bluuebunny/crossref_metadata_2025_split huggingface dataset:
The long-term broad-line responsivity in MKN 110
Authors: Homan D , Lawrence A , Ward M , Bruce A , Landt H , MacLeod C , Elvis M , Wilkes B , Huchra J P , Peterson B M 
Published: December 2022

ABSTRACT
We examine the long-term history of the optical spectrum of the extremely variable Active Galactic Nucleus (AGN) MKN 110. By combining various archival data with new data, we cover an unprecedented long period of ∼30 yr (1987–2019). We find that the He ii λ4686 emission line changes by a factor of forty and varies more strongly than the optical continuum. Following Ferland et al., we take He ii λ4686 as a proxy for the FUV continuum and compare the flux of several other line species against it. This comparison reveals a clear pattern, whereby lines respond close to linearly at low FUV fluxes, and saturate at high FUV fluxes. The saturation level of the response appears to depend on the excitation energy of the line species. In addition to this global pattern, we note changes among observational epochs, indicating a structural evolution in the broad line region (BLR). The line profiles in our spectra show an offset between the narrow and broad components of the He ii λ4686 and H β lines. This offset shows a significant negative correlation with the FUV flux and a positive correlation with the line velocity width. Our analysis reveals a complex BLR response to a changing continuum. The clear presence of a non-responsive component of the broad lines indicates the existence of multiple contributions to the line emission. We find there are several kinematic models of the BLR and inner regions of the AGN that match our data.
Origin of multifractality in solar wind turbulence: the role of current sheets
Authors: Gomes Leonardo F , Gomes Tiago F P , Rempel Erico L , Gama Sílvio 
Published: December 2022

ABSTRACT
In this work, a multifractal framework is proposed to investigate the effects of current sheets in solar wind turbulence. By using multifractal detrended fluctuation analysis coupled with surrogate methods and volatility, two solar wind magnetic field time series are investigated, one with current sheets and one without current sheets. Despite the lack of extreme-events intermittent bursts in the current sheet-free series, both series are shown to be strongly multifractal, although the current sheet-free series displays an almost linear behaviour for the scaling exponent of structure functions. Long-range correlations are shown to be the main source of multifractality for the series without current sheets, while a combination of heavy-tail distribution and non-linear correlations is responsible for multifractality in the series with current sheets. The multifractality in both time series is formally shown to be associated with an energy-cascade process using the p-model.
Pulsar revival in neutron star mergers: multimessenger prospects for the discovery of pre-merger coherent radio emission
Authors: Cooper A J , Gupta O , Wadiasingh Z , Wijers R A M J , Boersma O M , Andreoni I , Rowlinson A , Gourdji K 
Published: December 2022

ABSTRACT
We investigate pre-merger coherent radio emission from neutron star mergers arising due to the magnetospheric interaction between compact objects. We consider two plausible radiation mechanisms, and show that if one neutron star has a surface magnetic field Bs ≥ 1012G, coherent millisecond radio bursts with characteristic temporal morphology and inclination angle dependence are observable to Gpc distances with next-generation radio facilities. We explore multi-messenger and multi-wavelength methods of identification of a neutron star merger origin of radio bursts, such as in fast radio burst surveys, triggered observations of gamma-ray bursts and gravitational wave events, and optical/radio follow-up of fast radio bursts in search of kilonova and radio afterglow emission. We present our findings for current and future observing facilities, and make recommendations for verifying or constraining the model.
Machine learning classification of CHIME fast radio bursts – II. Unsupervised methods
Authors: Zhu-Ge Jia-Ming , Luo Jia-Wei , Zhang Bing 
Published: December 2022

