bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrative conformal p-values for out-of-distribution testing with labelled outliers
Authors: Liang Ziyi , Sesia Matteo , Sun Wenguang
Published: January 2024

This paper presents a conformal inference method for out-of-distribution testing that leverages side information from labelled outliers, which are commonly underutilized or even discarded by conventional conformal p-values. This solution is practical and blends inductive and transductive inference strategies to adaptively weight conformal p-values, while also automatically leveraging the most powerful model from a collection of one-class and binary classifiers. Further, this approach leads to rigorous false discovery rate control in multiple testing when combined with a conditional calibration strategy. Extensive numerical simulations show that the proposed method outperforms existing approaches.
Chikungunya infection in returned travellers: results from the GeoSentinel network, 2005–2020
Authors: Bierbrier Rachel , Javelle Emilie , Norman Francesca F , Chen Lin Hwei , Bottieau Emmanuel , Schwartz Eli , Leder Karin , Angelo Kristina M , Stoney Rhett J , Libman Michael , Hamer Davidson H , Huits Ralph , Connor Bradley A , Simon Fabrice , Barkati Sapha ,   for the GeoSentinel Network
Published: January 2024

Background

Chikungunya is an important travel-related disease because of its rapid geographical expansion and potential for prolonged morbidity. Improved understanding of the epidemiology of travel-related chikungunya infections may influence prevention strategies including education and vaccination.

Methods

We analysed data from travellers with confirmed or probable chikungunya reported to GeoSentinel sites from 2005 to 2020. Confirmed chikungunya was defined as a compatible clinical history plus either virus isolation, positive nucleic acid test or seroconversion/rising titre in paired sera. Probable chikungunya was defined as a compatible clinical history with a single positive serology result.

Results

1202 travellers (896 confirmed and 306 probable) with chikungunya were included. The median age was 43 years (range 0–91; interquartile range [IQR]: 31–55); 707 (58.8%) travellers were female. Most infections were acquired in the Caribbean (28.8%), Southeast Asia (22.8%), South Central Asia (14.2%) and South America (14.2%). The highest numbers of chikungunya cases reported to GeoSentinel were in 2014 (28.3%), 2015 (14.3%) and 2019 (11.9%). The most frequent reasons for travel were tourism (n = 592; 49.3%) and visiting friends or relatives (n = 334; 27.7%). The median time to presentation to a GeoSentinel site was 23 days (IQR: 7–52) after symptom onset. In travellers with confirmed chikungunya and no other reported illnesses, the most frequently reported symptoms included musculoskeletal symptoms (98.8%), fever/chills/sweats (68.7%) and dermatologic symptoms (35.5%). Among 917 travellers with information available, 296 (32.3%) had a pretravel consultation.

Conclusions

Chikungunya was acquired by international travellers in almost 100 destinations globally. Vector precautions and vaccination where recommended should be integrated into pretravel visits for travellers going to areas with chikungunya or areas with the potential for transmission. Continued surveillance of travel-related chikungunya may help public health officials and clinicians limit the transmission of this potentially debilitating disease by defining regions where protective measures (e.g. pretravel vaccination) should be strongly considered.
TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response
Authors: Chen Min , Dai Yani , Liao Jiamin , Wu Huan , Lv Qiang , Huang Yu , Liu Lichang , Feng Yu , Lv Hongxuan , Zhou Bo , Peng Dan
Published: January 2024

Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.
The CRISPR–Cas system in clinical strains of Acinetobacter baumannii: an in-silico analysis
Authors: Martínez-Trejo Arturo , Ruiz-Ruiz Juan Manuel , Gonzalez-Avila Luis Uriel , Saldaña-Padilla Andres , Hernández-Cortez Cecilia , de Jesús Colmenero-Solís Raúl , Bello-López Juan Manuel , Castro-Escarpulli Graciela
Published: January 2024

Acinetobacter baumannii is a relevant bacterium due to its high-resistance profile. It is well known that antimicrobial resistance is primarily linked to mutations and the acquisition of external genomic material, such as plasmids or phages, to which the Clustered Regularly Interspaced Short Palindromic Repeats associated with Cas proteins, or CRISPR–Cas, system is related. It is known that the system can influence the acquisition of foreign genetic material and play a role in various physiological pathways. In this study, we conducted an in-silico analysis using 91 fully assembled genomes of clinical strains obtained from the NCBI database. Among the analyzed genomes, the I-F1 subtype of the CRISPR–Cas system was detected showcasing variations in architecture and phylogeny. Using bioinformatic tools, we determined the presence, distribution, and specific characteristics of the CRISPR–Cas system. We found a possible association of the system with resistance genes but not with virulence determinants. Analysis of the system’s components, including spacer sequences, suggests its potential role in protecting against phage infections, highlighting its protective function.
Knowledge and regulation on fungal contamination of sand and water: Progress report and perspectives
Authors: Gangneux Jean-Pierre , Brandao Joao , Segal Ester ,   the ECMM/ISHAM MYCOSANDS study group, Arikan-Akdagli Sevtap , Barac Aleksandra , Bertout Sébastien , Bostanaru Andra-Cristina , Brito Sara , Bull Michelle , Çerikçioğlu Nilgün , Chapman Belinda , Delhaes Laurence , Efstratiou Maria , Ergin Çagri , Frenkel Michael , Guerra Alexis Danielle , Gitto Aurora , Gonçalves Cláudia Isabel , Guegan Hélène , Gunde-Cimerman Nina , Güran Mümtaz , Irinyi Laszlo , Jiang Sunny , Jonikaitė Egle , Jozić Slaven , Kataržytė Marija , Klingspor Lena , Mares Mihai , Meijer Wim , Melchers Willem , Meletiadis Joseph , Meyer Wieland , Nastasa Valentin , Novak-Babič Monika , Ogunc Dilara , Ozhak Betil , Prigitano Anna , Ranque Stéphane , Richardson Malcolm , Roger Frédéric , Rusu Raluca-Oana , Sabino Raquel , Sampaio Ana , Silva Susana , Solo-gabriele Helena , Stephens Jayne , Tehupeiory-Kooreman Marlou , Tortorano Anna-Maria , Velegraki Aristea , Veríssimo Cristina , Lušić Darija Vukić , Wunderlich Georgoa
Published: January 2024

