bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constraining reionization in progress at z = 5.7 with Lyman-α emitters: voids, peaks, and cosmic variance
Authors: Gangolli Nakul , D’Aloisio Anson , Nasir Fahad , Zheng Zheng 
Published: December 2020

ABSTRACT
A number of independent observations suggest that the intergalactic medium was significantly neutral at z = 7 and that reionization was, perhaps, still in progress at z = 5.7. The narrowband survey, SILVERRUSH, has mapped over 2000 Lyman-α emitters (LAEs) at these redshifts ( G58). Previous analyses have assumed that reionization was over by z = 5.7, but this data may actually sample the final stages of reionization when the last neutral islands were relegated to the cosmic voids. Motivated by these developments, we re-examine LAE void and peak statistics and their ability to constrain reionization. We construct models of the LAE distribution in (1 Gpc h−1)3 volumes, spanning a range of neutral fractions at z = 5.7 and 6.6. Models with a higher neutral fraction show an enhanced probability of finding holes in the LAE distribution. When comparing models at fixed mean surface density, however, LAEs obscured by neutral gas in the voids must be compensated by visible LAEs elsewhere. Hence, in these models, the likelihood of finding an overdense peak is also enhanced in the latter half of reionization. Compared to the widely used angular two-point correlation function (2PCF), we find that the void probability function (VPF) provides a more sensitive test of models during the latter half of reionization. By comparison, at neutral fractions $\sim 50{{\ \rm per\ cent}}$, the VPF and a simple peak thresholding statistic are both similar to the 2PCF in constraining power. Lastly, we find that the cosmic variance and large-scale asymmetries observed in the SILVERRUSH fields are consistent with large-scale structure in a ΛCDM universe.
The evolution of the low-density H i intergalactic medium from z = 3.6 to 0: data, transmitted flux, and H i column density,,
Authors: Kim T-S , Wakker B P , Nasir F , Carswell R F , Savage B D , Bolton J S , Fox A J , Viel M , Haehnelt M G , Charlton J C , Rosenwasser B E 
Published: December 2020

ABSTRACT
We present a new, uniform analysis of the H i transmitted flux (F) and H i column density ($N_{\mathrm{H\,{\small I}}}$) distribution in the low-density IGM as a function of redshift z for 0 &lt; z &lt; 3.6 using 55 HST/COS FUV (Δz = 7.2 at z &lt; 0.5), five HST/STIS + COS NUV (Δz = 1.3 at z ∼ 1) and 24 VLT/UVES, and Keck/HIRES (Δz = 11.6 at 1.7 &lt; z &lt; 3.6) AGN spectra. We performed a consistent, uniform Voigt profile analysis to combine spectra taken with different instruments, to reduce systematics and to remove metal-line contamination. We confirm previously known conclusions on firmer quantitative grounds in particular by improving the measurements at z ∼ 1. Two flux statistics at 0 &lt; F &lt; 1, the mean H i flux and the flux probability distribution function (PDF), show that considerable evolution occurs from z = 3.6 to z = 1.5, after which it slows down to become effectively stable for z &lt; 0.5. However, there are large sightline variations. For the H i column density distribution function (CDDF, f ∝ $N_{\rm H\,{\small I}}^{-\beta }$) at $\log (N_{\mathrm{H\,{\small I}}}/1\, {\mathrm{cm}^{-2}})$ ∈ [13.5, 16.0], β increases as z decreases from β = 1.60 at z ∼ 3.4 to β = 1.82 at z ∼ 0.1. The CDDF shape at lower redshifts can be reproduced by a small amount of clockwise rotation of a higher-z CDDF with a slightly larger CDDF normalization. The absorption line number per z (dn/dz) shows a similar evolutionary break at z ∼ 1.5 as seen in the flux statistics. High-$N_{\mathrm{H\,{\small I}}}$ absorbers evolve more rapidly than low-$N_{\mathrm{H\,{\small I}}}$ absorbers to decrease in number or cross-section with time. The individual dn/dz shows a large scatter at a given z. The scatter increases towards lower z, possibly caused by a stronger clustering at lower z.
Tilt angle and lifetime of sunspot groups
Authors: Nagovitsyn Yury A , Osipova Aleksandra A , Pevtsov Alexei A 
Published: December 2020

