bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding quadruply imaged quasars with machine learning – I. Methods
Authors: Akhazhanov A , More A , Amini A , Hazlett C , Treu T , Birrer S , Shajib A , Liao K , Lemon C , Agnello A , Nord B , Aguena M , Allam S , Andrade-Oliveira F , Annis J , Brooks D , Buckley-Geer E , Burke D L , Carnero Rosell A , Carrasco Kind M , Carretero J , Choi A , Conselice C , Costanzi M , da Costa L N , Pereira M E S , De Vicente J , Desai S , Dietrich J P , Doel P , Everett S , Ferrero I , Finley D A , Flaugher B , Frieman J , García-Bellido J , Gerdes D W , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Kim A G , Kuehn K , Kuropatkin N , Lahav O , Lima M , Lin H , Maia M A G , March M , Menanteau F , Miquel R , Morgan R , Palmese A , Paz-Chinchón F , Pieres A , Plazas Malagón A A , Sanchez E , Scarpine V , Serrano S , Sevilla-Noarbe I , Smith M , Soares-Santos M , Suchyta E , Swanson M E C , Tarle G , To C , Varga T N , Weller J ,   (DES Collaboration)
Published: April 2022

ABSTRACTStrongly lensed quadruply imaged quasars (quads) are extraordinary objects. They are very rare in the sky and yet they provide unique information about a wide range of topics, including the expansion history and the composition of the Universe, the distribution of stars and dark matter in galaxies, the host galaxies of quasars, and the stellar initial mass function. Finding them in astronomical images is a classic ‘needle in a haystack’ problem, as they are outnumbered by other (contaminant) sources by many orders of magnitude. To solve this problem, we develop state-of-the-art deep learning methods and train them on realistic simulated quads based on real images of galaxies taken from the Dark Energy Survey, with realistic source and deflector models, including the chromatic effects of microlensing. The performance of the best methods on a mixture of simulated and real objects is excellent, yielding area under the receiver operating curve in the range of 0.86–0.89. Recall is close to 100 per cent down to total magnitude i ∼ 21 indicating high completeness, while precision declines from 85 per cent to 70 per cent in the range i ∼ 17–21. The methods are extremely fast: training on 2 million samples takes 20 h on a GPU machine, and 108 multiband cut-outs can be evaluated per GPU-hour. The speed and performance of the method pave the way to apply it to large samples of astronomical sources, bypassing the need for photometric pre-selection that is likely to be a major cause of incompleteness in current samples of known quads.
Tracing stars in Milky Way satellites with a-sloth
Authors: Chen Li-Hsin , Magg Mattis , Hartwig Tilman , Glover Simon C O , Ji Alexander P , Klessen Ralf S 
Published: April 2022

ABSTRACT
We study the stellar mass-to-halo mass (SMHM) relation at z = 0 in 30 Milky Way (MW)-like systems down to the ultrafaint ($M_{\rm *}\lt 10^5\, {\rm M}_\odot$) regime using the semi-analytic model a-sloth. A new model allows us to follow star formation (SF) and the stochastic stellar feedback from individually sampled Pop II stars. Our fiducial model produces consistent results with the SMHM relation derived from abundance matching and the observed cumulative stellar mass function above the observational completeness. We find a plateau in the SMHM relation in the ultrafaint regime. The stellar mass of this plateau tells us how many stars formed before supernovae occur and regulate further SF, which is determined by the Pop II SF efficiency. We also find that the number of luminous satellites increases rapidly as M* decreases until $M_{\rm *}\approx 10^4\, {\rm M}_\odot$. Finally, we find that the relative streaming velocity between baryons and dark matter at a high redshift is important in determining the number of ultrafaint dwarf galaxies at z = 0. The new model in a-sloth provides a framework to study the stellar properties and the formation history of metal-poor stars in MW and its satellites.
A survey of disc thickness and viscosity in circumbinary accretion: Binary evolution, variability, and disc morphology
Authors: Dittmann Alexander J , Ryan Geoffrey 
Published: April 2022