Fungal flora in coastal/inland beach sand and recreational water is a neglected field of study, despite its potential impact on human health. A joint International Society for Human and Animal Mycology/European Confederation for Medical Mycology (ISHAM/ECMM) working group was formed in 2019 with the task to set up a vast international initiative aimed at studying the fungal contamination of beaches and bathing waters. Here we review the importance of the topic, and list the main results and achievements from 12 scientific publications. Fungal contamination exists at different levels, and the genera most frequently found were Aspergillus spp., Candida spp., Fusarium spp., and Cryptococcus spp., both in sand and in water. A site-blind median was found to be 89 colony-forming units of fungi per gram of sand in coastal/inland freshwaters. This threshold has been used for the sand quality criterion of the blue flag in Portugal. Additionally, our data were considered pivotal and therefore used for the first inclusion of fungi as a biological taxon of interest in water quality and sand monitoring recommendations of the World Health Organization’s new guidelines on recreational water quality (Vol.1–Chap7). The findings of the consortium also suggest how environmental conditions (climate, salinity, soil pH, nitrogen, etc.) influence microbial communities in different regions, and that yeast species like Candida glabrata, Clavispora lusitaniae, and Meyerozyma guilliermondii have been identified as potential fungal indicators of fecal contamination. Climate change and natural disasters may affect fungal populations in different environments, and because this is still a field of study under exploration, we also propose to depict the future challenges of research and unmet needs.
The dragon-II simulations – III. Compact binary mergers in clusters with up to 1 million stars: mass, spin, eccentricity, merger rate, and pair instability supernovae rate
Authors: Arca sedda Manuel , Kamlah Albrecht W H , Spurzem Rainer , Rizzuto Francesco Paolo , Giersz Mirek , Naab Thorsten , Berczik Peter
Published: January 2024

Compact binary mergers forming in star clusters may exhibit distinctive features that can be used to identify them among observed gravitational-wave sources. Such features likely depend on the host cluster structure and the physics of massive star evolution. Here, we dissect the population of compact binary mergers in the dragon-II simulation data base, a suite of 19 direct N-body models representing dense star clusters with up to 106 stars and $\lt 33~{{\ \rm per\ cent}}$ of stars in primordial binaries. We find a substantial population of black hole binary (BBH) mergers, some of them involving an intermediate-mass BH (IMBH), and a handful mergers involving a stellar BH and either a neutron star (NS) or a white dwarf (WD). Primordial binary mergers, $\sim 30~{{\ \rm per\ cent}}$ of the whole population, dominate ejected mergers. Dynamical mergers, instead, dominate the population of in-cluster mergers and are systematically heavier than primordial ones. Around 20 per cent of dragon-II mergers are eccentric in the Laser Interferometer Space Antenna (LISA) band and 5 per cent in the LIGO band. We infer a mean cosmic merger rate of $\mathcal {R}\sim 30(4.4)(1.2)$ yr−1 Gpc−3 for BBHs, NS–BH, and WD–BH binary mergers, respectively, and discuss the prospects for multimessenger detection of WD–BH binaries with LISA. We model the rate of pair-instability supernovae (PISNe) in star clusters and find that surveys with a limiting magnitude mbol = 25 can detect ∼1–15 yr−1 PISNe. Comparing these estimates with future observations could help to pin down the impact of massive star evolution on the mass spectrum of compact stellar objects in star clusters.
The benchmark M dwarf eclipsing binary CM Draconis with TESS: spots, flares, and ultra-precise parameters
Authors: Martin David V , Sethi Ritika , Armitage Tayt , Gilbert Gregory J , Rodríguez Martínez Romy , Gilbert Emily A
Published: January 2024

