bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prevalence of laboratory-confirmed Pneumocystis jirovecii in HIV-infected adults in Africa: A systematic review and meta-analysis
Authors: Wills Nicola K , Lawrence David S , Botsile Elizabeth , Tenforde Mark W , Jarvis Joseph N 
Published: January 2021

Abstract
Background: The epidemiology of Pneumocystis jirovecii, known to colonize the respiratory tract and cause a life-threatening HIV-associated pneumonia (PCP), is poorly described in Africa. We conducted a systematic review to evaluate P. jirovecii prevalence in African HIV-positive adults with or without respiratory symptoms. Methods: We searched Medline, Embase, Cochrane library, Africa-Wide, and Web of Science for studies employing PCR and/or microscopy for P. jirovecii detection in respiratory samples from HIV-positive adults in Africa between 1995 and 2020. Prevalence with respiratory symptoms was pooled using random-effect meta-analysis, and stratified by laboratory method, sample tested, study setting, CD4 count, and trimethoprim/sulfamethoxazole prophylaxis. Colonization prevalence in asymptomatic adults and in adults with non-PCP respiratory disease was described, and quantitative PCR (qPCR) thresholds to distinguish colonization from microscopy-confirmed PCP reviewed. Results: Thirty-two studies were included, with 27 studies (87%) at high risk of selection bias. P. jirovecii was detected in 19% [95% confidence interval (CI): 12–27%] of 3583 symptomatic and in 9% [95% CI: 0–45%] of 140 asymptomatic adults. Among symptomatic adults, prevalence was 22% [95% CI: 12–35%] by PCR and 15% [95% CI: 9–23%] by microscopy. Seven percent of 435 symptomatic adults had PCR-detected Pneumocystis colonization without evidence of PCP [95% CI: 5–10%, four studies]. One study established a qPCR cutoff of 78 copies/5μl of DNA in 305 induced sputum samples to distinguish Pneumocystis colonization from microscopy-confirmed PCP. Conclusion: Despite widened access to HIV services, P. jirovecii remains common in Africa. Prevalence estimates and qPCR-based definitions of colonization are limited, and overall quality of studies is low.
The black hole masses of extremely luminous radio-WISE selected galaxies
Authors: Ferris E R , Blain A W , Assef R J , Hatch N A , Kimball A , Kim M , Sajina A , Silva A , Stern D , Diaz-Santos T , Tsai C-W , Wylezalek D 
Published: January 2021

ABSTRACT
We present near-IR photometry and spectroscopy of 30 extremely luminous radio and mid-IR-selected galaxies. With bolometric luminosities exceeding ∼1013 $\rm {L_{\odot }}$ and redshifts ranging from z = 0.880 to 2.853, we use Very Large Telescope instruments X-shooter and Infrared Spectrometer and Array Camera to investigate this unique population of galaxies. Broad multicomponent emission lines are detected in 18 galaxies and we measure the near-IR lines $\rm {H\,\rm {\beta }}$, $\rm{[O\,{\small III}]}\, \rm {\lambda }\rm {\lambda }4959,5007$, and $\rm {H\,\rm {\alpha }}$ in 6, 15, and 13 galaxies, respectively, with 10 $\rm {Ly\,\alpha }$ and 5 C iv lines additionally detected in the UVB arm. We use the broad $\rm{[O\,{\small III}]}\, \rm {\lambda }5007$ emission lines as a proxy for the bolometric active galactic nucleus luminosity, and derive lower limits to supermassive black hole masses of 107.9–109.4 M⊙ with expectations of corresponding host masses of 1010.4–1012.0 M⊙. We measure $\rm {\lambda }_{Edd}$ &gt; 1 for eight of these sources at a 2σ significance. Near-IR photometry and SED fitting are used to compare stellar masses directly. We detect both Balmer lines in five galaxies and use these to infer a mean visual extinction of AV = 2.68 mag. Due to non-detections and uncertainties in our ${\rm H}\, \beta$ emission line measurements, we simulate a broad ${\rm H}\, \beta$ line of FWHM = 1480 $\rm {kms^{-1}}$ to estimate extinction for all sources with measured ${\rm H}\, \alpha$ emission. We then use this to infer a mean AV = 3.62 mag, demonstrating the highly obscured nature of these galaxies, with the consequence of increasing our estimates of black hole masses by a 0.5 orders of magnitude in the most extreme and obscured cases.
Radial oscillations and gravitational wave echoes of strange stars for various equations of state
Authors: Bora Jyatsnasree , Dev Goswami Umananda 
Published: January 2021

