bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial Neural Network classification of 4FGL sources
Authors: Germani S , Tosti G , Lubrano P , Cutini S , Mereu I , Berretta A 
Published: June 2021

ABSTRACT
The Fermi-LAT DR1 and DR2 4FGL catalogues feature more than 5000 gamma-ray sources of which about one fourth are not associated with already known objects, and approximately one third are associated with blazars of uncertain nature. We perform a three-category classification of the 4FGL DR1 and DR2 sources independently, using an ensemble of Artificial Neural Networks (ANNs) to characterize them based on the likelihood of being a Pulsar (PSR), a BL Lac type blazar (BLL) or a Flat Spectrum Radio Quasar (FSRQ). We identify candidate PSR, BLL, and FSRQ among the unassociated sources with approximate equipartition among the three categories and select 10 classification outliers as potentially interesting for follow-up studies.
Kinematics of Mg ii absorbers from the redshift-space distortion around massive quiescent galaxies
Authors: Zu Ying 
Published: June 2021

ABSTRACT
The kinematics of Mg ii absorbers is the key to understanding the origin of cool, metal-enriched gas clouds in the circumgalactic medium of massive quiescent galaxies. Exploiting the fact that the cloud line-of-sight velocity distribution is the only unknown for predicting the redshift-space distortion (RSD) of Mg ii absorbers from their 3D real-space distribution around galaxies, we develop a novel method to infer the cool cloud kinematics from the redshift-space galaxy–cloud cross-correlation ξs. We measure ξs for ∼104 Mg ii absorbers around ∼8 × 105 CMASS galaxies at 0.4 &lt; z &lt; 0.8. We discover that ξs does not exhibit a strong Fingers-of-God effect, but is heavily truncated at velocity ${\sim }300\, \mathrm{km}\, {\rm s}^{-1}$. We reconstruct both the redshift and real-space cloud number density distributions inside haloes, $\xi ^{s}_{1h}$ and ξ1h, respectively. Thus, for any model of cloud kinematics, we can predict $\xi ^{s}_{1h}$ from the reconstructed ξ1h, and self-consistently compare to the observed $\xi ^{s}_{1h}$. We consider four types of cloud kinematics, including an isothermal model with a single velocity dispersion, a satellite infall model in which cool clouds reside in the subhaloes, a cloud accretion model in which clouds follow the cosmic gas accretion, and a tired wind model in which clouds originate from the galactic wind-driven bubbles. All the four models provide statistically good fits to the RSD data, but only the tired wind model can reproduce the observed truncation by propagating ancient wind bubbles at ${\sim }250\, \mathrm{km}\, s^{-1}$ on scales ${\sim }400\, \, h^{-1}\, \mathrm{kpc}$. Our method provides an exciting path to decoding the dynamical origin of metal absorbers from the RSD measurements with upcoming spectroscopic surveys.
Comparison of the ion-to-electron temperature ratio prescription: GRMHD simulations with electron thermodynamics
Authors: Mizuno Yosuke , Fromm Christian M , Younsi Ziri , Porth Oliver , Olivares Hector , Rezzolla Luciano 
Published: June 2021

ABSTRACT
The Event Horizon Telescope (EHT) collaboration, an Earth-size sub-millimetre radio interferometer, recently captured the first images of the central supermassive black hole in M87. These images were interpreted as gravitationally lensed synchrotron emission from hot plasma orbiting around the black hole. In the accretion flows around low-luminosity active galactic nuclei such as M87, electrons and ions are not in thermal equilibrium. Therefore, the electron temperature, which is important for the thermal synchrotron radiation at EHT frequencies of 230 GHz, is not independently determined. In this work, we investigate the commonly used parametrized ion-to-electron temperature ratio prescription, the so-called R−β model, considering images at 230 GHz by comparing with electron-heating prescriptions obtained from general-relativistic magnetohydrodynamical (GRMHD) simulations of magnetized accretion flows in a Magnetically Arrested Disc (MAD) regime with different recipes for the electron thermodynamics. When comparing images at 230 GHz, we find a very good match between images produced with the R−β prescription and those produced with the turbulent- and magnetic reconnection-heating prescriptions. Indeed, this match is on average even better than that obtained when comparing the set of images built with the R−β prescription with either a randomly chosen image or with a time-averaged one. From this comparative study of different physical aspects, which include the image, visibilities, broad-band spectra, and light curves, we conclude that, within the context of images at 230 GHz relative to MAD accretion flows around supermassive black holes, the commonly used and simple R−β model is able to reproduce well the various and more complex electron-heating prescriptions considered here.
TnpAREP and REP sequences dissemination in bacterial genomes: REP recognition determinants
Authors: Corneloup Alix , Caumont-Sarcos Anne , Kamgoue Alain , Marty Brigitte , Le Phan Thai Nguyen , Siguier Patricia , Guynet Catherine , Ton-Hoang Bao 
Published: June 2021