A gold standard for the study of M dwarfs is the eclipsing binary CM Draconis. It is rare because it is bright (Jmag = 8.5) and contains twin fully convective stars on an almost perfectly edge-on orbit. Both masses and radii were previously measured to better than 1 per cent precision, amongst the best known. We use 15 sectors of data from the Transiting Exoplanet Survey Satellite (TESS) to show that CM Draconis is the gift that keeps on giving. Our paper has three main components. First, we present updated parameters, with radii and masses constrained to previously unheard-of precisions of ≈0.06 and ≈0.12 per cent, respectively. Secondly, we discover strong and variable spot modulation, suggestive of spot clustering and an activity cycle of the order of ≈4 yr. Thirdly, we discover 163 flares. We find a relationship between the spot modulation and flare rate, with flares more likely to occur when the stars appear brighter. This may be due to a positive correlation between flares and the occurrence of bright spots (plages). The flare rate is surprisingly not reduced during eclipse, but one flare may show evidence of being occulted. We suggest that the flares may be preferentially polar, which has positive implications for the habitability of planets orbiting M dwarfs.
Decoding the thermal history of the merging cluster Cygnus A
Authors: Majumder Anwesh , Wise M W , Simionescu A , de Vries M N
Published: January 2024

We report on a detailed spatial and spectral analysis of the large-scale X-ray emission from the merging cluster Cygnus A. We use 2.2 Ms Chandra and 40 ks XMM–Newton archival data sets to determine the thermodynamic properties of the intracluster gas in the merger region between the two subclusters in the system. These profiles exhibit temperature enhancements that imply significant heating along the merger axis. Possible sources for this heating include the shock from the ongoing merger, past activity of the powerful AGN in the core, or a combination of both. To distinguish between these scenarios, we compare the observed X-ray properties of Cygnus A with simple, spherical cluster models. These models are constructed using azimuthally averaged density and temperature profiles determined from the undisturbed regions of the cluster and folded through marx to produce simulated Chandra observations. The thermodynamic properties in the merger region from these simulated X-ray observations were used as a baseline for comparison with the actual observations. We identify two distinct components in the temperature structure along the merger axis, a smooth, large-scale temperature excess we attribute to the ongoing merger, and a series of peaks where the temperatures are enhanced by 0.5–2.5 keV. If these peaks are attributable to the central AGN, the location, and strength of these features imply that Cygnus A has been active for the past 300 Myr injecting a total of ∼1062 erg into the merger region. This corresponds to ∼10 per cent of the energy deposited by the merger shock.
The infalling elliptical galaxy M89: the chemical composition of the AGN disturbed hot atmosphere
Authors: Kara Sinancan , Plšek Tomáš , Protušová Klaudia , Breuer Jean-Paul , Werner Norbert , Mernier François , Ercan E Nihal
Published: January 2024

The chemical enrichment of X-ray-emitting hot atmospheres has hitherto been primarily studied in galaxy clusters. These studies revealed relative abundances of heavy elements that are remarkably similar to Solar. Here, we present measurements of the metal content of M89 (NGC 4552), an elliptical galaxy infalling into the Virgo cluster with a ∼10 kpc ram-pressure stripped X-ray tail. We take advantage of deep Chandra and XMM–Newton observations, and with particular attention to carefully modelling the spectra, we measure the O/Fe, Ne/Fe, Mg/Fe, Si/Fe, and S/Fe ratios. Contrary to previous measurements in galaxy clusters, our results for the hot atmosphere of M89 suggest super-Solar abundance ratios with respect to iron (i.e. α/Fe > 1), similar to its stellar components. Our analysis of the active galactic nucleus (AGN) activity in this system indicates that the AGN-induced outflow could have facilitated the stripping of the original galactic atmosphere, which has been replaced with fresh stellar mass-loss material with super-Solar α/Fe abundance ratios. Additionally, we report a new fitting bias in the RGS data of low-temperature plasma. The measured O/Fe ratios are >1σ lower in multitemperature models than a single temperature fit, leading to discrepancies in the calculations of supernova fractions derived from the metal abundances.
Pushchino multibeams pulsar search – IV. Detection of new pulsars at declinations −9° < δ < +55°
Authors: Tyul’bashev S A , Tyul’basheva G E , Kitaeva M A , Ovchinnikov I L , Oreshko V V , Logvinenko S V
Published: January 2024

The search for pulsars in monitoring data obtained at the radio telescope Large Phased Array (LPA) at a frequency of 111 MHz was carried out. Daily round-the-clock observations were carried out for about 3000 d. The duration of the observation session for each direction in the sky was 3.5 min d−1. The search for pulsars was carried out using power spectra. To search for weak pulsars, power spectra were summed up. The expected increase in sensitivity was 35–40 times compared to observations in one session. In a blind search, 330 pulsars with regular radiation were detected, with periods (P) from 0.0333 to 3.7455 s and dispersion measures (DMs) up to 249 pc cm−3. 39 pulsars turned out to be new. Average profiles were obtained for six pulsars. The DMs for seven pulsars previously detected on the LPA have been clarified.
The kinematic and dynamic properties of HBC 494’s wide-angle outflows
Authors: Fourkas Austen , Ruíz-Rodríguez Dary , Mundy Lee G , Williams Jonathan P
Published: January 2024

