bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning application to detect light echoes around black holes
Authors: Chainakun P , Mankatwit N , Thongkonsing P , Young A J 
Published: July 2021

ABSTRACT
X-ray reverberation has become a powerful tool to probe the disc-corona geometry near black holes. Here, we develop machine learning (ML) models to extract the X-ray reverberation features imprinted in the power spectral density (PSD) of active galactic nucleus (AGN). The machine is trained using simulated PSDs in the form of a simple power-law encoded with the relativistic echo features. Dictionary learning and sparse coding algorithms are used for the PSD reconstruction, by transforming the noisy PSD to a representative sparse version. Then, the support vector machine is employed to extract the interpretable reverberation features from the reconstructed PSD that holds the information of the source height. The results show that the accuracy of predicting the source height, h, is genuinely high and the misclassification is only found when h &gt; 15rg. When the test PSD has a bending power-law shape, which is completely new to the machine, the accuracy is still high. Therefore, the ML model does not require the intrinsic shape of the PSD to be determined in advance. By focusing on the PSD parameter space observed in real AGN data, classification for h ≤ 10rg can be determined with 100 per cent accuracy, even using a PSD in an energy band that contains a reflection flux as low as $10{{\ \rm per\ cent}}$ of the total flux. For h &gt; 10rg, the data, if misclassified, will have small uncertainties of Δh ∼ 2–4rg. This work shows, as a proof of concept, that the ML technique could shape new methodological directions in the X-ray reverberation analysis.
Weak lensing scattering transform: dark energy and neutrino mass sensitivity
Authors: Cheng (程思浩) Sihao , Ménard Brice 
Published: July 2021

ABSTRACT
As weak lensing surveys become deeper, they reveal more non-Gaussian aspects of the convergence field which can only be extracted using statistics beyond the power spectrum. In a companion paper, we showed that the scattering transform, a novel statistic borrowing mathematical concepts from convolutional neural networks, is a powerful tool for cosmological parameter estimation in the non-Gaussian regime. Here, we extend that analysis to explore its sensitivity to dark energy and neutrino mass parameters with weak lensing surveys. We first use image synthesis to show visually that, compared to the power spectrum and bispectrum, the scattering transform provides a better statistical vocabulary to characterize the perceptual properties of lensing mass maps. We then show that it is also better suited for parameter inference: (i) it provides higher sensitivity in the noiseless regime, and (ii) at the noise level of Rubin-like surveys, though the constraints are not significantly tighter than those of the bispectrum, the scattering coefficients have a more Gaussian sampling distribution, which is an important property for likelihood parametrization and accurate cosmological inference. We argue that the scattering coefficients are preferred statistics considering both constraining power and likelihood properties.
Searching water megamasers by using mid-infrared spectroscopy (I): Possible mid-infrared indicators
Authors: Lam Man I , Walcher C Jakob , Gao Feng , Yang Ming , Li Huan , Hao Lei 
Published: July 2021

ABSTRACT
Water megamasers at 22 GHz with a gas disc configuration in galaxies provide the most precise measurements of supermassive black hole masses, as well as independent constraints on the Hubble constant in the nearby universe. The existence of other maser types, such as jet or outflow masers, represents another tracer for AGN science. However, the detection rate of water megamasers in galaxies is extremely low. Over 40 yr, only ∼ 160 galaxies are found to harbour maser emission, and ∼30 per cent of them show features in their maser emission that indicate a disc-like geometry. Therefore, increasing the detection rate of masers is a crucial task to allow expanding on maser studies. We present a comparison of mid-infrared spectroscopic data between a maser galaxy sample and a Seyfert 2 control sample. We find that maser galaxies show significant peculiarities in their mid-infrared spectra: (1) Maser galaxies tend to present stronger silicate absorption at τ9.7 $\mu\mathrm{ m}$ than the control sample, (2) PAH 11.3 $\mu$m emission in maser galaxies is much weaker than in the control sample, (3) spectral indices at 20–30 $\mu$m are steeper in maser galaxies than in the control sample and tend to be mid-infrared enhanced population. We conclude that there may be good indicators in mid-infrared and far-infrared which could differentiate maser and non-maser Seyfert 2 galaxies. Upcoming infrared facilities, such as the James Webb Space Telescope, may be able to exploit these and other useful criteria and tracers for water megamaser observations.
Non-equilibrium in the solar neighbourhood using dynamical modelling with Gaia DR2
Authors: Kipper Rain , Tenjes Peeter , Tempel Elmo , de Propris Roberto 
Published: July 2021