Abstract
REP, diverse palindromic DNA sequences found at high copy number in many bacterial genomes, have been attributed important roles in cell physiology but their dissemination mechanisms are poorly understood. They might represent non-autonomous transposable elements mobilizable by TnpAREP, the first prokaryotic domesticated transposase associated with REP. TnpAREP, fundamentally different from classical transposases, are members of the HuH superfamily and closely related to the transposases of the IS200/IS605 family. We previously showed that Escherichia coli TnpAREP processes cognate single stranded REP in vitro and that this activity requires the integrity of the REP structure, in particular imperfect palindromes interrupted by a bulge and preceded by a conserved DNA motif. A second group of REPs rather carry perfect palindromes, raising questions about how the latter are recognized by their cognate TnpAREP. To get insight into the importance of REP structural and sequence determinants in these two groups, we developed an in vitro activity assay coupled to a mutational analysis for three different TnpAREP/REP duos via a SELEX approach. We also tackled the question of how the cleavage site is selected. This study revealed that two TnpAREP groups have co-evolved with their cognate REPs and use different strategies to recognize their REP substrates.
Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer–target gene regulatory interactions
Authors: Salviato Elisa , Djordjilović Vera , Hariprakash Judith Mary , Tagliaferri Ilario , Pal Koustav , Ferrari Francesco 
Published: June 2021

AbstractA growing amount of evidence in literature suggests that germline sequence variants and somatic mutations in non-coding distal regulatory elements may be crucial for defining disease risk and prognostic stratification of patients, in genetic disorders as well as in cancer. Their functional interpretation is challenging because genome-wide enhancer–target gene (ETG) pairing is an open problem in genomics. The solutions proposed so far do not account for the hierarchy of structural domains which define chromatin three-dimensional (3D) architecture. Here we introduce a change of perspective based on the definition of multi-scale structural chromatin domains, integrated in a statistical framework to define ETG pairs. In this work (i) we develop a computational and statistical framework to reconstruct a comprehensive map of ETG pairs leveraging functional genomics data; (ii) we demonstrate that the incorporation of chromatin 3D architecture information improves ETG pairing accuracy and (iii) we use multiple experimental datasets to extensively benchmark our method against previous solutions for the genome-wide reconstruction of ETG pairs. This solution will facilitate the annotation and interpretation of sequence variants in distal non-coding regulatory elements. We expect this to be especially helpful in clinically oriented applications of whole genome sequencing in cancer and undiagnosed genetic diseases research.
Dialysis dose and mortality in haemodialysis: is higher better?
Authors: Béguin Lisa , Krummel Thierry , Longlune Nathalie , Galland Roula , Couchoud Cécile , Hannedouche Thierry 
Published: June 2021

AbstractBackgroundThe effect of dialysis dose on mortality remains unsettled. Current guidelines recommend targeting a single-pool Kt/V (spKt/V) at 1.20–1.40 per thrice-weekly dialysis session. However, the optimal dialysis dose remains mostly disputed.MethodsIn a nationwide registry of all incident patients receiving thrice-weekly haemodialysis, 32 283 patients had available data on dialysis dose, estimated by Kt/V and its variants epuration volume per session (Kt) and Kt indexed to body surface area (Kt/A). Survival was analysed with a multivariate Cox model and a concurrent risk model accounting for renal transplantation. A predictive model of Kt in the upper quartile was developed.ResultsRegardless of the indicator, a higher dose of dialysis was consistently associated with better survival. The survival differential of Kt was the most discriminating, but marginally, compared with the survival differential according to Kt/V and Kt/A. Patient survival was higher in the upper quartile of Kt (&gt;69 L/session) then deteriorated as the Kt decreased, with a difference in survival between the upper and lower quartile of 23.6% at 5 years. Survival differences across Kt distribution were similar after accounting for kidney transplantation as a competing risk. Predictive factors for Kt in the upper quartile were arteriovenous fistula versus catheters and graft, haemodiafiltration versus haemodialysis, scheduled dialysis start versus emergency start, long weekly dialysis duration and spKt/V measurement versus double-pool equilibrated Kt/V.ConclusionsOur data confirm the existence of a relationship between dialysis dose and survival that persisted despite correcting for known confounders. A model for predicting a high dose of dialysis is proposed with practical relevance.
Reaching the Unreachable: Strategies for HCV Eradication in Patients With Refractory Opioid Addiction—A Real-world Experience
Authors: Sandmann Lisa , Deppe Julian , Beier Christoph , Ohlendorf Valerie , Schneider Julia , Wedemeyer Heiner , Wedegärtner Felix , Cornberg Markus , Maasoumy Benjamin 
Published: June 2021

