bluuebunny/crossref_metadata_2025_split huggingface dataset:
The climate and compositional variation of the highly eccentric planet HD 80606 b – the rise and fall of carbon monoxide and elemental sulfur
Authors: Tsai Shang-Min , Steinrueck Maria , Parmentier Vivien , Lewis Nikole , Pierrehumbert Raymond 
Published: February 2023

ABSTRACTThe gas giant HD 80606 b has a highly eccentric orbit (e ∼ 0.93). The variation due to the rapid shift of stellar irradiation provides a unique opportunity to probe the physical and chemical timescales and to study the interplay between climate dynamics and atmospheric chemistry. In this work, we present integrated models to study the atmospheric responses and the underlying physical and chemical mechanisms of HD 80606 b. We first run 3D general circulation models (GCMs) to establish the atmospheric thermal and dynamical structures for different atmospheric metallicities and internal heat. Based on the GCM output, we then adopted a 1D time-dependent photochemical model to investigate the compositional variation along the eccentric orbit. The transition of the circulation patterns of HD 80606 b matched the dynamics regimes in previous works. Our photochemical models show that efficient vertical mixing leads to deep quench levels of the major carbon and nitrogen species and the quenching behaviour does not change throughout the eccentric orbit. Instead, photolysis is the main driver of the time-dependent chemistry. While CH4 dominates over CO through most of the orbits, a transient state of [CO]/[CH4] &gt; 1 after periastron is confirmed for all metallicity and internal heat cases. The upcoming JWST Cycle 1 GO program will be able to track this real-time CH4–CO conversion and infer the chemical timescale. Furthermore, sulfur species initiated by sudden heating and photochemical forcing exhibit both short-term and long-term cycles, opening an interesting avenue for detecting sulfur on exoplanets.
Orbital and radiative properties of wandering intermediate-mass black holes in the ASTRID simulation
Authors: Weller Emma Jane , Pacucci Fabio , Ni Yueying , Chen Nianyi , Di Matteo Tiziana , Siwek Magdalena , Hernquist Lars 
Published: February 2023

ABSTRACT
Intermediate-Mass Black Holes (IMBHs) of $10^3-10^6\, {\rm M_\odot }$ are commonly found at the centre of dwarf galaxies. Simulations and observations convincingly show that a sizeable population of IMBHs could wander off-centre in galaxies. We use the cosmological simulation ASTRID to study the orbital and radiative properties of wandering IMBHs in massive galaxies at z ∼ 3. We find that this population of black holes has large orbital inclinations (60° ± 22°) with respect to the principal plane of the host. The eccentricity of their orbits is also significant (0.6 ± 0.2) and decreases with time. Wandering IMBHs undergo spikes of accretion activity around the pericentre of their orbits, with rates 10−3 − 10−5 times the Eddington rate and a median accretion duty cycle of $\sim 12{{\ \rm per\ cent}}$. Their typical spectral energy distribution peaks in the infrared at $\sim 11 \, \mu \rm m$ rest-frame. Assuming a standard value of $10{{\ \rm per\ cent}}$ for the matter-to-energy radiative efficiency, IMBHs reach 2 − 10 keV X-ray luminosities $\gt 10^{37} \, \mathrm{erg\, s^{-1}}$ for $\sim 10{{\ \rm per\ cent}}$ of the time. This luminosity corresponds to fluxes $\gt 10^{-15} \, \mathrm{erg \, s^{-1} \, cm^{-2}}$ within 10 Mpc. They could be challenging to detect because of competing emissions from X-ray binaries and the interstellar medium. X-ray luminosities $\gt 10^{41} \, \mathrm{erg \, s^{-1}}$, in the hyper-luminous X-ray sources (HLXs) regime, are reached by $\sim 7{{\ \rm per\ cent}}$ of the IMBHs. These findings suggest that HLXs are a small subset of the wandering IMBH population, which is characterized by luminosities 103 − 104 times fainter. Dedicated surveys are needed to assess the demographics of this missing population of black holes.
MusE GAs FLOw and Wind (MEGAFLOW) IX. The impact of gas flows on the relations between the mass, star formation rate, and metallicity of galaxies
Authors: Langan Ivanna , Zabl Johannes , Bouché Nicolas F , Ginolfi Michele , Popping Gergö , Schroetter Ilane , Wendt Martin , Schaye Joop , Boogaard Leindert , Freundlich Jonathan , Richard Johan , Matthee Jorryt , Mercier Wilfried , Contini Thierry , Guo Yucheng , Cherrey Maxime 
Published: February 2023