ABSTRACT
Fast radio bursts (FRBs) are one of the most mysterious astronomical transients. Observationally, they can be classified into repeaters and apparent non-repeaters. However, due to the lack of continuous observations, some apparent repeaters may have been incorrectly recognized as non-repeaters. In a series of two papers, we intend to solve such problem with machine learning. In this second paper of the series, we focus on an array of unsupervised machine learning methods. We apply multiple unsupervised machine learning algorithms to the first Canadian Hydrogen Intensity Mapping Experiment Fast Radio Burst catalogue to learn their features and classify FRBs into different clusters without any premise about the FRBs being repeaters or non-repeaters. These clusters reveal the differences between repeaters and non-repeaters. Then, by comparing with the identities of the FRBs in the observed classes, we evaluate the performance of various algorithms and analyse the physical meaning behind the results. Finally, we recommend a list of most credible repeater candidates as targets for future observing campaigns to search for repeated bursts in combination of the results presented in Paper I using supervised machine learning methods.
The impact of the AGN and the torus properties on the evolution of spiral galaxies
Authors: Abdulrahman M A , Gadallah K A K , Ahmed A , Elnawawy M S 
Published: December 2022

ABSTRACT
For spiral galaxies, the active galactic nucleus (AGN) and some physical parameters that concern the host galaxy such as spiral arm radius and density can play an important role in the morphological evolution of these galaxies. Considering the gravitational effect of the central black hole as a feeding mechanism, the gas flows from spiral arms to the accretion disk. Accordingly, we constructed our approach and derived an equation for the AGN luminosity that depends on parameters such as the black hole mass and the spiral arm density. The galaxy samples were taken from a catalog of type 1 AGN from SDSS-DR7. In our model, we present the relation between the AGN luminosity and the black hole mass depending on the above physical parameters. We also investigated the relation between the black hole mass and the star formation rate for the galaxy sample. The physical properties of the torus, such as the spiral arm radius, density, the torus length, and the gas mass, and the star formation rate were explained in terms of the variation of the AGN luminosity. These properties are more effective in the evolutionary scenario of the spiral galaxy. Relative to the variation of the AGN luminosity, the evolutionary track is different based quantitatively on the star formation rate. In which the variation in the star formation rate is positively correlated with the AGN luminosity.
Increased expression of the p-STAT3/IL-17 signaling pathway in patients with dermatomyositis
Authors: Li Dongmei , Jia Wen , Zhou Luyao , Hao Yiqun , Wang Kai , Yang Bo , Yang Jie , Luo Dongping , Fu Zili 
Published: December 2022

ABSTRACT

Objectives
The aim is to explore the roles of phosphorylated signal transduction and activator of transcription 3 (p-STAT3) and interleukin (IL)-17 in patients with dermatomyositis (DM).

Methods
A total of 20 DM patients and 12 healthy controls were enrolled. Flow cytometry combined with counting was used to detect the number of Th17 cells. Western blotting and immunohistochemistry were used to examine the muscle levels of p-STAT3 and IL-17, and serum levels of IL-17 were measured by enzyme-linked immunosorbent assays.

Results
Muscle p-STAT3 and IL-17 levels, the number of Th17 cells, and serum IL-17 levels were markedly increased in DM. p-STAT3 and IL-17 were co-expressed in the muscle of DM patients. The p-STAT3 levels were correlated with the number of Th17 cells as well as muscle and serum IL-17 levels. The correlations of the p-STAT3 level with elevated levels of transaminases, myocardial enzymes, and the health assessment questionnaire score were significantly positive, while the correlation with manual muscle testing-8 was significantly negative. A receiver operating characteristic curve indicated the good predictive value of p-STAT3 for the occurrence of DM.

Conclusions
The increased p-STAT3/IL-17 signaling pathway activation in DM patients may induce muscle inflammation and necrosis, and it may be a potential target for DM.
CYCLeR—a novel tool for the full isoform assembly and quantification of circRNAs
Authors: Stefanov Stefan R , Meyer Irmtraud M 
Published: December 2022