Abstract
To achieve global hepatitis C virus (HCV) eradication, barriers prohibiting treatment access need to be overcome. We established a strategy to initiate antiviral therapy in patients with severe, refractory heroin addiction. All patients achieved sustained virological response. Outreach programs of hepatologists might be a reasonable way to overcome barriers to HCV treatment.
Textural and Geochemical Evidence for Magnetite Production upon Antigorite Breakdown During Subduction
Authors: Vieira Duarte Joana F , Piccoli Francesca , Pettke Thomas , Hermann Jörg 
Published: June 2021

AbstractMagnetite stability in ultramafic systems undergoing subduction plays a major role in controlling redox states of the fluids liberated upon dehydration reactions, as well as of residual rocks. Despite their relevance for the evaluation of the redox conditions, the systematics and geochemistry of oxide minerals have remained poorly constrained in subducted ultramafic rocks. Here, we present a detailed petrological and geochemical study of magnetite in hydrous ultramafic rocks from Cerro del Almirez (Spain). Our results indicate that prograde to peak magnetite, ilmenite–hematite solid solution minerals, and sulfides coexist in both antigorite-serpentinite and chlorite-harzburgite at c. 670 °C and 1·6 GPa, displaying successive crystallization stages, each characterized by specific mineral compositions. In antigorite-serpentinite, magnetite inherited from seafloor hydration and recrystallized during subduction has moderate Cr (Cr2O3 &lt; 10 wt%) and low Al and V concentrations. In chlorite-harzburgite, polygonal magnetite is in textural equilibrium with olivine, orthopyroxene, chlorite, pentlandite, and ilmenite–hematite solid solution minerals. The Cr2O3 contents of this magnetite are up to 19 wt%, higher than any magnetite data obtained for antigorite-serpentinite, along with higher Al and V, derived from antigorite breakdown, and lower Mn concentrations. This polygonal magnetite displays conspicuous core to rim zoning as recognized on elemental maps. Cr–V–Al–Fe3+ mass-balance calculations, assuming conservative behavior of total Fe3+ and Al, were employed to model magnetite compositions and modes in the partially dehydrated product chlorite-harzburgite starting from antigorite-serpentinite, as well as in the serpentinite protolith starting from the chlorite-harzburgite. The model results disagree with measured Cr and V compositions in magnetite from antigorite-serpentinites and chlorite-harzburgites. This indicates that these two rock types had different initial bulk compositions and thus cannot be directly compared. Our mass-balance analysis also reveals that new magnetite formation is required across the antigorite-breakdown reaction to account for the mass conservation of fluid-immobile elements such as Cr–V–Al–Fe3+. Complete recrystallization and formation of new magnetite in equilibrium with peak olivine (Mg# 89–91), chlorite (Mg# ∼95), orthopyroxene (Mg# 90–91), and pentlandite buffer the released fluid to redox conditions of ∼1 log unit above the quartz–fayalite–magnetite buffer. This is consistent with the observation that the Fe–Ti solid solution minerals (hemo-ilmenite and ilmeno-hematite) crystallized as homogeneous phases and exsolved upon exhumation and cooling. We conclude that antigorite-dehydration reaction fluids carry only a moderate redox budget and therefore may not be the only reason why the magmas are comparatively oxidized.
Plant casein kinases phosphorylate and destabilize a cyclin-dependent kinase inhibitor to promote cell division
Authors: Qu Li , Wei Zhuang , Chen Hu-Hui , Liu Tao , Liao Kan , Xue Hong-Wei 
Published: June 2021