ABSTRACTMuch of the parameter space relevant to the evolution of astrophysical circumbinary accretion discs remains unexplored. We have carried out a suite of circumbinary disc simulations surveying both disc thickness and kinematic viscosity, using both constant-ν and constant-α prescriptions. We focus primarily on disc aspect ratios between 0.1 and 0.033, and on viscosities between ν = 0.0005 and ν = 0.008 (in units of binary semimajor axis and orbital frequency), and specialize to circular equal-mass binaries. Both factors strongly influence the evolution of the binary semimajor axis: at ν = 0.0005, inspirals occur at aspect ratios ≲ 0.059, while at ν = 0.004 inspirals occur only at aspect ratios ≲ 0.04. Inspirals occur largely because of the increasingly strong negative torque on the binary by streams of material which lag the binary, with negligible contributions from resonant torques excited in the circumbinary disc. We find that reductions in accretion rate occur when simulations are initialized too far from the eventual quasi-steady state driven by interaction with the binary, rather than being intrinsically linked to the disc aspect ratio. We find not only that the cavity size increases as viscosity is decreased, but that thinner circumbinary discs become more eccentric. Our results suggest that supermassive black hole binaries should be driven, more rapidly than previous estimates, from ∼parsec separations to distances where gravitational waves drive their inspiral, potentially reducing the number of binaries observable by pulsar timing arrays.
Average bolometric corrections and optical to X-ray flux measurements as a function of accretion rate for X-ray binaries
Authors: Anastasopoulou K , Zezas A , Steiner J F , Reig P 
Published: April 2022

ABSTRACT
In this paper, we use an RXTE library of spectral models from 10 black hole and 9 pulsar X-ray binaries, as well as model spectra available in the literature from 13 extra-galactic ultra-luminous X-ray sources (ULXs). We compute average bolometric corrections (BC = Lband/Lbol) for our sample as a function of different accretion rates. We notice the same behaviour between black hole and pulsar BCs only when ULX pulsars are included. These measurements provide a picture of the energetics of the accretion flow for an X-ray binary based solely on its observed luminosity in a given band. Moreover, it can be a powerful tool in X-ray binary population synthesis models. Furthermore, we calculate the X-ray (2–10 keV) to optical (V band) flux ratios originating from the disc/corona at different Eddington ratios for the black hole X-ray binaries in our sample. This provides a metric of the maximum contribution of the disc to the optical emission of a binary system and better constraints on its nature (donor type, etc.). We find that the optical to X-ray flux ratio shows very little variation as a function of accretion rate, but testing for different disc geometry scenarios we find that the optical contribution of the disc increases as the p value decreases [T(r) ∼ r−p]. Moreover, observational data are in agreement with a thicker disc scenario (p &lt; 0.65), which could also possibly explain the lack of observed high-inclination systems.
Escaping the maze: a statistical subgrid model for cloud-scale density structures in the interstellar medium
Authors: Buck Tobias , Pfrommer Christoph , Girichidis Philipp , Corobean Bogdan 
Published: April 2022

ABSTRACT
The interstellar medium (ISM) is a turbulent, highly structured multiphase medium. State-of-the-art cosmological simulations of the formation of galactic discs usually lack the resolution to accurately resolve those multiphase structures. However, small-scale density structures play an important role in the life cycle of the ISM, and determine the fraction of cold, dense gas, the amount of star formation, and the amount of radiation and momentum leakage from cloud-embedded sources. Here, we derive a statistical model to calculate the unresolved small-scale ISM density structure from coarse-grained, volume-averaged quantities such as the gas clumping factor, $\mathcal {C}$, and mean density 〈ρ〉V. Assuming that the large-scale ISM density is statistically isotropic, we derive a relation between the three-dimensional clumping factor, $\mathcal {C}_\rho$, and the clumping factor of the 4$\pi$ column density distribution on the cloud surface, $\mathcal {C}_\Sigma$, and find $\mathcal {C}_\Sigma =\mathcal {C}_\rho ^{2/3}$. Applying our model to calculate the covering fraction, i.e. the 4$\pi$ sky distribution of optically thick sightlines around sources inside interstellar gas clouds, we demonstrate that small-scale density structures lead to significant differences at fixed physical ISM density. Our model predicts that gas clumping increases the covering fraction by up to 30 per cent at low ISM densities compared to a uniform medium. On the other hand, at larger ISM densities, gas clumping suppresses the covering fraction and leads to increased scatter such that covering fractions can span a range from 20 per cent to 100 per cent at fixed ISM density. All data and example code are publicly available at GitHub.
A case of intestinal amoebiasis mimicking intestinal Behçet’s disease
Authors: Fukui Ayaka , Nakayama Yoichi , Yoshida Tsuneyasu , Murakami Kosaku , Kadoba Keiichiro , Onizawa Hideo , Akizuki Shuji , Nakashima Ran , Yoshifuji Hajime , Ohmura Koichiro , Sugimoto Akihiko , Yamamoto Shuji , Morinobu Akio 
Published: April 2022