ABSTRACT
We use the Catalogue of Solar Activity (CSA) to study the latitudinal variations of tilt of solar active regions. The tilt angles β are computed taking into account changes of the heliographic grid with latitude φ. We show that when sunspot groups of different sizes and lifetimes are included, a classical representation of the Joy’s law as a linear function of latitude (β ∝ φ) is only the first approximation valid within a limited range of latitudes (−25° ≤ φ ≤ +25°). Outside this range, the functional dependence β = f(φ) becomes non-linear. Separating the data set on large long-living groups (LLG) and small short-living groups (SSG) reveals two quite different dependencies in β = f(φ): non-linearity in tilt is only present in LLGs and the steepness of linear section of β = f(φ) fit is higher for LLGs. This suggests a difference in the physical properties of two populations of solar groups, which could be hypothesized as an indication of different localization of subsurface zones of their formation in the framework of a distributed dynamo. However, since CSA contains the coordinates of sunspots averaged over the lifetime (or disc passage) of each group, one cannot rule out that the difference in tilts of SSG and LLG groups may be affected by the evolution of tilt angles during the lifetime/disc passage of the groups.
Regulatory protein genes and microRNAs in response to selenium stimuli in Pueraria lobata (Willd.) Ohwi
Authors: Li Yanni , He Meijun , Li Jishuang , Yao Yiwei , Zhu Li , Wu Bin 
Published: December 2020

Abstract
Regulatory protein genes and microRNAs (miRNAs) play important roles in response to abiotic and biotic stress, and the biosynthesis of secondary metabolites in plants. However, their responses to selenium (Se) stimuli have not been comprehensively studied in Pueraria lobata (Willd.) Ohwi, a selenocompound-rich medicinal and edible plant. In this study, we identified a total of 436/556/1161/624 transcription factors, 134/157/308/172 transcriptional regulators, and 341/456/250/518 protein kinases, which were co-expressed with at least one selenocompound-related structural gene/sulfate transporter or phosphate transporter/reactive oxygen species (ROS) scavenging structural gene/isoflavone-related structural gene, respectively. Then, we identified a total of 87 expressed miRNAs by Se disposure, in which 11 miRNAs, including miR171f-3p, miR390b-3P, miR-N111b, miR-N118, miR-N30, miR-N38-3P, miR-N61a, miR-N61b, miR-N80-3p, miR-N84-3P, and miR-N90.2-3P, were significantly upregulated. We also identified a total of 1172 target genes for the 87 expressed miRNAs. Gene Ontology enrichment analysis of these target genes showed that regulation of transcription, DNA-templated, integral component of membrane, nucleus, ATP binding, and plasma membrane are the top five subclassifications. Finally, we revealed that 5 miRNAs targeted 10 regulatory protein genes, which are highly correlated with at least one selenocompound-related structural gene or transporter gene; 5 miRNAs targeted 10 regulatory protein genes, which are highly correlated with at least one ROS scavenging structural gene; and 5 miRNAs targeted 9 regulatory protein genes, which are potentially involved in the isoflavone biosynthesis. Overall, the study provides us the comprehensive insight into the roles of regulatory proteins and miRNAs in response to Se stimuli in P. lobata.
Single-molecule visualization of human RECQ5 interactions with single-stranded DNA recombination intermediates
Authors: Xue Chaoyou , Molnarova Lucia , Steinfeld Justin B , Zhao Weixing , Ma Chujian , Spirek Mario , Kaniecki Kyle , Kwon Youngho , Beláň Ondrej , Krejci Katerina , Boulton Simon J , Sung Patrick , Greene Eric C , Krejci Lumir 
Published: December 2020