Abstract
Cell cycle is one of the most fundamentally conserved biological processes of plants and mammals. Casein kinase1s (CK1s) are critical for cell proliferation in mammalian cells; however, how CK1s coordinate cell division in plants remains unknown. Through genetic and biochemical studies, here we demonstrated that plant CK1, Arabidopsis (Arabidopsis thaliana) EL1-like (AELs), regulate cell cycle/division by modulating the stability and inhibitory effects of Kip-related protein6 (KRP6) through phosphorylation. Cytological analysis showed that AELs deficiency results in suppressed cell-cycle progression mainly due to the decreased DNA replication rate at S phase and increased period of G2 phase. AELs interact with and phosphorylate KRP6 at serines 75 and 109 to stimulate KRP6’s interaction with E3 ligases, thus facilitating the KRP6 degradation through the proteasome. These results demonstrate the crucial roles of CK1s/AELs in regulating cell division through modulating cell-cycle rates and elucidate how CK1s/AELs regulate cell division by destabilizing the stability of cyclin-dependent kinase inhibitor KRP6 through phosphorylation, providing insights into the plant cell-cycle regulation through CK1s-mediated posttranslational modification.
The Varieties of Agnosticism
Authors: Ferrari Filippo , Incurvati Luca 
Published: June 2021

AbstractWe provide a framework for understanding agnosticism. The framework accounts for the varieties of agnosticism while vindicating the unity of the phenomenon. This combination of unity and plurality is achieved by taking the varieties of agnosticism to be represented by several agnostic stances, all of which share a common core provided by what we call the minimal agnostic attitude. We illustrate the fruitfulness of the framework by showing how it can be applied to several philosophical debates. In particular, several philosophical positions can be aptly conceived of as instances of agnosticism whilst retaining their differences and distinguishing features.
Factors associated with homelessness among women: a cross-sectional survey of outpatient mental health service users at The Banyan, India
Authors: Krishnadas Preetha , Narasimhan Lakshmi , Joseph Tanya , Bunders Joske , Regeer Barbara 
Published: June 2021

ABSTRACT

Background
Homelessness has multifaceted and damaging effects on women with mental illness. This makes it imperative to identify and address the factors leading to homelessness among women with mental illness in order to inform policy on providing relevant services for this vulnerable population.

Method
A cross-sectional survey was conducted among 346 women in active contact with one of four outpatient clinics at The Banyan, a non-profit organization in the Indian state of Tamil Nadu. A semi-structured instrument and modified version of the List of Threatening Experiences Questionnaire was used for data collection. Multivariate logistic regression analysis was used to examine predictive variables for homelessness among women with mental illness.

Result
32.65% of participants reported a history of homelessness. Less than 5 years of schooling (OR = 2.914, 95% CI = 1.027–8.269, P &lt; 0.05) and disrupted relationships (OR = 1.807, 95% CI = 1.23–2.655, P &lt; 0.01) were associated with a greater likelihood of women with mental illness to experience homelessness.

Conclusion
In the study cohort, this was explained mainly by factors rooted in gender-based disadvantage. Further practice and research are needed to develop interventions that address issues with a sociological basis to mental illness and prevent these predictive factors.
Behçet’s disease and activities of daily living
Authors: Nagano Aoi , Takeuchi Masaki , Horita Nobuyuki , Teshigawara Takeshi , Kawagoe Tatsukata , Mizuki Yuki , Meguro Akira , Nakano Hiroto , Kirino Yohei , Takase-Minegishi Kaoru , Yoshimi Ryusuke , Kurosawa Michiko , Fukumoto Takeshi , Takeno Mitsuhiro , Kaneko Takeshi , Mizuki Nobuhisa 
Published: June 2021

Abstract

Objectives
No large-scale registration study has comprehensively evaluated the activities of daily living (ADL) in patients with Behçet’s disease.

Methods
The Japanese government provided us with a dataset of confirmed or suspected Behçet’s disease cases derived from ongoing national registration. ADL were categorized and analysed into four categories in patients who satisfied the International Criteria for Behçet’s Disease.