ABSTRACT
Intestinal amoebiasis is caused by Entamoeba histolytica (E. histolytica) and is characterised by cecal lesions, multiple lesions, aphthae, and multiple exudative erosions. Intestinal Behçet’s disease (BD) is a chronic inflammatory disorder that is characterised by multiple ulcers. Although the aetiologies of these two bowel diseases are unrelated, they are difficult to distinguish because they present similarly with inflammation and ulcers, especially if evidence of specific pathogens is not detected. Herein, we report a case of intestinal amoebiasis in a patient with BD. The patient underwent colonoscopy four times before intestinal amoebiasis was diagnosed. As intestinal BD was initially suspected, she received high-dose glucocorticoid therapy, which exacerbated her condition. Following exacerbation, she underwent colonoscopy, and E. histolytica was revealed. Deliberate care should be taken to distinguish between intestinal amoebiasis and intestinal BD, as the appropriate treatments for these diseases are entirely different.
Multivalent DNA and nucleosome acidic patch interactions specify VRK1 mitotic localization and activity
Authors: Budziszewski Gabrielle R , Zhao Yani , Spangler Cathy J , Kedziora Katarzyna M , Williams Michael R , Azzam Dalal N , Skrajna Aleksandra , Koyama Yuka , Cesmat Andrew P , Simmons Holly C , Arteaga Eyla C , Strauss Joshua D , Kireev Dmitri , McGinty Robert K 
Published: April 2022

AbstractA key role of chromatin kinases is to phosphorylate histone tails during mitosis to spatiotemporally regulate cell division. Vaccinia-related kinase 1 (VRK1) is a serine–threonine kinase that phosphorylates histone H3 threonine 3 (H3T3) along with other chromatin-based targets. While structural studies have defined how several classes of histone-modifying enzymes bind to and function on nucleosomes, the mechanism of chromatin engagement by kinases is largely unclear. Here, we paired cryo-electron microscopy with biochemical and cellular assays to demonstrate that VRK1 interacts with both linker DNA and the nucleosome acidic patch to phosphorylate H3T3. Acidic patch binding by VRK1 is mediated by an arginine-rich flexible C-terminal tail. Homozygous missense and nonsense mutations of this acidic patch recognition motif in VRK1 are causative in rare adult-onset distal spinal muscular atrophy. We show that these VRK1 mutations interfere with nucleosome acidic patch binding, leading to mislocalization of VRK1 during mitosis, thus providing a potential new molecular mechanism for pathogenesis.
A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters
Authors: Wang Wenmeng , Qiao Shiyao , Li Guangyue , Cheng Jiahui , Yang Cuicui , Zhong Chen , Stovall Daniel B , Shi Jinming , Teng Chunbo , Li Dangdang , Sui Guangchao 
Published: April 2022

Abstract
As an oncogenic transcription factor, Yin Yang 1 (YY1) regulates enhancer and promoter connection. However, gaps still exist in understanding how YY1 coordinates coactivators and chromatin enhancer elements to assemble enhancers and super-enhancers. Here, we demonstrate that a histidine cluster in YY1’s transactivation domain is essential for its formation of phase separation condensates, which can be extended to additional proteins. The histidine cluster is also required for YY1-promoted cell proliferation, migration, clonogenicity and tumor growth. YY1-rich nuclear puncta contain coactivators EP300, BRD4, MED1 and active RNA polymerase II, and colocalize with histone markers of gene activation, but not that of repression. Furthermore, YY1 binds to the consensus motifs in the FOXM1 promoter to activate its expression. Wild-type YY1, but not its phase separation defective mutant, connects multiple enhancer elements and the FOXM1 promoter to form an enhancer cluster. Consistently, fluorescent in situ hybridization (FISH) assays reveal the colocalization of YY1 puncta with both the FOXM1 gene locus and its nascent RNA transcript. Overall, this study demonstrates that YY1 activates target gene expression through forming liquid-liquid phase separation condensates to compartmentalize both coactivators and enhancer elements, and the histidine cluster of YY1 plays a determinant role in this regulatory mechanism.
nMOWChIP-seq: low-input genome-wide mapping of non-histone targets
Authors: Liu Zhengzhi , Naler Lynette B , Zhu Yan , Deng Chengyu , Zhang Qiang , Zhu Bohan , Zhou Zirui , Sarma Mimosa , Murray Alexander , Xie Hehuang , Lu Chang 
Published: April 2022