Abstract
RECQ5 is one of five RecQ helicases found in humans and is thought to participate in homologous DNA recombination by acting as a negative regulator of the recombinase protein RAD51. Here, we use kinetic and single molecule imaging methods to monitor RECQ5 behavior on various nucleoprotein complexes. Our data demonstrate that RECQ5 can act as an ATP-dependent single-stranded DNA (ssDNA) motor protein and can translocate on ssDNA that is bound by replication protein A (RPA). RECQ5 can also translocate on RAD51-coated ssDNA and readily dismantles RAD51–ssDNA filaments. RECQ5 interacts with RAD51 through protein–protein contacts, and disruption of this interface through a RECQ5–F666A mutation reduces translocation velocity by ∼50%. However, RECQ5 readily removes the ATP hydrolysis-deficient mutant RAD51–K133R from ssDNA, suggesting that filament disruption is not coupled to the RAD51 ATP hydrolysis cycle. RECQ5 also readily removes RAD51–I287T, a RAD51 mutant with enhanced ssDNA-binding activity, from ssDNA. Surprisingly, RECQ5 can bind to double-stranded DNA (dsDNA), but it is unable to translocate. Similarly, RECQ5 cannot dismantle RAD51-bound heteroduplex joint molecules. Our results suggest that the roles of RECQ5 in genome maintenance may be regulated in part at the level of substrate specificity.
The mTOR regulated RNA-binding protein LARP1 requires PABPC1 for guided mRNA interaction
Authors: Smith Ewan M , Benbahouche Nour El Houda , Morris Katherine , Wilczynska Ania , Gillen Sarah , Schmidt Tobias , Meijer Hedda A , Jukes-Jones Rebekah , Cain Kelvin , Jones Carolyn , Stoneley Mark , Waldron Joseph A , Bell Cameron , Fonseca Bruno D , Blagden Sarah , Willis Anne E , Bushell Martin 
Published: December 2020

AbstractThe mammalian target of rapamycin (mTOR) is a critical regulator of cell growth, integrating multiple signalling cues and pathways. Key among the downstream activities of mTOR is the control of the protein synthesis machinery. This is achieved, in part, via the co-ordinated regulation of mRNAs that contain a terminal oligopyrimidine tract (TOP) at their 5′ends, although the mechanisms by which this occurs downstream of mTOR signalling are still unclear. We used RNA-binding protein (RBP) capture to identify changes in the protein-RNA interaction landscape following mTOR inhibition. Upon mTOR inhibition, the binding of LARP1 to a number of mRNAs, including TOP-containing mRNAs, increased. Importantly, non-TOP-containing mRNAs bound by LARP1 are in a translationally-repressed state, even under control conditions. The mRNA interactome of the LARP1-associated protein PABPC1 was found to have a high degree of overlap with that of LARP1 and our data show that PABPC1 is required for the association of LARP1 with its specific mRNA targets. Finally, we demonstrate that mRNAs, including those encoding proteins critical for cell growth and survival, are translationally repressed when bound by both LARP1 and PABPC1.
The fission yeast Pin1 peptidyl-prolyl isomerase promotes dissociation of Sty1 MAPK from RNA polymerase II and recruits Ssu72 phosphatase to facilitate oxidative stress induced transcription
Authors: Wang Yi-Ting , Hsiao Wan-Yi , Wang Shao-Win 
Published: December 2020