ABSTRACT
Matter distribution models of the Milky Way galaxy are usually stationary, although there are known to be wave-like perturbations in the disc at ∼10 per cent level of the total density. Modelling of the overall acceleration field by allowing non-equilibrium is a complicated task. We must learn to distinguish whether density enhancements are persistent or not by their nature. In this paper, we elaborate our orbital arc method to include the effects of massless perturbations and non-stationarities in the modelling. The method is tested by modelling of simulation data and shown to be valid. We apply the method to the Gaia Data Release 2 (DR2) data within a region of ∼0.5 kpc from the Sun and confirm that acceleration field in the solar neighbourhood has a perturbed nature – the phase-space density along the orbits of stars grow in the order of $h\lesssim 5$ per cent per Myr due to non-stationarity. This result is a temporally local value and can be used only within the time frame of a few Myr. An attempt to pinpoint the origin of the perturbation shows that the stars having larger absolute angular momentum are the main carriers of the local perturbation. As they are faster than the average thin disc star, they are either originating further away and are close in their pericentre or they are perturbed locally by a fast comoving perturber, such as gas disc inhomogeneities.
A transmission hologram for slitless spectrophotometry on a convergent telescope beam. 1. Focus and resolution
Authors: Moniez M , Neveu J , Dagoret-Campagne S , Gentet Y , Le Guillou L ,   The LSST Dark Energy Science Collaboration, Bongard S , Copin Y , Coughlin M 
Published: July 2021

ABSTRACT
We report in this paper the test of a plane holographic optical element to be used as an aberration-corrected grating for a slitless spectrograph, inserted in a convergent telescope beam. Our long-term objective is the optimization of a specific hologram to switch the auxiliary telescope imager of the Vera Rubin Observatory into an accurate slitless spectrograph, dedicated to the atmospheric transmission measurement. We present and discuss here the promising results of tests performed with prototype holograms at the CTIO $0.9\,$m telescope during a run of 17 nights in 2017 May–June. After their on-sky geometrical characterization, the performances of the holograms as aberration-balanced dispersive optical elements have been established by analysing spectra obtained from spectrophotometric standard stars and narrow-band emitter planetary nebulae. Thanks to their additional optical function, our holographic disperser prototypes allow us to produce significantly better focused spectra within the full visible wavelength domain $[370,1050]\,$nm than a regular grating, which suffers from strong defocusing and aberrations when used in similar conditions. We show that the resolution of our slitless on-axis spectrograph equipped with the hologram approaches its theoretical performance. While estimating the benefits of a hologram for the spectrum resolution, the roadmap to produce a competitive holographic element for the Vera Rubin Observatory auxiliary telescope has been established.
TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution
Authors: Yuan Wei , Al-Hadid Qais , Wang Zhihao , Shen Lei , Cho Hyejin , Wu Xiwei , Yang Yanzhong 
Published: July 2021

Abstract
R-loops, which consist of a DNA/RNA hybrid and a displaced single-stranded DNA (ssDNA), are increasingly recognized as critical regulators of chromatin biology. R-loops are particularly enriched at gene promoters, where they play important roles in regulating gene expression. However, the molecular mechanisms that control promoter-associated R-loops remain unclear. The epigenetic ‘reader’ Tudor domain-containing protein 3 (TDRD3), which recognizes methylarginine marks on histones and on the C-terminal domain of RNA polymerase II, was previously shown to recruit DNA topoisomerase 3B (TOP3B) to relax negatively supercoiled DNA and prevent R-loop formation. Here, we further characterize the function of TDRD3 in R-loop metabolism and introduce the DExH-box helicase 9 (DHX9) as a novel interaction partner of the TDRD3/TOP3B complex. TDRD3 directly interacts with DHX9 via its Tudor domain. This interaction is important for recruiting DHX9 to target gene promoters, where it resolves R-loops in a helicase activity-dependent manner to facilitate gene expression. Additionally, TDRD3 also stimulates the helicase activity of DHX9. This stimulation relies on the OB-fold of TDRD3, which likely binds the ssDNA in the R-loop structure. Thus, DHX9 functions together with TOP3B to suppress promoter-associated R-loops. Collectively, these findings reveal new functions of TDRD3 and provide important mechanistic insights into the regulation of R-loop metabolism.
Difference in the Clinical Outcome of Bloodstream Infections Caused by Klebsiella aerogenes and Enterobacter cloacae Complex
Authors: Jeon Minji , Huh Kyungmin , Ko Jae-Hoon , Cho Sun Young , Huh Hee Jae , Lee Nam Yong , Kang Cheol-In , Chung Doo Ryeon , Peck Kyong Ran 
Published: July 2021

Abstract

Background
The difference in clinical outcomes between Klebsiella aerogenes (formerly Enterobacter aerogenes) bacteremia (KAB) and Enterobacter cloacae complex bacteremia (ECB) is controversial.