ABSTRACT
We study the radial oscillations of non-rotating strange stars (SSs) and their characteristic echo frequencies for three equations of state (EoS), viz., MIT Bag model EoS, linear EoS, and polytropic EoS. The frequencies of radial oscillations of these compact stars are computed for these EoSs. In total, 22 lowest radial frequencies for each of these three EoSs have been computed. First, for each EoS, we have integrated Tolman–Oppenheimer–Volkoff equations numerically to calculate the radial and pressure perturbations of SSs. Next, the mass–radius relationships for these stars are obtained using these three EoSs. Then the radial frequencies of oscillations for these EoSs are calculated. Further, the characteristic gravitational wave echo frequencies and the repetition of echo frequencies of SSs are computed for these EoSs. Our numerical results show that the radial frequencies and also echo frequencies vastly depend on the model and on the value of the model parameter. Our results also show that the radial frequencies of strange stars are maximum for polytropic EoS in comparison to MIT Bag model EoS and linear EoS. Moreover, SSs with MIT Bag model EoS and linear EoS are found to emit gravitational wave echoes. Whereas, SSs with polytropic EoS are not emitting gravitational wave echoes.
Quasi-periodic oscillations in the long-term radio light curves of the blazar AO 0235+164
Authors: Tripathi Ashutosh , Gupta Alok C , Aller Margo F , Wiita Paul J , Bambi Cosimo , Aller Hugh , Gu Minfeng 
Published: January 2021

ABSTRACT
We present time series analyses of three-decade long radio observations of the BL Lacertae object AO 0235+164 made at the University of Michigan Radio Astronomical Observatory operating at three central frequencies of 4.8, 8.0, and 14.5 GHz. We detected a quasi-periodic oscillation of ∼965 d in all three frequency bands in the light curve of the effectively simultaneous observations, along with strong signals at ∼1950, ∼1350, and ∼660 d. The periodicity is analysed with three methods: data-compensated discrete Fourier transform, generalized Lomb–Scargle periodogram, and Weighted Wavelet Z-transform. These methods are chosen as they have different analysis approaches toward robust measurement of claimed periodicities. The quasi-periodic oscillation at 965 ± 50 d is found to be significant (at least 3.5σ) and is persistent throughout the observation for all three radio frequencies, and the others, which may be harmonics, are comparably significant in at least the 8.0 and 14.5 GHz bands. We briefly discuss plausible explanations for the origin of such long and persistent periodicity.
Orbital analysis of small bodies in co-orbital motion with Jupiter through the torus structure
Authors: Qi Yi , de Ruiter Anton 
Published: January 2021

ABSTRACT
In this paper, based on the torus structure, we investigate the orbital characteristics of Jupiter Trojans and Jupiter-family comets (JFCs) in co-orbital motion with Jupiter. The motivation of this paper is to test whether the semi-analytical approach and conclusions of the torus structure proposed in the circular restricted three-body problem are still valid for real small bodies in the ephemeris model, and how long they follow the prediction of the semi-analytical approach. Based on the topological structure of the co-orbital motion in the torus space, we propose a method for estimating the libration amplitude for Trojans. 873 Jupiter Trojans with well-determined orbits are picked as examples to demonstrate the validity of our estimation method. Numerical analysis reveals that the difference between the osculating semimajor axes of the Trojan and Jupiter can influence the accuracy of our estimation method significantly. Based on the semi-analytical approach, we predict orbital behaviours of three JFCs, 85P/Boethin, P/2012 US27 (Siding Spring), and P/2019 A1 (PANSTARRS). Numerical integration in the ephemeris model indicates that their real orbital behaviours are consistent with our predictions. In particular, we find that the current quasi-satellite state of P/2012 US27 (Siding Spring) can remain for about 1.5 × 105 yr, much longer than those that correspond to other previously reported QS companions of Jupiter.
The Three Hundred Project: Substructure in hydrodynamical and dark matter simulations of galaxy groups around clusters
Authors: Haggar Roan , Pearce Frazer R , Gray Meghan E , Knebe Alexander , Yepes Gustavo 
Published: January 2021