We present Atacama Large Millimeter/sub-millimeter Array (ALMA) Cycle-5 observations of HBC 494, as well as calculations of the kinematic and dynamic variables which represent the object’s wide-angle bipolar outflows. HBC 494 is a binary FU Orionis type object located in the Orion A molecular cloud. We take advantage of combining the ALMA main array, Atacama Compact Array (ACA), and Total Power (TP) array in order to map HBC 494’s outflows and thus, estimate their kinematic parameters with higher accuracy in comparison to prior publications. We use 12CO, 13CO, C18O, and SO observations to describe the object’s outflows, envelope, and disc, as well as estimate the mass, momentum, and kinetic energy of the outflows. After correcting for optical opacity near systemic velocities, we estimate a mass of 3.0 × 10−2 M⊙ for the southern outflow and 2.8 × 10−2 M⊙ for northern outflow. We report the first detection of a secondary outflow cavity located approximately 15 arcsec north of the central binary system, which could be a remnant of a previous large-scale accretion outburst. Furthermore, we find CO spatial features in HBC 494’s outflows corresponding to position angles of ∼35° and ∼145°. This suggests that HBC 494’s outflows are most likely a composite of overlapping outflows from two different sources, i.e. HBC 494a and HBC 494b, the two objects in the binary system.
A dark siren measurement of the Hubble constant using gravitational wave events from the first three LIGO/Virgo observing runs and DELVE
Authors: Alfradique V , Bom C R , Palmese A , Teixeira G , Santana-Silva L , Drlica-Wagner A , Riley A H , Martínez-Vázquez C E , Sand D J , Stringfellow G S , Medina G E , Carballo-Bello J A , Choi Y , Esteves J , Limberg G , Mutlu-Pakdil B , Noël N E D , Pace A B , Sakowska J D , Wu J F
Published: January 2024

The current and next observation seasons will detect hundreds of gravitational waves (GWs) from compact binary systems coalescence at cosmological distances. When combined with independent electromagnetic measurements, the source redshift will be known, and we will be able to obtain precise measurements of the Hubble constant H0 via the distance–redshift relation. However, most observed mergers are not expected to have electromagnetic counterparts, which prevents a direct redshift measurement. In this scenario, one possibility is to use the dark sirens method that statistically marginalizes over all the potential host galaxies within the GW location volume to provide a probabilistic source redshift. Here we presented H0 measurements using two new dark sirens compared to previous analyses using DECam data: GW190924$\_$021846 and GW200202$\_$154313. The photometric redshifts of the possible host galaxies of these two events are acquired from the DECam Local Volume Exploration Survey (DELVE) carried out on the Blanco telescope at Cerro Tololo. The combination of the H0 posterior from GW190924$\_$021846 and GW200202$\_$154313 together with the bright siren GW170817 leads to $H_{0} = 68.84^{+15.51}_{-7.74}\, \rm {km\, s^{-1}\, Mpc^{-1}}$. Including these two dark sirens improves the 68  per cent confidence interval (CI) by 7  per cent over GW170817 alone. This demonstrates that the addition of well-localized dark sirens in such analysis improves the precision of cosmological measurements. Using a sample containing 10 well-localized dark sirens observed during the third LIGO/Virgo observation run, without the inclusion of GW170817, we determine a measurement of $H_{0} = 76.00^{+17.64}_{-13.45}\, \rm {km\, s^{-1}\, Mpc^{-1}}$.
A full reconstruction of two galaxy clusters intra-cluster medium with strong gravitational lensing
Authors: Allingham Joseph F V , Bœhm Céline , Eckert Dominique , Jauzac Mathilde , Lagattuta David , Mahler Guillaume , Hilton Matt , Lewis Geraint F , Ettori Stefano
Published: January 2024

Whilst X-rays and Sunyaev–Zel’dovich observations allow to study the properties of the intra-cluster medium (ICM) of galaxy clusters, their gravitational potential may be constrained using strong gravitational lensing. Although being physically related, these two components are often described with different physical models. Here, we present a unified technique to derive the ICM properties from strong lensing for clusters in hydrostatic equilibrium. In order to derive this model, we present a new universal and self-similar polytropic temperature profile, which we fit using the X-COP sample of clusters. We subsequently derive an analytical model for the electron density, which we apply to strong lensing clusters MACS J0242.5-2132 and MACS J0949.8+1708. We confront the inferred ICM reconstructions to XMM-Newton and ACT observations. We contrast our analytical electron density reconstructions with the best canonical β-model. The ICM reconstructions obtained prove to be compatible with observations. However they appear to be very sensitive to various dark matter halo parameters constrained through strong lensing (such as the core radius), and to the halo scale radius (fixed in the lensing optimizations). With respect to the important baryonic effects, we make the sensitivity on the scale radius of the reconstruction an asset, and use the inferred potential to constrain the dark matter density profile using ICM observations. The technique here developed should allow to take a new, and more holistic path to constrain the content of galaxy clusters.
Outflow-related radio emission in radio-quiet quasars
Authors: Liao Mai , Wang Junxian , Ren Wenke , Zhou Minhua
Published: January 2024