Methods
We compared the clinical outcomes of patients with KAB and ECB and examined the risk factors associated with mortality. We conducted a retrospective case-control study of hospitalized patients with monobacterial KAB and ECB between January 2011 and June 2020. The primary outcome measure was 30-day all-cause mortality. Multiple logistic regression and propensity-score (PS) matching were used to identify independent risk factors for mortality. The models included demographic characteristics, comorbidities, recent healthcare contact, patient status at the onset of bacteremia, and severity of infection as covariates.

Results
A total of 282 patients with KAB or ECB were included, among whom 194 patients were selected after PS matching. The 30-day all-cause mortality rate was higher in the ECB group than in the KAB group (24.1% vs 10.6%, P = .003). In a multivariable model, ECB was an independent risk factor for 30-day mortality in both overall and PS-matched cohorts (adjusted odds ratio, 3.528; 95% confidence interval, 1.614–7.714; P = .002). Stay in the intensive care unit at the onset of bacteremia and higher Pitt bacteremia score were found to be independent risk factors for 30-day mortality.

Conclusions
In our study, mortality was significantly higher in patients with ECB than in those with KAB. Further studies are warranted to clarify the virulence mechanisms of E cloacae complex.
Pricing Implications of Covariances and Spreads in Currency Markets
Authors: Maurer Thomas , Tô Thuy-Duong , Tran Ngoc-Khanh 
Published: July 2021

Abstract
We introduce a covariance and spread (i.e., exchange rate forward discount) adjusted carry factor that prices the cross-section of FX market returns, where many other single- and multifactor models fail. Both the covariance matrix of exchange rate growths and forward discounts contain important information for pricing that is not captured by well-known factors. The time-varying conditional covariance matrix and forward discounts forecast future realized currency returns. (JEL F31, F37, G12, G15, G17)
Treatment strategies for Sjögren’s syndrome with childhood onset: a systematic review of the literature
Authors: Doolan Georgia , Faizal Nor Mohd , Foley Charlene , Al-Obaidi Muthana , Jury Elizabeth C , Price Elizabeth , Ramanan Athimalaipet V , Lieberman Scott M , Ciurtin Coziana 
Published: July 2021

Abstract

Objectives
SS with childhood onset is a rare autoimmune disease characterized by heterogeneous presentation. The lack of validated classification criteria makes it challenging to diagnose. Evidence-based guidelines for treatment of juvenile SS are not available due to the rarity of disease and the paucity of research in this patient population. This systematic review aims to summarize and appraise the current literature focused on pharmacological strategies for management of SS with childhood onset.

Methods
PubMed and MEDLINE/Scopus databases up to December 2020 were screened for suitable reports highlighting pharmacological treatment of SS with childhood onset using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2009 reporting checklist. Animal studies were excluded.

Results
A total of 43 studies (34 case reports, 8 mini case series and 1 pilot study) were eligible for analysis. The studies retrieved included girls in 88% (120/137) of cases and had very low confidence levels. HCQ was prescribed for parotid swelling, as well as in association with MTX and NSAIDs in patients with arthritis and arthralgia. Corticosteroids such as long courses of oral prednisone and i.v. methylprednisolone were commonly prescribed for children with severe disease presentations. Rituximab was mainly indicated for mucosa-associated lymphoid tissue lymphoma and renal and nervous system complications. Other conventional DMARDs were prescribed in selected cases with extraglandular manifestations.

Conclusion
Various therapies are used for the management of juvenile SS and are prescribed based on expert clinician’s opinion. There are currently no good-quality studies that allow clinical recommendations for treatment of SS with childhood onset.
How Efficacious Are Antipsychotic Drugs for Schizophrenia? An Interpretation Based on 13 Effect Size Indices
Authors: Leucht Stefan , Siafis Spyridon , Engel Rolf R , Schneider-Thoma Johannes , Bighelli Irene , Cipriani Andrea , Furukawa Toshi A , Davis John M 
Published: July 2021

Abstract

Background
The magnitude of the superiority of antipsychotics over placebo is debated. One reason is that the effect-size index which is usually used in meta-analyses is in standard deviation units. Many other indices, some of which are more intuitive, exist.