ABSTRACT
Dark matter-only simulations are able to produce the cosmic structure of a Lambda cold dark matter universe, at a much lower computational cost than more physically motivated hydrodynamical simulations. However, it is not clear how well smaller substructure is reproduced by dark matter-only simulations. To investigate this, we directly compare the substructure of galaxy clusters and of surrounding galaxy groups in hydrodynamical and dark matter-only simulations. We utilize thethreeHundred project, a suite of 324 simulations of galaxy clusters that have been simulated with hydrodynamics, and in dark matter-only. We find that dark matter-only simulations underestimate the number density of galaxies in the centres of groups and clusters relative to hydrodynamical simulations, and that this effect is stronger in denser regions. We also look at the phase space of infalling galaxy groups, to show that dark matter-only simulations underpredict the number density of galaxies in the centres of these groups by about a factor of four. This implies that the structure and evolution of infalling groups may be different to that predicted by dark matter-only simulations. Finally, we discuss potential causes for this underestimation, considering both physical effects, and numerical differences in the analysis.
The growth of intracluster light in XCS-HSC galaxy clusters from 0.1 &lt; z &lt; 0.5
Authors: Furnell Kate E , Collins Chris A , Kelvin Lee S , Baldry Ivan K , James Phil A , Manolopoulou Maria , Mann Robert G , Giles Paul A , Bermeo Alberto , Hilton Matthew , Wilkinson Reese , Romer A Kathy , Vergara Carlos , Bhargava Sunayana , Stott John P , Mayers Julian , Viana Pedro 
Published: January 2021

ABSTRACT
We estimate the intracluster light (ICL) component within a sample of 18 clusters detected in the XMM Cluster Survey (XCS) data using the deep (∼26.8 mag) Hyper Suprime-Cam Subaru Strategic Programme data release 1 i-band data. We apply a rest-frame μB = 25 mag arcsec−2 isophotal threshold to our clusters, below which we define light as the ICL within an aperture of RX,500 (X-ray estimate of R500) centred on the brightest cluster galaxy (BCG). After applying careful masking and corrections for flux losses from background subtraction, we recover ∼20 per cent of the ICL flux, approximately four times our estimate of the typical background at the same isophotal level (${\sim}5{{\ \rm per\ cent}}$). We find that the ICL makes up about ${\sim}24{{\ \rm per\ cent}}$ of the total cluster stellar mass on average (∼41 per cent including the flux contained in the BCG within 50 kpc); this value is well matched with other observational studies and semi-analytic/numerical simulations, but is significantly smaller than results from recent hydrodynamical simulations (even when measured in an observationally consistent way). We find no evidence for any links between the amount of ICL flux with cluster mass, but find a growth rate of 2–4 for the ICL between 0.1 &lt; z &lt; 0.5. We conclude that the ICL is the dominant evolutionary component of stellar mass in clusters from z ∼ 1. Our work highlights the need for a consistent approach when measuring ICL alongside the need for deeper imaging, in order to unambiguously measure the ICL across as broad a redshift range as possible (e.g. 10-yr stacked imaging from the Vera C. Rubin Observatory).
The luminosity functions and redshift evolution of satellites of low-mass galaxies in the COSMOS survey
Authors: Roberts Daniella M , Nierenberg Anna M , Peter Annika H G 
Published: January 2021

ABSTRACT
The satellite populations of the Milky Way, and Milky Way mass galaxies in the local Universe, have been extensively studied to constrain dark matter and galaxy evolution physics. Recently, there has been a shift to studying satellites of hosts with stellar masses between that of the Large Magellanic Cloud and the Milky Way, since they can provide further insight on hierarchical structure formation, environmental effects on satellites, and the nature of dark matter. Most work is focused on the Local Volume, and little is still known about low-mass host galaxies at higher redshift. To improve our understanding of the evolution of satellite populations of low-mass hosts, we study satellite galaxy populations as a function of host stellar mass 9.5 &lt; log (M*/M⊙) &lt; 10.5 and redshifts 0.1 &lt; $z$ &lt; 0.8 in the COSMOS survey, making this the first study of satellite systems of low-mass hosts across half the age of the universe. We find that the satellite populations of low-mass host galaxies, which we measure down to satellite masses equivalent to the Fornax dwarf spheroidal satellite of the Milky Way, remain mostly unchanged through time. We observe a weak dependence between host stellar mass and number of satellites per host, which suggests that the stellar masses of the hosts are in the power-law regime of the stellar mass to halo mass relation (M*–Mhalo) for low-mass galaxies. Finally, we test the constraining power of our measured cumulative luminosity function to calculate the low-mass end slope of the M*–Mhalo relation. These new satellite luminosity function measurements are consistent with Lamda cold dark matter predictions.
Dynamics of the HD regulatory subdomain of PARP-1; substrate access and allostery in PARP activation and inhibition
Authors: Ogden Tom E H , Yang Ji-Chun , Schimpl Marianne , Easton Laura E , Underwood Elizabeth , Rawlins Philip B , McCauley Michael M , Langelier Marie-France , Pascal John M , Embrey Kevin J , Neuhaus David 
Published: January 2021