Abstract
Splicing is one key mechanism determining the state of any eukaryotic cell. Apart from linear splice variants, circular splice variants (circRNAs) can arise via non-canonical splicing involving a back-splice junction (BSJ). Most existing methods only identify circRNAs via the corresponding BSJ, but do not aim to estimate their full sequence identity or to identify different, alternatively spliced circular isoforms arising from the same BSJ. We here present CYCLeR, the first computational method for identifying the full sequence identity of new and alternatively spliced circRNAs and their abundances while simultaneously co-estimating the abundances of known linear splicing isoforms. We show that CYCLeR significantly outperforms existing methods in terms of F score and quantification of transcripts in simulated data. In a in a comparative study with long-read data, we also show the advantages of CYCLeR compared to existing methods. When analysing Drosophila melanogaster data, CYCLeR uncovers biological patterns of circRNA expression that other methods fail to observe.
Cells with stochastically increased methyltransferase to restriction endonuclease ratio provide an entry for bacteriophage into protected cell population
Authors: Kirillov Alexander , Morozova Natalia , Kozlova Svetlana , Polinovskaya Vasilisa , Smirnov Sergey , Khodorkovskii Mikhail , Zeng Lanying , Ispolatov Yaroslav , Severinov Konstantin 
Published: December 2022

Abstract
The action of Type II restriction–modification (RM) systems depends on restriction endonuclease (REase), which cleaves foreign DNA at specific sites, and methyltransferase (MTase), which protects host genome from restriction by methylating the same sites. We here show that protection from phage infection increases as the copy number of plasmids carrying the Type II RM Esp1396I system is increased. However, since increased plasmid copy number leads to both increased absolute intracellular RM enzyme levels and to a decreased MTase/REase ratio, it is impossible to determine which factor determines resistance/susceptibility to infection. By controlled expression of individual Esp1396I MTase or REase genes in cells carrying the Esp1396I system, we show that a shift in the MTase to REase ratio caused by overproduction of MTase or REase leads, respectively, to decreased or increased protection from infection. Consistently, due to stochastic variation of MTase and REase amount in individual cells, bacterial cells that are productively infected by bacteriophage have significantly higher MTase to REase ratios than cells that ward off the infection. Our results suggest that cells with transiently increased MTase to REase ratio at the time of infection serve as entry points for unmodified phage DNA into protected bacterial populations.
Toehold clipping: A mechanism for remote control of DNA strand displacement
Authors: Faheem Hiba , Mathivanan Johnsi , Talbot Hannah , Zeghal Hana , Vangaveti Sweta , Sheng Jia , Chen Alan A , Chandrasekaran Arun Richard 
Published: December 2022

Abstract
The ability to create stimuli-responsive DNA nanostructures has played a prominent role in dynamic DNA nanotechnology. Primary among these is the process of toehold-based strand displacement, where a nucleic acid molecule can act as a trigger to cause conformational changes in custom-designed DNA nanostructures. Here, we add another layer of control to strand displacement reactions through a 'toehold clipping' process. By designing DNA complexes with a photocleavable linker-containing toehold or an RNA toehold, we show that we can use light (UV) or enzyme (ribonuclease) to eliminate the toehold, thus preventing strand displacement reactions. We use molecular dynamics simulations to analyze the structural effects of incorporating a photocleavable linker in DNA complexes. Beyond simple DNA duplexes, we also demonstrate the toehold clipping process in a model DNA nanostructure, by designing a toehold containing double-bundle DNA tetrahedron that disassembles when an invading strand is added, but stays intact after the toehold clipping process even in the presence of the invading strand. This work is an example of combining multiple physical or molecular stimuli to provide additional remote control over DNA nanostructure reconfiguration, advances that hold potential use in biosensing, drug delivery or molecular computation.
Wondering If I’d Get There Quicker If I Was a Man: Factors Contributing to Delayed Academic Advancement of Women in Infectious Diseases
Authors: Stead Wendy , Manne-Goehler Jennifer , Blackshear Leslie , Marcelin Jasmine R , Salles Arghavan , del Rio Carlos , Krakower Douglas 
Published: December 2022

Abstract

Background
Gender inequities in academic advancement persist in many specialties, including Infectious Diseases (ID). Prior studies of advancement disparities have been predominantly quantitative, utilizing large physician databases or surveys. We used qualitative methods to explore ID physicians’ experiences and beliefs about causes and ways to mitigate gender inequities in advancement.

Methods
We conducted semistructured focus group discussions with academic ID physicians in the United States at IDWeek 2019 to explore perceived barriers and facilitators to academic advancement. Participants were assigned to focus groups based on their academic rank and gender. We analyzed focus group transcripts using content analysis to summarize emergent themes.