ABSTRACTWe study the link between gas flow events and key galaxy scaling relations: the relations between star formation rate (SFR) and stellar mass (the main sequence, MS); gas metallicity and stellar mass (the mass–metallicity relation, MZR); and gas metallicity, stellar mass, and SFR (the fundamental metallicity relation, FMR). Using all star-forming galaxies (SFGs) in the 22 MUSE fields of the MusE GAs FLOw and Wind (MEGAFLOW) survey, we derive the MS, MZR, and FMR scaling relations for 385 SFGs with $M_\star = 10^{8} - 10^{11.5}\, {\rm M}_\odot$ at redshifts 0.35 &lt; z &lt; 0.85. Using the MUSE data and complementary X-Shooter spectra at 0.85 &lt; z &lt; 1.4, we determine the locations of 21 SFGs associated with inflowing or outflowing circumgalactic gas (i.e. with strong Mg ii absorption in background quasar spectra) relative to these scaling relations. Compared to a control sample of galaxies without gas flows (i.e. without Mg ii absorption within 70 kpc of the quasar), SFGs with inflow events (i.e. Mg ii absorption along the major axis) are preferentially located above the MS, while SFGs with outflow events (i.e. Mg ii absorption along the minor axis) are preferentially more metal rich. Our observations support the scenario in which gas accretion increases the SFR while diluting the metal content and where circumgalactic outflows are found in more metal-rich galaxies.
Electron heating mechanisms at quasi-perpendicular shocks – revisited with magnetospheric multiscale measurements
Authors: Stasiewicz Krzysztof , Eliasson Bengt 
Published: February 2023

ABSTRACTWe demonstrate that measurements obtained from NASA’s magnetospheric multiscale (MMS) mission support quasi-adiabatic electron heating in quasi-perpendicular shocks with temperature Te⊥ ∝ B1 + α, where B is the magnetic field strength and α represents departure from adiabaticity. Adiabatic heating (α = 0) results from the conservation of magnetic moment on spatially increasing magnetic field inside the shock ramp. Negative α &lt; 0 is observed in most situations, where perpendicular energy gain from adiabatic heating is redistributed by interactions with waves to the parallel direction leading to a lower isotropic temperature increase. Positive α is observed when the stochastic heating of electrons is activated by the E × B wave acceleration mechanism by electrostatic waves leading to a higher temperature increase. By using test-particle simulations in a realistic shock model we have elucidated the process of stochastic wave acceleration. We have also shown the equivalence of adiabatic heating and acceleration by gradient B drift at shocks with low Mach numbers and demonstrated that the cross-shock potential does not contribute to the electron heating. Signatures of quasi-adiabatic heating and/or stochastic heating of electrons are observed in all shocks analysed with measurements by the MMS.
Does a radio jet drive the massive multiphase outflow in the ultra-luminous infrared galaxy IRAS 10565 + 2448?
Authors: Su Renzhi , Mahony Elizabeth K , Gu Minfeng , Sadler Elaine M , Curran S J , Allison James R , Yoon Hyein , Aditya J N H S , Chandola Yogesh , Chen Yongjun , Moss Vanessa A , Wu Zhongzu , Shao Xi , Liu Xiang , Glowacki Marcin , Whiting Matthew T , Weng Simon 
Published: February 2023