Abstract
PARP-1 is a key early responder to DNA damage in eukaryotic cells. An allosteric mechanism links initial sensing of DNA single-strand breaks by PARP-1’s F1 and F2 domains via a process of further domain assembly to activation of the catalytic domain (CAT); synthesis and attachment of poly(ADP-ribose) (PAR) chains to protein sidechains then signals for assembly of DNA repair components. A key component in transmission of the allosteric signal is the HD subdomain of CAT, which alone bridges between the assembled DNA-binding domains and the active site in the ART subdomain of CAT. Here we present a study of isolated CAT domain from human PARP-1, using NMR-based dynamics experiments to analyse WT apo-protein as well as a set of inhibitor complexes (with veliparib, olaparib, talazoparib and EB-47) and point mutants (L713F, L765A and L765F), together with new crystal structures of the free CAT domain and inhibitor complexes. Variations in both dynamics and structures amongst these species point to a model for full-length PARP-1 activation where first DNA binding and then substrate interaction successively destabilise the folded structure of the HD subdomain to the point where its steric blockade of the active site is released and PAR synthesis can proceed.
Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs
Authors: Fei Yue , Nyikó Tünde , Molnar Attila 
Published: January 2021

Abstract
Short non-coding RNA molecules (sRNAs) play a fundamental role in gene regulation and development in higher organisms. They act as molecular postcodes and guide AGO proteins to target nucleic acids. In plants, sRNA-targeted mRNAs are degraded, reducing gene expression. In contrast, sRNA-targeted DNA sequences undergo cytosine methylation referred to as RNA-directed DNA methylation (RdDM). Cytosine methylation can suppress transcription, thus sRNAs are potent regulators of gene expression. sRNA-mediated RdDM is involved in genome stability through transposon silencing, mobile signalling for epigenetic gene control and hybrid vigour. Since cytosine methylation can be passed on to subsequent generations, RdDM contributes to transgenerational inheritance of the epigenome. Using a novel approach, which can differentiate between primary (inducer) and secondary (amplified) sRNAs, we show that initiation of heritable RdDM does not require complete sequence complementarity between the sRNAs and their nuclear target sequences. sRNAs with up to four regularly interspaced mismatches are potent inducers of RdDM, however, the number and disruptive nature of nucleotide polymorphisms negatively correlate with their efficacy. Our findings contribute to understanding how sRNA can directly shape the epigenome and may be used in designing the next generation of RNA silencing constructs.
Predation assessment of the invasive ctenophore Mnemiopsis leidyi in a French Mediterranean lagoon
Authors: Marchessaux Guillaume , Belloni Bruno , Gadreaud Justine , Thibault Delphine 
Published: January 2021

Abstract
Since 2000, the invasive ctenophore Mnemiopsis leidyi has been recorded in Mediterranean brackish lagoons. Quantitative data on its feeding behavior (i.e. potential ecological impact) in these particular environments are non-existent. In this study, we describe in situ predation dynamics of M. leidyi in the Berre Lagoon (south-eastern France) over a 22-month survey. Ctenophores were fixed in a solution of formalin in brackish water, allowing the study of the prey items in the gastric cavities at different time scales. The number of prey items ingested is influenced by the ctenophore biovolume, from 8 (0.5 mL) to 1 207 prey ind−1 (35 mL), and by temperature of 3.4°C (2 ± 2 prey ind−1) to 23.2°C (517 ± 295 prey ind−1). Gut evacuation time is strongly related to temperature and ranged from 80 (25°C) to 160 min (9°C). Mnemiopsis leidyi diet changed seasonally following in situ concentrations of prey. The less mobile preys such as mollusks and barnacles were the most impacted. The ctenophore predation pressure on the zooplankton assemblage could lead at time to a release of grazing pressure on phytoplankton and favor the eutrophication of the lagoon.
Which physicochemical variables should zooplankton ecologists measure when they conduct field studies?
Authors: Gray Derek K , Elmarsafy Mariam , Vucic Jasmina M , Teillet Matthew , Pretty Thomas J , Cohen Rachel S , Huynh Mercedes 
Published: January 2021