Abstract
Genome-wide profiling of interactions between genome and various functional proteins is critical for understanding regulatory processes involved in development and diseases. Conventional assays require a large number of cells and high-quality data on tissue samples are scarce. Here we optimized a low-input chromatin immunoprecipitation followed by sequencing (ChIP-seq) technology for profiling RNA polymerase II (Pol II), transcription factor (TF), and enzyme binding at the genome scale. The new approach produces high-quality binding profiles using 1,000–50,000 cells. We used the approach to examine the binding of Pol II and two TFs (EGR1 and MEF2C) in cerebellum and prefrontal cortex of mouse brain and found that their binding profiles are highly reflective of the functional differences between the two brain regions. Our analysis reveals the potential for linking genome-wide TF or Pol II profiles with neuroanatomical origins of brain cells.
Evolutionarily Conserved and Non-Conserved Roles of Heterotrimeric Gα Proteins of Plants
Authors: Pandey Sona , Roy Choudhury Swarup , Ha Chien Van , Mohanasundaram Boominathan , Li Mao , Dodds Audrey 
Published: April 2022

AbstractHeterotrimeric G-proteins modulate multiple signaling pathways in many eukaryotes. In plants, G-proteins have been characterized primarily from a few model angiosperms and a moss. Even within this small group, they seem to affect plant phenotypes differently: G-proteins are essential for survival in monocots, needed for adaptation but are nonessential in eudicots, and are required for life cycle completion and transition from the gametophytic to sporophytic phase in the moss Physcomitrium (Physcomitrella) patens. The classic G-protein heterotrimer consists of three subunits: one Gα, one Gβ and one Gγ. The Gα protein is a catalytically active GTPase and, in its active conformation, interacts with downstream effectors to transduce signals. Gα proteins across the plant evolutionary lineage show a high degree of sequence conservation. To explore the extent to which this sequence conservation translates to their function, we complemented the well-characterized Arabidopsis Gα protein mutant, gpa1, with Gα proteins from different plant lineages and with the yeast Gpa1 and evaluated the transgenic plants for different phenotypes controlled by AtGPA1. Our results show that the Gα protein from a eudicot or a monocot, represented by Arabidopsis and Brachypodium, respectively, can fully complement all gpa1 phenotypes. However, the basal plant Gα failed to complement the developmental phenotypes exhibited by gpa1 mutants, although the phenotypes that are exhibited in response to various exogenous signals were partially or fully complemented by all Gα proteins. Our results offer a unique perspective on the evolutionarily conserved functions of G-proteins in plants.
Development of a liquid argon detector with high light collection efficiency using tetraphenyl butadiene and a silicon photomultiplier array
Authors: Aoyama Kazutaka , Tanaka Masashi , Kimura Masato , Yorita Kohei 
Published: April 2022

Abstract
To increase the light collection efficiency of a liquid argon (LAr) detector, we optimized the evaporation technique of tetraphenyl butadiene (TPB) on the detector surface and tested the operability of a silicon photomultiplier at LAr temperature. TPB converts LAr scintillations (vacuum ultraviolet light) to visible light, which can be detected using high-sensitivity photosensors. Because the light collection efficiency depends on the deposition mass of TPB on the inner surface of the detector, we constructed a well-controlled TPB evaporator to ensure reproducibility and measured the TPB deposition mass using a quartz crystal microbalance sensor. After optimizing the deposition mass of TPB (30 $\rm \mu g/cm^2$ on the photosensor window and 42 $\rm \mu g/cm^2$ on the detector wall), the observed light yield was 12.8 ± 0.3 p.e./keVee using photomultiplier tubes with a quantum efficiency of approximately 30% for TPB-converted light. We also tested the low-temperature tolerance of the silicon photomultiplier, which has a high photon detection efficiency, in a LAr environment. It detected the LAr scintillations converted by TPB with a photon detection efficiency exceeding 50%.
Evaluation of loop formation dynamics in a chromatin fiber during chromosome condensation
Authors: Yokota Hiroshi , Tachikawa Masashi 
Published: April 2022