Methods
We explain the formulae, advantages, and limitations of 13 effect-size indices: Mean Difference (MD), Standardized-Mean-Difference (SMD), Correlation Coefficient, Ratio-of-Means (RoM, endpoint and change data), Improvement Fraction (IF), Drug-Response Fraction (DRF), Minimally-Clinically-Important-Difference-Units (MCIDU), Number-Needed-to-Treat-derived from SMD (NNT), Odds Ratio (OR), Relative Risk (RR), and Risk Difference (RD) derived from SMD, Drug-response and Placebo-response in percent. We applied these indices to meta-analyses comparing antipsychotic drugs with placebo for acute schizophrenia.

Results
The difference of all antipsychotics pooled vs placebo (105 trials with 22741 participants) was: MD 9.4 (95% CI 8.4,10.2) PANSS points, SMD 0.47 (0.42,0.51), Correlation coefficient 0.23 (0.21,0.25), RoM endpoint 0.83 (0.81,0.85), RoM change 1.94 (1.84,2.02), IF (%) 49 (46,51), DRF (%) 94 (84,102), MCIDU 0.63 (0.56,0.68), NNT 5 (5,6), OR 2.34 (2.14, 2.52), RR 1.67 (1.59,1.73), RD 20% (18–22), and 50% (48, 52) improved on drug compared to 30% on placebo. Results of individual drugs compared to placebo are presented, as well.

Conclusions
Taken together these indices show a substantial, but not a large superiority of antipsychotics compared to placebo. The general chronicity of the patients in the trials must be considered. Future meta-analyses should report other effect size indices in addition to the Standardized-Mean-Difference, in particular percentage responders in the drug and placebo groups. They can be easily derived and would enhance the interpretation of research findings.
Co-occurring Deficits in Clinical and Cognitive Insight in Prolonged Schizophrenia-Spectrum Disorders: Relationship to Metacognitive Deficits
Authors: Mervis Joshua E , Bonfils Kelsey A , Cooper Samuel E , Wiesepape Courtney , Lysaker Paul H 
Published: July 2021

AbstractPeople diagnosed with schizophrenia have been broadly observed to experience deficits in clinical and cognitive insight; however, less is understood about how these deficits are related. One possibility is that these deficits co-occur among people when other deficits in cognition are present, such as in executive function, social cognition, and metacognition, which may either promote the development of both forms of poor insight or allow one to negatively influence the other. To explore this possibility, we conducted a cluster analysis using assessments of clinical and cognitive insight among 95 adults with a schizophrenia spectrum disorder. As predicted, this analysis yielded a group with concurrently poor clinical and cognitive insight (n = 36). Additional groups were found with concurrently good clinical and cognitive insight (n = 28) and poor clinical insight and good cognitive insight (n = 31). Groups were then compared on assessments of executive function, social cognition, and metacognition. The group with concurrently lower levels of cognitive and clinical insight had significantly poorer metacognition relative to the other groups. In particular, they tended to form more fragmented and less integrated ideas about themselves and others. No differences were found for executive function or social cognition. The result may suggest that while clinical and cognitive insight is partially orthogonal phenomena, relatively lower levels of metacognition, or difficulties forming integrated ideas about oneself and others, maybe a condition leading to the confluence of lower clinical and cognitive insight. Interventions targeting metacognition may be of particular use for this group.
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support
Authors: Gosselin Sophia , Fullmer Matthew S , Feng Yutian , Gogarten Johann Peter 
Published: July 2021