Results
Data from 2960 patients (men 38.9%, women 61.1%; median age 39 years) were assessed. While 1767 patients (59.7%) had normal ADL, the others had impaired ADL comprising limited but not assisted [n = 1058 (35.7%)], partially assisted [n = 116 (3.9%)] and fully assisted [n = 19 (0.6%)]. Logistic regression analysis showed that chronic ocular lesions [odds ratio (OR) 1.85 (95% CI 1.46, 2.35), P &lt; 0.001], paralysis [OR 2.51 (95% CI 1.58, 3.97), P &lt; 0.001], psychosis [OR 3.16 (95% CI 2.02, 4.95), P &lt; 0.001] and arthritis [OR 1.69 (95% CI 1.44, 1.99), P &lt; 0.001] led to the risk of impaired ADL. Chronic ocular lesions [OR 3.61 (95% CI 2.27, 5.72), P &lt; 0.001], paralysis [OR 3.43 (95% CI 1.87, 6.30), P &lt; 0.001] and psychosis [OR 3.60 (95% CI 2.00, 6.50), P &lt; 0.001] were related to the requirement of physical assistance (partially or fully assisted), although arthritis [OR 1.39 (95% CI 0.93, 2.06), P = 0.108] was not a significant factor in this model.

Conclusion
Ocular lesions, neurological manifestations and arthritis affected ADL. Patients with ocular lesions or neurological manifestations more frequently required physical assistance.
Bidirectional association between systemic lupus erythematosus and macrophage activation syndrome: a nationwide population-based study
Authors: Huang Lu-Wei , Wei James Cheng-Chung , Chen Der-Yuan , Chen Yen-Ju , Tang Kuo-Tung , Ko Tai-Ming , Chen Hsin-Hua 
Published: June 2021

Abstract

Objectives
To determine the bidirectional relationship between macrophage activation syndrome (MAS) and SLE.

Methods
Using the 1997–2013 Taiwan National Health Insurance Research Database, we identified patients with newly diagnosed SLE from 2001 to 2013 and selected individuals without SLE from a 1 million representative population. Propensity score (PS) matching was performed to balance incident SLE patients and individuals without SLE according to age, sex, comorbidities and medical utilization. The association between a history of MAS and SLE was studied using conditional logistic regression analysis shown as an adjusted odds ratio (aOR). The risk of MAS associated with SLE was analysed using Cox proportional regression analysis, shown as an adjusted hazard ratio (aHR), and we conducted a sensitivity analysis using various definitions of MAS.

Results
We included 10 481 SLE patients and 20 962 PS-matched (1:2) non-SLE individuals. The correlation between a history of MAS and SLE did not reach statistical significance after adjustment for potential confounders [aOR 1.18 (95% CI, 0.80, 1.75)] in the age-/sex-matched populations. In the 1:2 PS-matched populations, the risk of MAS markedly increased in patients with SLE [aHR 7.18 (95% CI 4.97, 10.36)]. Other risk factors for MAS included female gender, age ≥65 years, low income, a history of inflammatory bowel disease and a history of MAS.

Conclusion
This nationwide, population-based study revealed that a history of MAS was not significantly associated with SLE risk. However, the risk of MAS was markedly associated with SLE and a history of MAS.
VIRTUAL CLINICAL TRIALS IN MEDICAL IMAGING SYSTEM EVALUATION AND OPTIMISATION
Authors: Barufaldi Bruno , Maidment Andrew D A , Dustler Magnus , Axelsson Rebecca , Tomic Hanna , Zackrisson Sophia , Tingberg Anders , Bakic Predrag R 
Published: June 2021

Abstract
Virtual clinical trials (VCTs) can be used to evaluate and optimise medical imaging systems. VCTs are based on computer simulations of human anatomy, imaging modalities and image interpretation. OpenVCT is an open-source framework for conducting VCTs of medical imaging, with a particular focus on breast imaging. The aim of this paper was to evaluate the OpenVCT framework in two tasks involving digital breast tomosynthesis (DBT). First, VCTs were used to perform a detailed comparison of virtual and clinical reading studies for the detection of lesions in digital mammography and DBT. Then, the framework was expanded to include mechanical imaging (MI) and was used to optimise the novel combination of simultaneous DBT and MI. The first experiments showed close agreement between the clinical and the virtual study, confirming that VCTs can predict changes in performance of DBT accurately. Work in simultaneous DBT and MI system has demonstrated that the system can be optimised in terms of the DBT image quality. We are currently working to expand the OpenVCT software to simulate MI acquisition more accurately and to include models of tumour growth. Based on our experience to date, we envision a future in which VCTs have an important role in medical imaging, including support for more imaging modalities, use with rare diseases and a role in training and testing artificial intelligence (AI) systems.