara , Goecke Michaela , Hanewinkel Reiner 
Published: August 2021

Abstract

Introduction
Experimentation with e-cigarettes is rising among youth, and there are concerns that e-cigarettes could be a new risk factor for initiating substance use. This study aimed to investigate whether e-cigarette use longitudinally predicts experimentation with cannabis.

Aims and Methods
During 2017–2019, a prospective cohort study with an observation period of 18 months was conducted with 3040 students from Germany who had never used cannabis (mean age = 14.8, range: 13–18 years). A multiple Poisson regression was used to investigate whether e-cigarette use was an independent predictor of future cannabis use.

Results
Lifetime e-cigarette use was reported by 29.4% of the survey population (n = 894) at baseline, and 17.4% (n = 529) initiated cannabis use during the observation period. Among e-cigarette ever users, the initiation rate was 34.5% compared with 10.4% of never users. Results were robust to adjustment for age, sex, migrant status, type of school, sensation seeking, peer cannabis use, the use of alcohol and conventional cigarettes (ARR = 1.83; 95% CI: 1.48–2.25). Further analyses revealed that the association between e-cigarette use and cannabis experimentation was stronger among youth with low sensation-seeking scores (ARR = .77, CI: .61–.97) and no conventional cigarette use (ARR = .48, CI: .37–.64) at baseline.

Conclusions
E-cigarette use is associated with a subsequent initiation of cannabis use. This association seems to be stronger for youth who have a lower risk for substance use in general. Future studies need to investigate whether this is only true for experimental or also more frequent cannabis use.

Implications
The study indicates a prospective association between e-cigarette use and initiation of cannabis experimentation independent of other risk factors. It suggests that e-cigarette use is more strongly associated with cannabis initiation for youth with a lower propensity to use substances (low sensation-seekers and non-smokers).