AbstractPin1 is a peptidyl-prolyl isomerase that regulates the structure and function of eukaryotic RNA polymerase II (Pol II) through interaction with the C-terminal domain (CTD) of Rpb1, the largest subunit of Pol II. We demonstrated that this function is important for cellular response to oxidative stress in the fission yeast Schizosaccharomyces pombe. In response to oxidative stress, the Atf1 transcription factor targets Sty1, the mitogen-activated protein kinase (MAPK), to specific stress-responsive promoters. Anchored Sty1 recruits Pol II through direct association with Rpb1-CTD and phosphorylates the reiterated heptad sequence at Serine 5. Pin1 binds phosphorylated CTD to promote dissociation of Sty1 from it, and directly recruits Ssu72 phosphatase to facilitate dephosphorylation of CTD for transcription elongation. In the absence of Pin1, the association of Sty1-Atf1 with Rpb1 persists on stress-responsive promoters failed to generate transcripts of the corresponding genes effectively. The identified characteristic features of the fission yeast Pin1 are conserved in humans. We demonstrated that elevated Pin1 level in cancer cells might help to sustain survival under oxidative stress generated from their altered metabolic pathways. Together, these results suggest a conserved function of Pin1 in cellular response to oxidative stress among eukaryotic cells that might have clinical implication.
Tumor cell network integration in glioma represents a stemness feature
Authors: Xie Ruifan , Kessler Tobias , Grosch Julia , Hai Ling , Venkataramani Varun , Huang Lulu , Hoffmann Dirk C , Solecki Gergely , Ratliff Miriam , Schlesner Matthias , Wick Wolfgang , Winkler Frank 
Published: December 2020

Abstract

Background
Malignant gliomas including glioblastomas are characterized by a striking cellular heterogeneity, which includes a subpopulation of glioma cells that becomes highly resistant by integration into tumor microtube (TM)-connected multicellular networks.

Methods
A novel functional approach to detect, isolate, and characterize glioma cell subpopulations with respect to in vivo network integration is established, combining a dye staining method with intravital two-photon microscopy, Fluorescence-Activated Cell Sorting (FACS), molecular profiling, and gene reporter studies.

Results
Glioblastoma cells that are part of the TM-connected tumor network show activated neurodevelopmental and glioma progression gene expression pathways. Importantly, many of them revealed profiles indicative of increased cellular stemness, including high expression of nestin. TM-connected glioblastoma cells also had a higher potential for reinitiation of brain tumor growth. Long-term tracking of tumor cell nestin expression in vivo revealed a stronger TM network integration and higher radioresistance of the nestin-high subpopulation. Glioblastoma cells that were both nestin-high and network-integrated were particularly able to adapt to radiotherapy with increased TM formation.

Conclusion
Multiple stem-like features are strongly enriched in a fraction of network-integrated glioma cells, explaining their particular resilience.
Global blue carbon accumulation in tidal wetlands increases with climate change
Authors: Wang Faming , Sanders Christian J , Santos Isaac R , Tang Jianwu , Schuerch Mark , Kirwan Matthew L , Kopp Robert E , Zhu Kai , Li Xiuzhen , Yuan Jiacan , Liu Wenzhi , Li Zhi'an 
Published: December 2020

Abstract
Coastal tidal wetlands produce and accumulate significant amounts of organic carbon (C) that help to mitigate climate change. However, previous data limitations have prevented a robust evaluation of the global rates and mechanisms driving C accumulation. Here, we go beyond recent soil C stock estimates to reveal global tidal wetland C accumulation and predict changes under relative sea level rise, temperature and precipitation. We use data from literature study sites and our new observations spanning wide latitudinal gradients and 20 countries. Globally, tidal wetlands accumulate 53.65 (95%CI: 48.52–59.01) Tg C yr−1, which is ∼30% of the organic C buried on the ocean floor. Modeling based on current climatic drivers and under projected emissions scenarios revealed a net increase in the global C accumulation by 2100. This rapid increase is driven by sea level rise in tidal marshes, and higher temperature and precipitation in mangroves. Countries with large areas of coastal wetlands, like Indonesia and Mexico, are more susceptible to tidal wetland C losses under climate change, while regions such as Australia, Brazil, the USA and China will experience a significant C accumulation increase under all projected scenarios.
High-velocity impact of a hybrid CBN nanotubes
Authors: Armani Enzo , Autreto Pedro A S 
Published: December 2020