Abstract
Over the last century, a rich literature has developed describing how the physical and chemical environment influences zooplankton communities, but there is little guidance on the suite of limnological variables that should be measured by zooplankton ecologists. We performed a literature review to assess (i) which variables were measured most often by zooplankton ecologists, (ii) which of these variables were consistently related to zooplankton abundance and richness and (iii) whether key variables were overlooked by investigators. Our results show that there is a core group of nine limnological variables that are measured most frequently, including lake surface area, pH, phosphorus, nitrogen, dissolved oxygen, conductivity, chlorophyll-a, maximum depth and temperature. These variables were among those most often associated with variation in zooplankton, but several others, including dissolved organic carbon, alkalinity and nitrate, were sampled infrequently, despite showing promise as important explanatory variables. The selection of variables in past studies did not correlate with how often those variables were significant in the literature, but instead, might have been related to their ease of measurement. Neglecting to measure important variables could have implications for fundamental and applied studies that aim to understand the factors structuring zooplankton communities and their response to environmental change.
Brassinosteroid homeostasis is critical for the functionality of the Medicago truncatula pulvinus
Authors: Kong Yiming , Meng Zhe , Wang Hongfeng , Wang Yan , Zhang Yuxue , Hong Limei , Liu Rui , Wang Min , Zhang Jing , Han Lu , Bai Mingyi , Yu Xiaolin , Kong Fanjiang , Mysore Kirankumar S , Wen Jiangqi , Xin Peiyong , Chu Jinfang , Zhou Chuanen 
Published: January 2021

Abstract
Many plant species open their leaves during the daytime and close them at night as if sleeping. This leaf movement is known as nyctinasty, a unique and intriguing phenomenon that been of great interest to scientists for centuries. Nyctinastic leaf movement occurs widely in leguminous plants, and is generated by a specialized motor organ, the pulvinus. Although a key determinant of pulvinus development, PETIOLULE-LIKE PULVINUS (PLP), has been identified, the molecular genetic basis for pulvinus function is largely unknown. Here, through an analysis of knockout mutants in barrelclover (Medicago truncatula), we showed that neither altering brassinosteroid (BR) content nor blocking BR signal perception affected pulvinus determination. However, BR homeostasis did influence nyctinastic leaf movement. BR activity in the pulvinus is regulated by a BR-inactivating gene PHYB ACTIVATION TAGGED SUPPRESSOR1 (BAS1), which is directly activated by PLP. A comparative analysis between M. truncatula and the non-pulvinus forming species Arabidopsis and tomato (Solanum lycopersicum) revealed that PLP may act as a factor that associates with unknown regulators in pulvinus determination in M. truncatula. Apart from exposing the involvement of BR in the functionality of the pulvinus, these results have provided insights into whether gene functions among species are general or specialized.
Diversity of Pain Medicine Trainees and Faculty in the United States: A Cross-Sectional Analysis of Fellowship Training from 2009–2019
Authors: Odonkor Charles A , Leitner Brooks , Taraben Salam , Adekoya Peju , Orhurhu Vwaire , Hirani Salman , Ike Kenneth , Lee Roger , Vanterpool Stephanie , Goree Johnathan H , Sully Kate , Poree Lawrence 
Published: January 2021

Abstract

Objective
Diversity and equity in medicine remain pivotal to care delivery. Data analysis on sex and racial diversity of pain medicine fellowship trainees and faculty in the United States are scant. We sought to characterize demographic and retention patterns among pain medicine fellows and faculty, who represent the emerging chronic pain management workforce.

Design
cross-sectional retrospective analysis.

Method
We conducted an analysis of data from the American Association of Medical Colleges (AAMC) and the United States Accreditation Council on Graduate Medical Education (ACGME)-approved residency and fellowship training-programs for each year from 2009 through 2019, inclusively. We compared changes in sex, racial/ethnicity composition and retention rates of fellows and faculty in the United States by practice setting.

Results
From 2009 to 2019, there was a 14% increase in the number of ACGME pain fellowship programs. From 2009 to 2019, the ratio of men to women pain fellows ranged from 5:1 to 3.7:1. Compared with their self-identified White peers, Asian (OR 0.44; 95% CI: 0.34–0.58), Black (OR 0.46; 95% CI: 0.30–0.72), and Native American/Alaskan Native (OR 0.26; 95% CI: 0.08–0.80) identifying individuals had significantly lower odds of being a pain fellow, P &lt; 0.05. There was no significant difference in female (OR = 0.4, 95% CI: 0.148-1.09) and Black (OR 0.36; 95% CI: 0.11–1.12) program-directors. Pain-fellow in-state retention was 53%.

Conclusions
The demographics of pain medicine training programs reflect a persistent male vs. female gap with underrepresentation of racial minorities. Further research is needed to elucidate reasons underlying these disparities.