Results
We convened 3 women-only focus groups (1 for instructors/assistant professors, 1 for associate professors, and 1 for full professors) and 1 men-only focus group of full professors (total N = 50). Our analyses identified several major themes on barriers to equitable academic advancement, including (1) interpersonal and institutional gender bias, (2) difficulty balancing the demands of family life with work life, and (3) gender differences in negotiation strategies.

Conclusions
Barriers to gender equity in academic advancement are myriad and enduring and span the professional and personal lives of ID physicians. In addition to swift enactment of policy changes directed at critical issues such as ending workplace harassment and ensuring adequate parental leaves for birth and nonbirth parents, leaders in academic medicine must shine a bright light on biases within the system at large and within themselves to correct these disparities with the urgency required.
Early stage of radiological expertise modulates resting-state local coherence in the inferior temporal lobe
Authors: Dong Minghao , Zhang Peiming , Chai Weilu , Zhang Xiaoyan , Chen Bihong T , Wang Hongmei , Wu Jia , Chen Chao , Niu Yi , Liang Jimin , Shi Guangming , Jin Chenwang 
Published: December 2022

AbstractBackgroundThe visual system and its inherent functions undergo experience-dependent changes through the lifespan, enabling acquisition of new skills. Previous fMRI studies using tasks reported increased specialization in a number of cortical regions subserving visual expertise. Although ample studies focused on representation of long-term visual expertise in the brain, i.e. in terms of year, monthly-based early-stage representation of visual expertise remains unstudied. Given that spontaneous neuronal oscillations actively encode previous experience, we propose brain representations in the resting state is fundamentally important.ObjectiveThe current study aimed to investigate how monthly-based early-stage visual expertise are represented in the resting state using the expertise model of radiologists.MethodsIn particular, we investigated the altered local clustering pattern of spontaneous brain activity using regional homogeneity (ReHo). A cohort group of radiology interns (n = 22) after one-month training in X-ray department and matched laypersons (n = 22) were recruited after rigorous behavioral assessment.ResultsThe results showed higher ReHo in the right hippocampus (HIP) and the right ventral anterior temporal lobe (vATL) (corrected by Alphasim correction, P &lt; 0.05). Moreover, ReHo in the right HIP correlated with the number of cases reviewed during intern radiologists’ training (corrected by Alphasim correction, P &lt; 0.05).ConclusionsIn sum, our results demonstrated that the early stage of visual expertise is more concerned with stabilizing visual feature and domain-specific knowledge into long-term memory. The results provided novel evidence regarding how early-stage visual expertise is represented in the resting brain, which help further elaborate how human visual expertise is acquired. We propose that our current study may provide novel ideas for developing new training protocols in medical schools.
WDPhotTools – a white dwarf photometric toolkit in Python
Authors: Lam M C , Yuen K W , Green M J , Li W 
Published: December 2022

Abstract
From data collection to photometric fitting and analysis of white dwarfs, to generating a white dwarf luminosity function requires numerous astrophysical, mathematical, and computational domain knowledge. The steep learning curve makes it difficult to enter the field, and often individuals have to reinvent the wheel to perform identical data reduction and analysis tasks. We have gathered a wide range of publicly available white dwarf cooling models and synthetic photometry to provide a toolkit that allows (i) visualization of various models, (ii) photometric fitting of a white dwarf with or without distance and reddening, and (iii) the computing of white dwarf luminosity functions with a choice of initial mass function, main-sequence evolution model, star-formation history, initial–final mass relation, and white dwarf cooling model. We have recomputed and compared the effective temperature of the white dwarfs from the Gaia EDR3 white dwarf catalogue. The two independent works show excellent agreement in the temperature solutions.
A Method to Explore Variations of Ventilator-Associated Event Surveillance Definitions in Large Critical Care Databases in the United States
Authors: Wong An-Kwok Ian , Kim Han , Charpignon Marie-Laure , Carvalho Leandro , Monares-Zepeda Enrique , Madushani R. W. M. A. , Adhikari Lasith , Kindle Ryan D. , Kutner Michael , Celi Leo Anthony , Lough Mary E. , Mireles-Cabodevila Eduardo 
Published: December 2022