In this work, we revisit the relationship between [O iii] line width w90 (as the indicator of active galactic nucleus outflow velocity) and the radio emission in radio-quiet quasars (RQQs) by employing a large sample of Type I quasars (∼37 000) selected from the Sloan Digital Sky Survey (SDSS) Data Release 16. By median stacking the radio images (to include the dominant fraction of individually radio non-detected RQQs) of Karl G. Jansky Very Large Array Sky Survey for subsamples of RQQs with different w90, our study demonstrates that the correlation between w90 and radio emission in our SDSS RQQs is significant, and remains solid after controlling the effects of black hole mass, quasar luminosity, Eddington ratio, and redshift. This intrinsic link supports that the [O iii] outflows in quasars, most likely resulting from wide-angled sub-relativistic quasar winds launched from the accretion disc, could make a dominant contribution to radio emission in the general RQQs. Alternatively, the correlation may be attributed to low-power jets in RQQs if they are ubiquitous and could efficiently enhance the [O iii] width through interacting with the interstellar medium. Meanwhile, the star formation rates traced by the flux ratio of [Ne v]/[O ii] emission lines display no dependence on w90 after controlling the effects of black hole mass, quasar luminosity, Eddington ratio, and redshift. This suggests that the stronger radio emission in RQQs with larger w90 could not be attributed to outflow-enhanced (positive feedback) star formation in the hosts. However, this also indicates that the outflows, though exhibiting robust correlation with radio power, produce neither positive nor negative feedback to the star formation in their hosts.
Discovery of novel microRNA mimic repressors of ribosome biogenesis
Authors: Bryant Carson J , McCool Mason A , Rosado González Gabriela T , Abriola Laura , Surovtseva Yulia V , Baserga Susan J
Published: January 2024

While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A (p21) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We provide evidence that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3′ UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.
Improved detection and consistency of RNA-interacting proteomes using DIA SILAC
Authors: Tan Thomas C J , Spanos Christos , Tollervey David
Published: January 2024

The RNA-interacting proteome is commonly characterized by UV-crosslinking followed by RNA purification, with protein recovery quantified using SILAC labeling followed by data-dependent acquisition (DDA) of proteomic data. However, the low efficiency of UV-crosslinking, combined with limited sensitivity of the DDA approach often restricts detection to relatively abundant proteins, necessitating multiple mass spec injections of fractionated peptides for each biological sample. Here we report an application of data-independent acquisition (DIA) with SILAC in a total RNA-associated protein purification (TRAPP) UV-crosslinking experiment. This gave 15% greater protein detection and lower inter-replicate variation relative to the same biological materials analyzed using DDA, while allowing single-shot analysis of the sample. As proof of concept, we determined the effects of arsenite treatment on the RNA-bound proteome of HEK293T cells. The DIA dataset yielded similar GO term enrichment for RNA-binding proteins involved in cellular stress responses to the DDA dataset while detecting extra proteins unseen by DDA. Overall, the DIA SILAC approach improved detection of proteins over conventional DDA SILAC for generating RNA-interactome datasets, at a lower cost due to reduced machine time. Analyses are described for TRAPP data, but the approach is suitable for proteomic analyses following essentially any RNA-binding protein enrichment technique.
Tobacco Use and Uptake of COVID-19 Vaccinations in Finland: A Population-Based Study
Authors: Peña Sebastián , Zhou Zhi , Kestilä Laura , Galanti Maria Rosaria , Shaaban Ahmed Nabil , Caspersen Ida Henriette , Magnus Per , Geraldo Pablo , Rojas-Saunero Paloma , Parikka Suvi , Nohynek Hanna , Karvonen Sakari
Published: January 2024

Introduction

People who smoke are at higher risk of Coronavirus Disease-2019 (COVID-19) hospitalizations and deaths and might benefit greatly from high COVID-19 vaccination coverage. Studies on tobacco use and COVID-19 vaccine uptake in the general population are lacking.

Aims and Methods

We conducted a cohort study utilizing linked data from 42 935 participants from two national surveys in Finland (FinSote 2018 and 2020). Exposures were smoking and smokeless tobacco (snus) use. The primary outcome was the uptake of two COVID-19 vaccine doses. Secondary outcomes were the uptake of one COVID-19 vaccine dose; three COVID-19 vaccine doses; time between the first and second dose; and time between the second and third dose. We examined the association between tobacco use and COVID-19 vaccine uptake and between-dose spacing in Finland.

Results

People who smoke had a 7% lower risk of receiving two COVID-19 vaccine doses (95% confidence interval [CI] = 0.91; 0.96) and a 14% lower risk of receiving three doses (95% CI = 0.78; 0.94) compared to never smokers. People who smoked occasionally had a lower risk of receiving three vaccine doses. People who currently used snus had a 28% lower uptake of three doses (95% CI = 0.56; 0.93) compared to never users but we did not find evidence of an association for one or two doses. We did not find evidence of an association between tobacco use and spacing between COVID-19 vaccine doses.

Conclusions

People who smoke tobacco products daily, occasionally, and use snus had a lower uptake of COVID-19 vaccines. Our findings support a growing body of literature on lower vaccination uptake among people who use tobacco products.

Implications

People who smoke or use snus might be a crucial target group of public health efforts to increase COVID-19 vaccinations and plan future vaccination campaigns.