Abstract
Chromatin fibers composed of DNA and proteins fold into consecutive loops to form rod-shaped chromosomes in mitosis. Although the loop growth dynamics has been investigated in several studies, its detailed processes are unclear. Here, we describe the time evolution of the loop length for thermal-driven loop growth processes as an iterative map by calculating the physical quantities involved in the processes. We quantify the energy during the chromatin loop formation by calculating the free energies of unlooped and looped chromatins using the Domb–Joyce model of a lattice polymer chain incorporating the bending elasticity for thermal-driven loop growth processes. The excluded volume interaction among loops is integrated by employing the mean-field theory. We compare the loop formation energy with the thermal energy and evaluate the growth of the loop length via thermal fluctuation. By assuming the dependence of the excluded volume parameter on the loop length, we construct an iterative map for the loop growth dynamics. The map demonstrates that the growth length of the loop for a single reaction cycle decreases with time to reach the condensin size, where the loop growth dynamics can be less stochastic and be regarded as the direct power stroke of condensin as a kind of motor protein.
Assessment of Negative Symptoms in Clinical Trials of Acute Schizophrenia: Test of a Novel Enrichment Strategy
Authors: Hopkins Seth C , Tomioka Sasagu , Ogirala Ajay , Loebel Antony , Koblan Kenneth S , Marder Stephen R 
Published: April 2022

Abstract
Drug trials for negative symptoms in schizophrenia select patients based on the severity and stability of negative symptoms, using criteria that are not suitable for trials of acute exacerbation of schizophrenia. Here we present a method to prognostically enrich subjects having a predefined factor structure in PANSS and apply it to the measurement of negative symptoms specifically in trials of acute schizophrenia. A vector of 1335 elements based on between- and within-item variances, covariances, and differences of PANSS items was created to calculate an index of heterogeneity and to enrich for a predetermined symptom construct in PANSS. Using prerandomization PANSS scores across N = 4876 subjects in 13 trials of acute schizophrenia, we demonstrate an ability to select for a subpopulation having the greatest amount of variance explained across the 7-items of the Marder PANSS negative symptom (MPNS) construct. Network analyses on subjects enriched for MPNS construct confirm that negative symptoms were most influential in overall psychopathology, distinct from subjects without the MPNS construct. As expected for D2 antagonists, drug-placebo differences on negative symptoms with lurasidone were not specific to the subpopulation having the MPNS construct. In contrast, the novel TAAR1 agonist ulotaront demonstrated specific improvements in negative symptoms which were greatest in the MPNS subpopulation. These results demonstrate the utility of a novel prognostic enrichment strategy that can address heterogeneity in clinical trials, where patients can be selected on the basis of a greater likelihood of having the measured symptom construct (negative symptoms) related to the disorder (schizophrenia).
ClinicalTrials.gov Identifiers: NCT0296938, NCT00088634, NCT00549718, NCT00615433, NCT00790192
Insomnia as a predictor of recurrent cardiovascular events in patients with coronary heart disease
Authors: Frøjd Lars Aastebøl , Dammen Toril , Munkhaugen John , Weedon-Fekjær Harald , Nordhus Inger Hilde , Papageorgiou Costas , Sverre Elise 
Published: April 2022

AbstractStudy ObjectivesInsomnia is highly prevalent in patients with coronary heart disease (CHD). However, the potential effect of insomnia on the risk of recurrent major adverse cardiovascular events (MACE) remains uncertain.MethodsThis prospective cohort study included 1082 consecutive patients 2–36 (mean 16) months after myocardial infarction and/or coronary revascularization. Data on clinical insomnia, coronary risk factors, and comorbidity were collected at baseline. Clinical insomnia was assessed using the Bergen Insomnia Scale (BIS). The primary composite endpoint of MACE (cardiovascular death, hospitalization due to myocardial infarction, revascularization, stroke, or heart failure) was assessed with an average follow-up of 4.2 (SD 0.3) years after baseline. Data were analyzed using Cox proportional hazard regression models stratified by prior coronary events before the index event.ResultsAt baseline, mean age was 62 years, 21% were females, and 45% reported clinical insomnia. A total of 346 MACE occurred in 225 patients during the follow-up period. For clinical insomnia, the relative risk of recurrent MACE was 1.62 (95% confidence interval [CI]: 1.24–2.11, p &lt; .001) adjusted for age, gender, and previous coronary events. In a multi-adjusted analysis, including coronary risk factors, cardiovascular comorbidity, symptoms of anxiety, and depression, the relative risk was 1.41 (95% CI: 1.05–1.89, p = .023). Clinical insomnia accounted for 16% of the MACE in attributable risk fraction analyses, being third in importance after smoking (27%) and low physical activity (21%).ConclusionsClinical insomnia was associated with increased risk of recurrent MACE. These results emphasize the importance of identifying and managing insomnia in CHD outpatients.