AbstractWhole-genome comparisons based on average nucleotide identities (ANI) and the genome-to-genome distance calculator have risen to prominence in rapidly classifying prokaryotic taxa using whole-genome sequences. Some implementations have even been proposed as a new standard in species classification and have become a common technique for papers describing newly sequenced genomes. However, attempts to apply whole-genome divergence data to the delineation of higher taxonomic units and to phylogenetic inference have had difficulty matching those produced by more complex phylogenetic methods. We present a novel method for generating statistically supported phylogenies of archaeal and bacterial groups using a combined ANI and alignment fraction-based metric. For the test cases to which we applied the developed approach, we obtained results comparable with other methodologies up to at least the family level. The developed method uses nonparametric bootstrapping to gauge support for inferred groups. This method offers the opportunity to make use of whole-genome comparison data, that is already being generated, to quickly produce phylogenies including support for inferred groups. Additionally, the developed ANI methodology can assist the classification of higher taxonomic groups.[Average nucleotide identity (ANI); genome evolution; prokaryotic species delineation; taxonomy.]
Peripunctal Mass Lesions: Clinicopathological Analysis and Surgical Outcomes—A Multicentric Series
Authors: Nair Akshay Gopinathan , Mukherjee Bipasha , Kamal Saurabh , Singh Swati , Alam Md. Shahid , Nisar Sonam Poonam , Koka Kirthi , Gopinathan Indumati 
Published: July 2021

Purpose:
To report the epidemiology, histopathological spectrum, and surgical outcomes of peripunctal mass lesions.

Methods:
Multicentric retrospective case series involving 6 centers in India. All cases of peripunctal masses with histopathological diagnoses and minimum follow up of 3 months were included. Demographic data, clinical photographs, objective assessments of clinical improvement were assessed before and after treatment.

Results:
A total of 50 patients were included. The mean age was 46.4 years (range: 12–76 years). The mean duration of complaints was 27.4 months (range: 1–120 months) and mean follow-up period after surgery was 15.8 months (range: 3–120 months). The most common presenting complaints were a mass lesion/cosmetic concern (82%), followed by epiphora (48%) and foreign body sensation (16%). The most common lesion was melanocytic nevus (19/50; 38%), followed by squamous papilloma (8/50; 16%), hidrocystoma (7/50; 14%), and epidermoid cyst (7/50; 14%). Three cases of malignant tumors were diagnosed: 2 cases of sebaceous gland carcinoma and 1 case of squamous cell carcinoma. In all, 21 of 50 (42%) cases underwent excision with the placement of a Mini-Monoka stent, whereas the remaining 29 cases underwent only excision. At final follow up, a healed punctal opening was visible in 46 of 50 (92%) of the cases; 2 (4%) cases had a slit-like punctum and in 1 case (2%), a stenosed punctum was visible. However, only 1 case (2%) reported epiphora at follow up.

Conclusions:
Peripunctal masses are largely benign and present most commonly on the lower eyelid. Melanocytic nevus is the most common peripunctal mass lesion. In the series, stent placement did not play a significant role in the functional outcome.
Real-world incidence of monofocal toric intraocular lens repositioning: analysis of the American Academy of Ophthalmology IRIS Registry
Authors: Kramer Brent A. , Berdahl John , Gu Xiaolin , Merchea Mohinder 
Published: July 2021

Purpose:
To determine the 12-month incidence of reoperation to realign 2 commercially available types of implanted monofocal toric acrylic intraocular lenses (IOLs).

Setting:
American Academy of Ophthalmology IRIS (Intelligent Research in Sight) Registry.

Design:
Registry retrospective study.

Methods:
Eyes that underwent cataract extraction and were implanted with a TECNIS or AcrySof monofocal toric IOL in 2016 and 2017 were identified. The rate of reoperation for IOL realignment (Current Procedural Terminology code 66825) within 365 days of implantation was determined for each IOL group. Risk factors for repositioning were evaluated using logistic regression modeling.

Results:
A total of 6482 eyes were implanted with a monofocal toric IOL, including 2013 (31.06%) with a TECNIS and 4469 (68.94%) with an AcrySof IOL. During the first postoperative year, 87 (1.3%) eyes underwent surgical IOL repositioning. The incidence of repositioning was significantly higher (P < .0001) for TECNIS-implanted (3.1%, 62/2013) than for AcrySof-implanted (0.6%, 25/4469) eyes (odds ratio [OR] 5.6; 95% CI, 3.5-8.9). Younger age (OR 0.76; 95% CI, 0.67-0.86 per 5-year increase) was associated with a higher risk for IOL repositioning.

Conclusions:
Real-world analysis of U.S. patients in the IRIS Registry revealed that the rate of surgical IOL repositioning was 5 times higher in eyes implanted with TECNIS than with AcrySof monofocal toric IOLs for astigmatic correction at the time of cataract surgery. These findings should be considered when selecting a toric IOL for correction of astigmatism in cataract patients, particularly in younger patients with a higher risk for misalignment requiring repositioning.