Clinical Trials Registration Number

NCT05479383
Sex Differences in Alterations of Brain Functional Network in Tobacco Use Disorder
Authors: Qiu Xianxin , Han Xu , Wang Yao , Ding Weina , Sun Yawen , Lei Hao , Zhou Yan , Lin Fuchun
Published: January 2024

Introduction

Many studies have found sex differences in alterations of brain function in cigarette-smoking adults from the perspective of functional activity or connectivity. However, no studies have systematically found different alteration patterns in brain functional topology of cigarette-smoking men and women from three perspectives: nodal and network efficiency and modular connections.

Aims and Methods

Fifty-six tobacco use disorder (TUD) participants (25 women) and 66 non-TUD participants (28 women) underwent a resting-state functional magnetic resonance imaging scan. The whole-brain functional networks were constructed, and a two-way analysis of covariance with false discovery rate correction (q < 0.05) was performed to investigate whether men and women TUD participants had different alterations in the topological features at global, modular, and nodal levels.

Results

Compared to non-TUD participants, men but not women TUD participants showed significantly lower global efficiency (lower intermodular connections between the visual and executive control and between the visual and subcortical modules did not pass the correction) and significantly lower nodal global efficiency in the right superior occipital gyrus, bilateral fusiform gyrus, the right pallidum, right putamen, the bilateral paracentral lobule, the postcentral gyrus, and lower nodal local efficiency in the left paracentral lobule.

Conclusions

Men and women TUD participants have different topological properties of brain functional network, which may contribute to our understanding of neural mechanisms underlying sex differences in TUD.

Implications

Compared to non-TUD participants, we found men but not women TUD participants with significantly lower network metrics at global, modular, and nodal levels, which could improve our understanding of neural mechanisms underlying sex differences in TUD and lay a solid foundation for future sex-based TUD prevention and treatment.
The influence of pediatric cancer treatment on taste perception and food hedonics: a systematic review
Authors: Curtis Annie R , Tan Sze Yen , Boltong Anna , Cohen Jennifer , Kiss Nicole
Published: January 2024

Context

Children with cancer are at risk of poor nutritional status during treatment and into survivorship. Objectively measured taste perception and self-reported food hedonics are 2 factors that may influence food intake.

Objective

This 2-armed systematic review examined whether chemotherapy and radiotherapy affect (1) taste perception and (2) hedonic experiences of children and survivors of childhood cancer.

Data Source

A 2-armed systematic literature search was conducted in the Medline, CINAHL, Embase, and PsychInfo database until June 2022. The effects of cancer treatment on objective taste perception or food hedonics (ie, food liking or aversion and appetite) were examined.

Data Extraction

Peer-reviewed articles published in English of studies that included children (aged <18 years) or survivors of childhood cancer (any age) were reviewed. Risk of bias was determined using the Evidence Analysis Library by the Academy of Nutrition and Dietetics.

Data Analysis

A total of 1417 articles in the taste search arm and 3862 articles in the hedonics search arm were identified. Of these, 9 and 4 articles were eligible for review, respectively. Cancer treatment had highly variable effects on taste perception during treatment and into survivorship. Learned food aversions were experienced by children receiving chemotherapy treatment and liking of meats and salty foods by children with cancer was affected. The impact of treatment on appetite varied.

Conclusions

Cancer treatment did not uniformly affect taste perception. Food liking may be negatively affected, and learned food aversions may develop during cancer treatment. To establish the clinical relevance of childhood cancer treatment on taste perception and food hedonics, more research is required.

Systematic Review Registration

PROSPERO registration no.CRD42020207127.
Re-defining evidence-based policing
Authors: Klose Stephan
Published: January 2024

This article re-defines evidence-based policing as ‘a decision-making process which integrates the best available evidence, professional judgement and community values, preferences and circumstances’. The article argues that this definition serves to position evidence-based policing more clearly as a research-informed, practitioner-centred, and community-oriented approach to policing practice. It moreover advances links between evidence-based policing and related concepts—such as evidence-based medicine—which, in turn, promises to address misunderstandings in (and streamline) debates about evidence-based practice across disciplinary lines. The article provides an in-depth discussion of each key element of its proposed three-pronged definition—best available evidence, professional judgement, and community values, preferences, and circumstances—through a review of ongoing discussions about evidence-based policing in the field of criminology and evolving discussions (and conceptualizations) of evidence-based practice across other disciplines. Finally, the article outlines how its proposed definition—and its three integral elements—can guide the future development of an evidence-based policing agenda.
Sectors versus borders: interest group cleavages and struggles over corporate governance in the age of asset management
Authors: Voss Dustin
Published: January 2024

Universally invested asset managers like BlackRock have established a dominant position in equity markets around the globe. While extant contributions have explored their voting behaviour and role in shaping corporate governance at the firm level, less is known about their potential to build interest coalitions with other business groups, and their leverage over state-level corporate governance institutions. This article investigates conflict over a far-reaching reform to co-determination in Germany. Qualitative content analysis of over 100 stakeholder statements yields that asset managers forge coalitions with short-term-oriented investors to abolish key tenets of corporatist institutions. However, a domestic countercoalition of financial and non-financial firms prevented momentous institutional change. This article improves our understanding of international asset managers’ preferences and highlights coalition building as a key determinant of the political power of international finance. By aligning the costs of institutional change for incumbents, corporatist institutions continue to act as shields against financialization.
Plant secondary metabolites involved in the stress tolerance of long-lived trees
Authors: Cui Jiawen , Li Xiang , Lu Zhaogeng , Jin Biao
Published: January 2024