ABSTRACT
We present new upgraded Giant Metrewave Radio Telescope H i 21-cm observations of the ultra-luminous infrared galaxy IRAS 10565 + 2448, previously reported to show blueshifted, broad, and shallow H i absorption indicating an outflow. Our higher spatial resolution observations have localized this blueshifted outflow, which is ∼ 1.36 kpc southwest of the radio centre and has a blueshifted velocity of $\sim 148\, \rm km\, s^{-1}$ and a full width at half maximum of $\sim 581\, \rm km\, s^{-1}$. The spatial extent and kinematic properties of the H i outflow are consistent with the previously detected cold molecular outflows in IRAS 10565 + 2448, suggesting that they likely have the same driving mechanism and are tracing the same outflow. By combining the multiphase gas observations, we estimate a total outflowing mass rate of at least $140\, \rm M_\odot \, yr^{-1}$ and a total energy loss rate of at least $8.9\times 10^{42}\, \rm erg\, s^{-1}$, where the contribution from the ionized outflow is negligible, emphasizing the importance of including both cold neutral and molecular gas when quantifying the impact of outflows. We present evidence of the presence of a radio jet and argue that this may play a role in driving the observed outflows. The modest radio luminosity $L_{\rm 1.4GHz}\, \sim 1.3\times 10^{23}\, {\rm W\, Hz^{-1}}$ of the jet in IRAS 10565 + 2448 implies that the jet contribution to driving outflows should not be ignored in low radio luminosity active galactic nuclei.
Probing gas kinematics towards the high-mass protostellar object G358.46−0.39
Authors: Ugwu C J , Chibueze J O , Morgan J , Csengeri T , Chukwude A E , van der Walt D J , Alhassan J A 
Published: February 2023

ABSTRACTWe investigated the nature of protostellar objects in G358.46−0.39 and their gas kinematics using ALMA data, with the aim of understanding the ongoing star formation activities in the region. The dust continuum map reveals multiple cores (MM1a, MM1b, MM1c, and MM2) dominated by MM1a, with no detectable free–free emission. We calculated the masses and the column densities of the various objects (MM1a, MM1b, MM1c, and MM2). A total of 33, 10, 10, and 9 molecular transitions are detected towards MM1a, MM1b, MM1c, and MM2, respectively. The differences in the number of molecular lines detected towards each of the cores support different excitation conditions at different positions. We derived the kinetic temperature ranges of MM1a, MM1b, MM1c, and MM2 to be ∼96–118, 96–114, 72–74, and 80–84 K, respectively. A highly collimated bipolar outflow traced by 12CO emission is observed to be associated with MM1a, with knots along the outflow lobes, which could be an indication of episodic ejection. The C17O emission is observed to be likely tracing a slowly rotating envelope of gas around MM1a. The velocity field map of CH3OH (22, 1 − 31, 2) emission suggests the presence of a rotating structure, possibly a disc. The physical and kinematic properties of MM1a are strong indication of a massive young stellar object, with ongoing outflow activity and accretion in its early stage of formation.
the three hundredproject: a machine learning method to infer clusters of galaxy mass radial profiles from mock Sunyaev–Zel’dovich maps
Authors: Ferragamo A , de Andres D , Sbriglio A , Cui W , De Petris M , Yepes G , Dupuis R , Jarraya M , Lahouli I , De Luca F , Gianfagna G , Rasia E 
Published: February 2023