OBJECTIVES:
The Centers for Disease Control has well-established surveillance programs to monitor preventable conditions in patients supported by mechanical ventilation (MV). The aim of the study was to develop a data-driven methodology to examine variations in the first tier of the ventilator-associated event surveillance definition, described as a ventilator-associated condition (VAC). Further, an interactive tool was designed to illustrate the effect of changes to the VAC surveillance definition, by applying different ventilator settings, time-intervals, demographics, and selected clinical criteria.

DESIGN:
Retrospective, multicenter, cross-sectional analysis.

SETTING:
Three hundred forty critical care units across 209 hospitals, comprising 261,910 patients in both the electronic Intensive Care Unit Clinical Research Database and Medical Information Mart for Intensive Care III databases.

PATIENTS:
A total of 14,517 patients undergoing MV for 4 or more days.

MEASUREMENTS AND MAIN RESULTS:
We designed a statistical analysis framework, complemented by a custom interactive data visualization tool to depict how changes to the VAC surveillance definition alter its prognostic performance, comparing patients with and without VAC. This methodology and tool enable comparison of three clinical outcomes (hospital mortality, hospital length-of-stay, and ICU length-of-stay) and provide the option to stratify patients by six criteria in two categories: patient population (dataset and ICU type) and clinical features (minimum Fio
2, minimum positive end-expiratory pressure, early/late VAC, and worst first-day respiratory Sequential Organ Failure Assessment score). Patient population outcomes were depicted by heatmaps with mortality odds ratios. In parallel, outcomes from ventilation setting variations and clinical features were depicted with Kaplan-Meier survival curves.

CONCLUSIONS:
We developed a method to examine VAC using information extracted from large electronic health record databases. Building upon this framework, we developed an interactive tool to visualize and quantify the implications of variations in the VAC surveillance definition in different populations, across time and critical care settings. Data for patients with and without VAC was used to illustrate the effect of the application of this method and visualization tool.
The Spillover Effects of Quality Improvement Beyond Target Populations in Mechanical Ventilation
Authors: Greenwald Andrew S. , Hauw-Berlemont Caroline , Shan Mingxu , Wang Shuang , Yip Natalie , Kurlansky Paul , Argenziano Michael , Bennett Bridgette , Langone Danielle , Moitra Vivek 
Published: December 2022

OBJECTIVES:
To assess the impact of a mechanical ventilation quality improvement program on patients who were excluded from the intervention.

DESIGN:
Before-during-and-after implementation interrupted time series analysis to assess the effect of the intervention between coronary artery bypass grafting (CABG) surgery patients (included) and left-sided valve surgery patients (excluded).

SETTING:
Academic medical center.

PATIENTS:
Patients undergoing CABG and left-sided valve procedures were analyzed.

INTERVENTIONS:
A postoperative mechanical ventilation quality improvement program was developed for patients undergoing CABG.

MEASUREMENTS AND MAIN RESULTS:
Patients undergoing CABG had a median mechanical ventilation time of 11 hours during P0 (“before” phase) and 6.22 hours during P2 (“after” phase; p < 0.001). A spillover effect was observed because mechanical ventilation times also decreased from 10 hours during P0 to 6 hours during P2 among valve patients who were excluded from the protocol (p < 0.001). The interrupted time series analysis demonstrated a significant level of change for ventilation time from P0 to P2 for both CABG (p < 0.0001) and valve patients (p < 0.0001). There was no significant difference in the slope of change between the CABG and valve patient populations across time cohorts (P0 vs P1 [p = 0.8809]; P1 vs P2 [p = 0.3834]; P0 vs P2 [p = 0.7672]), which suggests that the rate of change in mechanical ventilation times was similar between included and excluded patients.

CONCLUSIONS:
Decreased mechanical ventilation times for patients who were not included in a protocol suggests a spillover effect of quality improvement and demonstrates that quality improvement can have benefits beyond a target population.