Ancient trees are natural wonders because of their longevity, having lived for hundreds or thousands of years, and their ability to withstand changing environments and a variety of stresses. These long-lived trees have sophisticated defense mechanisms, such as the production of specialized plant metabolites (SPMs). In this review, we provide an overview of the major biotic and abiotic stresses that long-lived trees often face, as well as an analysis of renowned ancient tree species and their unique protective SPMs against environmental stressors. We also discuss the synthesis and accumulation of defensive SPMs induced by environmental factors and endophytes in these trees. Furthermore, we conducted a comparative genomic analysis of 17 long-lived tree species and discovered significant expansions of SPM biosynthesis gene families in these species. Our comprehensive review reveals the crucial role of SPMs in high resistance in long-lived trees, providing a novel natural resource for plant defense, crop improvement and even the pharmaceutical industry.
Uniform carbon reserve dynamics along the vertical light gradient in mature tree crowns
Authors: Zahnd Cedric , Zehnder Miro , Arend Matthias , Kahmen Ansgar , Hoch Günter
Published: January 2024

Understanding the within-tree variability of non-structural carbohydrates (NSC) is crucial for interpreting point measurements and calculating whole-tree carbon balances. Yet, little is known about how the vertical light gradient within tree crowns influences branch NSC concentrations and dynamics. We measured NSC concentrations, irradiance and key leaf traits in uppermost, sun-exposed and lowest, shaded branches in the crowns of mature, temperate trees from nine species with high temporal resolution throughout one growing season. Measurements from two additional years allowed us to test the generality of our findings amongst climatically contrasting years. Despite the vertical light gradient, we found very similar seasonal NSC dynamics and concentrations between sun and shade branches in most species. This can at least partially be explained by acclimations in specific leaf area and photosynthetic leaf traits compensating the different light availability between the top and bottom canopy. Only in the ring-porous species Quercus petraea x robur and Fraxinus  excelsior was starch refilling after budbreak slower in lower branches. End-of-season NSC concentrations were similar between canopy positions and amongst observation years. Only Fagus sylvatica had 40 and 29% lower starch concentrations by the end of the extremely dry year 2020, relative to the other 2 years. We show that NSC measured anywhere in a tree crown is often representative of the whole crown. Overall, our results suggest that carbon reserve dynamics in trees are largely insensitive to both microclimatic gradients and inter-annual climatic variation, and only deviate under severe carbon deficits, as was presumably the case with Fagus in our study.
Nuclear‐localized androgen receptor content following resistance exercise training is associated with hypertrophy in males but not females
Authors: Hatt Aidan A. , Kamal Michael , Mikhail Andrew I. , Fortino Stephen A. , Wageh Mai , Kumbhare Dinesh , Parise Gianni
Published: January 2024

Androgen receptor (AR) content has been implicated in the differential response between high and low responders following resistance exercise training (RET). However, the influence of AR expression on acute skeletal muscle damage and whether it may influence the adaptive response to RET in females is poorly understood. Thus, the purpose of this exploratory examination was to 1) investigate changes in AR content during skeletal muscle repair and 2) characterize AR‐mediated sex‐based differences following RET. A skeletal muscle biopsy from the vastus lateralis was obtained from 26 healthy young men (n = 13) and women (n = 13) at baseline and following 300 eccentric kicks. Subsequently, participants performed 10 weeks of full‐body RET and a final muscle biopsy was collected. In the untrained state, AR mRNA expression was associated with paired box protein‐7 (PAX7) mRNA in males. For the first time in human skeletal muscle, we quantified AR content in the myofiber and localized to the nucleus where AR has been shown to trigger cellular outcomes related to growth. Upon eccentric damage, nuclear‐associated AR (nAR) content increased (p < .05) in males and not females. Males with the greatest increase in cross‐sectional area (CSA) post‐RET had more (p < .05) nAR content than females with the greatest gain CSA. Collectively, skeletal muscle damage and RET increased AR protein, and both gene and hypertrophy measures revealed sex differences in relation to AR. These findings suggest that AR content but more importantly, nuclear localization, is a factor that differentiates RET‐induced hypertrophy between males and females.
Novel ferroptosis gene biomarkers and immune infiltration profiles in diabetic kidney disease via bioinformatics
Authors: Huang Yixiong , Yuan Xinke
Published: January 2024