ABSTRACTWe develop a machine learning algorithm to infer the three-dimensional cumulative radial profiles of total and gas masses in galaxy clusters from thermal Sunyaev–Zel’dovich effect maps. We generate around 73 000 mock images along various lines of sight using 2522 simulated clusters from the three hundred project at redshift z &lt; 0.12 and train a model that combines an auto-encoder and a random forest. Without making any prior assumptions about the hydrostatic equilibrium of the clusters, the model is capable of reconstructing the total mass profile as well as the gas mass profile, which is responsible for the Sunyaev–Zel’dovich effect. We show that the recovered profiles are unbiased with a scatter of about 10 per cent, slightly increasing towards the core and the outskirts of the cluster. We selected clusters in the mass range of $10^{13.5} \le M_{200} /({{\, h^{-1}\,{\rm {{\rm M}_{\odot }}}}}) \le 10^{15.5}$, spanning different dynamical states, from relaxed to disturbed haloes. We verify that both the accuracy and precision of this method show a slight dependence on the dynamical state, but not on the cluster mass. To further verify the consistency of our model, we fit the inferred total mass profiles with a Navarro–Frenk–White model and contrast the concentration values with those of the true profiles. We note that the inferred profiles are unbiased for higher concentration values, reproducing a trustworthy mass–concentration relation. The comparison with a widely used mass estimation technique, such as hydrostatic equilibrium, demonstrates that our method recovers the total mass that is not biased by non-thermal motions of the gas.
Implications of post-kick jets in core-collapse supernovae
Authors: Soker Noam 
Published: February 2023

ABSTRACTI examine the assumption that the jets that shape the axisymmetrical morphological features of core-collapse supernova (CCSN) remnants are post-kick jets, i.e. the neutron star (NS) launches these jets after the explosion and after it acquired its natal kick velocity. I find that this assumption implies that the pre-collapse cores of CCSN progenitors have sufficient angular momentum fluctuations to support jittering jets that explode the star. From the finding that the shaping-jets neither tend to be aligned with the kick velocity nor to be perpendicular to it I argue that the assumption that the shaping-jets are post-kick jets has the following implications. (1) The NS accretes mass at a radius of $r_{\rm acc} \approx 5000 {~\rm km}$ from the centre of the explosion at $\approx 10 {~\rm s}$ after explosion. (2) The required angular momentum fluctuations of the accreted gas to explain the medium values of jets-kick angles are also sufficient to support an intermittent pre-kick accretion disc, just before and during the explosion. Such an intermittent accretion disc is likely to launch jets that explode the star in the frame of the jittering jets explosion mechanism. This suggests that most likely the shaping-jets are the last jets in the jittering jets explosion mechanism rather than post-kick jets. (3) The jittering jets explosion mechanism expects that black holes have small natal kick velocities.
Clinical disease activity is a major determinant of plasma D-dimer elevation in outpatients with rheumatoid arthritis: A hospital-based cross-sectional study
Authors: Mori Shunsuke , Soejima Hirofumi , Hokamaki Jun , Tsujita Kenichi 
Published: February 2023

ABSTRACT

Objectives
To identify factors associated with plasma D-dimer levels in outpatients with rheumatoid arthritis (RA).

Methods
We consecutively recruited 460 RA patients who visited our hospital for routine follow-ups between June and October 2021. Plasma D-dimer, RA-related characteristics, comorbidities, and cardiovascular and venous thromboembolism (VTE) risk factors were examined at enrolment. Patients with elevated D-dimer levels underwent whole-leg venous ultrasonography to diagnose deep vein thrombosis (DVT).

Results
Participants had no DVT signs or symptoms. Among them, 252 (54.8%) were positive for plasma D-dimer (≥0.5 μg/ml) and 40 (8.7%) had high D-dimer levels (≥3 μg/ml). The mean was 1.07 μg/ml. After adjustments, age [odds ratio (OR) 1.88 per additional 10 years, P = .003], high and moderate clinical disease activity index (OR 8.79, P &lt; .001), and the presence of comorbidities or cardiovascular/VTE risk factors (OR 2.94, P = .017) were identified as the factors independently associated with high D-dimer levels. Among patients with D-dimer levels ≥3 μg/ml, 10 (25%) had DVT in their lower limbs, and D-dimer levels were significantly higher in patients with DVT compared with those without it (mean 6.0  vs. 4.1 μg/ml, P &lt; .001).

Conclusions
Clinical disease activity is a major contributor to plasma D-dimer elevation in RA outpatients.
Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures
Authors: Akcan Toray S , Vilov Sergey , Heinig Matthias 
Published: February 2023

AbstractPromoter-proximal Polymerase II (Pol II) pausing is a key rate-limiting step for gene expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have been identified. However, we lack a quantitative model of how interactions of these factors determine pausing, therefore the relative importance of implicated factors is unknown. Moreover, previously unknown regulators might exist. Here we address this gap with a machine learning model that accurately predicts the extent of promoter-proximal Pol II pausing from large-scale genome and transcriptome binding maps and gene annotation and sequence composition features. We demonstrate high accuracy and generalizability of the model by validation on an independent cell line which reveals the model's cell line agnostic character. Model interpretation in light of prior knowledge about molecular functions of regulatory factors confirms the interconnection of pausing with other RNA processing steps. Harnessing underlying feature contributions, we assess the relative importance of each factor, quantify their predictive effects and systematically identify previously unknown regulators of pausing. We additionally identify 16 previously unknown 7SK ncRNA interacting RNA-binding proteins predictive of pausing. Our work provides a framework to further our understanding of the regulation of the critical early steps in transcriptional elongation.
A clade of RHH proteins ubiquitous in Sulfolobales and their viruses regulates cell cycle progression
Authors: Li Xuyang , Lozano-Madueño Cristina , Martínez-Alvarez Laura , Peng Xu 
Published: February 2023

AbstractCell cycle regulation is crucial for all living organisms and is often targeted by viruses to facilitate their own propagation, yet cell cycle progression control is largely underexplored in archaea. In this work, we reveal a cell cycle regulator (aCcr1) carrying a ribbon-helix-helix (RHH) domain and ubiquitous in the Thermoproteota of the order Sulfolobales and their viruses. Overexpression of several aCcr1 members including gp21 of rudivirus SIRV2 and its host homolog SiL_0190 of Saccharolobus islandicus LAL14/1 results in impairment of cell division, evidenced by growth retardation, cell enlargement and an increase in cellular DNA content. Additionally, both gp21 and SiL_0190 can bind to the motif AGTATTA conserved in the promoter of several genes involved in cell division, DNA replication and cellular metabolism thereby repressing or inducing their transcription. Our results suggest that aCcr1 silences cell division and drives progression to the S-phase in Sulfolobales, a function exploited by viruses to facilitate viral propagation.
SMAD3 promotes expression and activity of the androgen receptor in prostate cancer
Authors: Jeon Hee-Young , Pornour Majid , Ryu Hyunju , Khadka Sudeep , Xu Rui , Jang Jihyun , Li Deqiang , Chen Hegang , Hussain Arif , Fazli Ladan , Gleave Martin , Dong Xuesen , Huang Furong , Wang Qianben , Barbieri Christopher , Qi Jianfei 
Published: February 2023

AbstractOverexpression of androgen receptor (AR) is the primary cause of castration-resistant prostate cancer, although mechanisms upregulating AR transcription in this context are not well understood. Our RNA-seq studies revealed that SMAD3 knockdown decreased levels of AR and AR target genes, whereas SMAD4 or SMAD2 knockdown had little or no effect. ChIP-seq analysis showed that SMAD3 knockdown decreased global binding of AR to chromatin. Mechanistically, we show that SMAD3 binds to intron 3 of the AR gene to promote AR expression. Targeting these binding sites by CRISPRi reduced transcript levels of AR and AR targets. In addition, ∼50% of AR and SMAD3 ChIP-seq peaks overlapped, and SMAD3 may also cooperate with or co-activate AR for AR target expression. Functionally, AR re-expression in SMAD3-knockdown cells partially rescued AR target expression and cell growth defects. The SMAD3 peak in AR intron 3 overlapped with H3K27ac ChIP-seq and ATAC-seq peaks in datasets of prostate cancer. AR and SMAD3 mRNAs were upregulated in datasets of metastatic prostate cancer and CRPC compared with primary prostate cancer. A SMAD3 PROTAC inhibitor reduced levels of AR, AR-V7 and AR targets in prostate cancer cells. This study suggests that SMAD3 could be targeted to inhibit AR in prostate cancer.
Early-onset grade 2-3 diffuse gliomas and schwannomas increase the risk of central nervous system tumors among the patients’ relatives
Authors: Alanen Eljas , Heikkinen Sanna , Nurminen Riikka , Nykter Matti , Haapasalo Hannu , Hirvonen Elli , Pitkäniemi Janne , Rautajoki Kirsi J 
Published: February 2023