Diabetic kidney disease (DKD) is the primary cause of end‐stage renal disease, exhibiting high disability and mortality rates. Ferroptosis is vital for the progression of DKD, but the exact mechanism remains unclear. This study aimed to explore the potential mechanism of ferroptosis‐related genes in DKD and their relationship with the immune and to identify new diagnostic biomarkers to help treat and diagnose DKD. GSE30122 and GSE47185 were obtained from the Gene Expression Omnibus database and were integrated into a merged dataset, followed by functional enrichment analysis. Then potential differentially expressed genes were screened. Ferroptosis‐related differentially‐expressed genes were identified, followed by gene ontology analysis. Protein–protein interaction networks were constructed and hub genes were screened. The immune cell‐infiltrating state in the dataset was assessed using appropriate algorithms. Immune signature subtypes were constructed using the consensus clustering analysis. Hub gene expression was validated using qRT‐PCR and immunohistochemistry. A total of Eleven screened ferroptosis‐related differentially expressed genes were screened. Six potentially diagnostically favorable ferroptosis‐related hub genes were identified. Significantly increased expression of γδT cells, resting mast cells, and macrophages infiltration was observed in the DKD group. Additionally, two distinct immune signature subgroups were identified. Ferroptosis‐related hub genes were significantly correlated with differentially infiltrated immune cells. Six hub genes were significantly upregulated in HK‐2 cells following high glucose treatment and in human kidney tissues of patients with DKD. Six ferroptosis‐related hub genes were identified as potential biomarkers of diabetic kidney disease, but further validation is needed.
Role of ecto‐5′‐nucleotidase in bladder function
Authors: Barge Sagar , Wu Ali , Zhang Lanlan , Robson Simon C. , Olumi Aria , Alper Seth L. , Zeidel Mark L. , Yu Weiqun
Published: January 2024

Purinergic signaling plays an important role in regulating bladder contractility and voiding. Abnormal purinergic signaling is associated with lower urinary tract symptoms (LUTS). Ecto‐5′‐nucleotidase (NT5E) catalyzes dephosphorylation of extracellular AMP to adenosine, which in turn promotes adenosine‐A2b receptor signaling to relax bladder smooth muscle (BSM). The functional importance of this mechanism was investigated using Nt5e knockout (Nt5eKO) mice. Increased voiding frequency of small voids revealed by voiding spot assay was corroborated by urodynamic studies showing shortened voiding intervals and decreased bladder compliance. Myography indicated reduced contractility of Nt5eKO BSM. These data support a role for NT5E in regulating bladder function through modulation of BSM contraction and relaxation. However, the abnormal bladder phenotype of Nt5eKO mice is much milder than we previously reported in A2b receptor knockout (A2bKO) mice, suggesting compensatory response(s) in Nt5eKO mouse bladder. To better understand this compensatory mechanism, we analyzed changes in purinergic and other receptors controlling BSM contraction and relaxation in the Nt5eKO bladder. We found that the relative abundance of muscarinic CHRM3 (cholinergic receptor muscarinic 3), purinergic P2X1, and A2b receptors was unchanged, whereas P2Y12 receptor was significantly downregulated, suggesting a negative feedback response to elevated ADP signaling. Further studies of additional ecto‐nucleotidases indicated significant upregulation of the nonspecific urothelial alkaline phosphatase ALPL, which might mitigate the degree of voiding dysfunction by compensating for Nt5e deletion. These data suggest a mechanistic complexity of the purinergic signaling network in bladder and imply a paracrine mechanism in which urothelium‐released ATP and its rapidly produced metabolites coordinately regulate BSM contraction and relaxation.
Associations of per- and polyfluoroalkyl substances and nonalcoholic fatty liver disease in the United States adult population, 2003–2018
Authors: Momo Harry D. , Alvarez Christian S. , Purdue Mark P. , Graubard Barry I. , McGlynn Katherine A.
Published: January 2024

Background:

Nonalcoholic fatty liver disease (NAFLD) is the most common liver disorder worldwide and a leading cause of liver-related mortality. Prior studies have linked per- and polyfluoroalkyl substances (PFAS) exposure to liver dysfunction and alterations in metabolic pathways, but the extent of a PFAS-NAFLD relationship is unclear. Thus, the aim of the current study was to examine whether there were associations between PFAS exposures and NAFLD in the US adult population over a 16-year period.

Methods:

Data from 10,234 persons who participated in the National Health and Nutrition Examination Survey between 2003 and 2018 were analyzed. Odds ratios and 95% confidence intervals were calculated using multivariable logistic regression for the associations between PFAS and NAFLD, defined by the Hepatic Steatosis Index (NAFLD-HSI), the Fatty Liver Index (NAFLD-FLI), and by Transient Elastography with Controlled Attenuation Parameter (NAFLD-TE-CAP).

Results:

Overall, there was a significant inverse association between total PFAS and NAFLD-HSI (P-trend = 0.04). Significant inverse associations were also found between perfluorohexane sulfonic acid (PFHxS) and NAFLD-HSI (P-trend = 0.04), and NAFLD-FLI (P-trend = 0.03). Analysis by time period, 2003–2010 versus 2011–2018, found that while inverse associations were more apparent during the latter period when total PFAS (P-trend = 0.02), PFHxS (P-trend = 0.04), and perfluorooctanoic acid (PFOA) (P-trend = 0.03) were inversely associated with NAFLD-HSI and PFOA was inversely associated with NAFLD-FLI (P-trend = 0.05), there were no significant interaction effects. No significant associations between the PFAS and NAFLD-TE-CAP were found.

Conclusions:

The current study found no evidence of a positive association between the most common PFAS and NAFLD in the US population.