AbstractBackgroundCentral nervous system (CNS) tumors are a heterogeneous group of tumors that include several aggressive malignancies with a high mortality rate. This study aimed to evaluate the familial relative risk of CNS tumors in family members of early-onset index cases (probands) in and between diffuse glioma, non-diffuse glioma, meningioma, and other CNS tumors.MethodsWe retrieved tumor data from the Finnish cancer registry and familial relationships data from the population information system. We ascertained 5408 probands diagnosed with primary CNS tumors (age ≤40 years) between 1970 and 2012 in Finland. We report the standardized incidence ratios as a measure of familial aggregation using Poisson regression.ResultsThe risk of early-onset diffuse glioma increased among siblings of probands with the same tumor [SIR 3.85, 95% confidence interval (CI): 1.66–7.59], with association mainly returning to grade 2–3 diffuse gliomas. Early-onset other CNS tumors were associated with an increased risk of other CNS tumors, early-onset meningioma, and late-onset diffuse glioma in 1st-degree relatives. The elevated risk of other CNS tumors was largely caused by schwannomas (SIR 59.44, 95% CI: 27.18–112.84 for 1st-degree relatives) and associated with neurofibromatosis. No tumor syndrome was associated with an increased risk of diffuse gliomas.ConclusionsThe early onset of grade 2–3 diffuse gliomas is associated with an increased risk of similar tumor entities. Early-onset schwannomas dramatically increase CNS tumor risk with a broader tumor-type profile. In future studies, it would be important to identify the underlying shared hereditary factors that contribute to the development of familial diffuse gliomas.
Symbiont diversity in the eukaryotic microbiomes of marine crustacean zooplankton
Authors: Savage Rose-Lynne , Maud Jacqueline L , Kellogg Colleen T E , Hunt Brian P V , Tai Vera 
Published: February 2023

AbstractProtists (eukaryotic microorganisms) commonly form symbiotic associations with crustacean zooplankton, but their diversity, prevalence and ecological roles are underestimated due to the limited scope of previous investigations. Using metabarcoding of the V4 region of the 18S rRNA gene, we characterized the eukaryotic microbiomes of the dominant crustacean zooplankton, specifically copepods, euphausiids, amphipods and ostracods, from the Strait of Georgia, Canada. Sequence reads from the alveolates dominated all zooplankton examined, which mostly comprised ciliates and dinoflagellates of known symbiont lineages. These lineages included not only those of parasitoids but also those of uncharacterized species. Apostome ciliate reads were the most abundant in all hosts except for cyclopoid copepods, which were dominated by the parasitic Syndiniales. Most symbiont lineages showed some degree of host preference, particularly Pseudocolliniidae ciliate parasites with ostracods, but were often detected in all hosts indicating broad host specificity. Reads from free-living protists, including diatoms and surprisingly hydrozoans, were inferred to be part of their diet. Hydrozoans may have been ingested from free organic matter, such as detritus or marine snow, suggesting a likely underestimated pathway of carbon cycling. This investigation contributes to resolving the interactions between zooplankton and protists and the potential ecological significance of symbioses on zooplankton productivity.