Abstract
Nanomaterials under extreme conditions can behave in a completely different manner. High-velocity impact, for example, can produce nanoribbons without any chemical approach via carbon or boron nitride nanotubes unzipping. Although hybrid nanostructures have been used to create stronger structures, few studies on these materials under extreme conditions have been employed. In this work, we studied, using fully atomistic reactive molecular dynamics simulations an experimentally synthesized hybrid nanotube (boron nitride and carbon nanotubes concentrically assembled) under the high-velocity impact. Our results show that the combination of elastic and brittle materials can produce different structures, such as nanoribbons and boron nitride atomic chains. These results can have a significant impact on the production of new nanostructures.
Collateral Runs
Authors: Infante Sebastian , Vardoulakis Alexandros P 
Published: December 2020

Abstract
This paper models an unexplored source of liquidity risk large broker-dealers face: a withdrawal of collateral providers. By setting different contracting terms on repurchase agreements with cash borrowers and lenders, dealers can source funds for their own activities. Cash borrowers internalize the risk of losing their collateral in case their dealer defaults, prompting them to withdraw it. This incentive creates strategic complementarities among collateral providers, reducing a dealer’s liquidity position and compromising their solvency. Collateral runs are triggered by a contraction in dealers’ assets making them markedly different than traditional wholesale funding runs. Mitigating these risks involves different policy recommendations.
Incidence and severeness of COVID-19 hospitalization in patients with inflammatory rheumatic disease: a nationwide cohort study from Denmark
Authors: Cordtz René , Lindhardsen Jesper , Soussi Bolette G , Vela Jonathan , Uhrenholt Line , Westermann Rasmus , Kristensen Salome , Nielsen Henrik , Torp-Pedersen Christian , Dreyer Lene 
Published: December 2020

Abstract

Objectives
To estimate the incidence of COVID-19 hospitalization in patients with inflammatory rheumatic disease (IRD); in patients with RA treated with specific DMARDs; and the incidence of severe COVID-19 infection among hospitalized patients with RA.

Methods
A nationwide cohort study from Denmark between 1 March and 12 August 2020. The adjusted incidence of COVID-19 hospitalization was estimated for patients with RA; spondyloarthritis including psoriatic arthritis; connective tissue disease; vasculitides; and non-IRD individuals. Further, the incidence of COVID-19 hospitalization was estimated for patients with RA treated and non-treated with TNF-inhibitors, HCQ or glucocorticoids, respectively. Lastly, the incidence of severe COVID-19 infection (intensive care, acute respiratory distress syndrome or death) among hospital-admitted patients was estimated for RA and non-IRD sp - individudals.

Results
Patients with IRD (n = 58 052) had an increased partially adjusted incidence of hospitalization with COVID-19 compared with the 4.5 million people in the general population [hazard ratio (HR) 1.46, 95% CI: 1.15, 1.86] with strongest associations for patients with RA (n = 29 440, HR 1.72, 95% CI: 1.29, 2.30) and vasculitides (n = 4072, HR 1.82, 95% CI: 0.91, 3.64). There was no increased incidence of COVID-19 hospitalization associated with TNF-inhibitor, HCQ nor glucocorticoid use. COVID-19 admitted patients with RA had a HR of 1.43 (95% CI: 0.80, 2.53) for a severe outcome.

Conclusion
Patients with IRD were more likely to be admitted with COVID-19 than the general population, and COVID-19 admitted patients with RA could be at higher risk of a severe outcome. Treatment with specific DMARDs did not affect the risk of hospitalization.
Adult-onset Still’s disease with neurological involvement: a single-centre report
Authors: Zhao Mengzhu , Wu Di , Shen Min 
Published: December 2020

Abstract

Objectives
Adult-onset Still’s disease (AOSD) is a multifactorial systemic autoinflammatory disease. Neurological damage has been rarely reported in AOSD. We aimed to characterize the clinical features of AOSD patients with neurological involvement.

Methods
A total of 187 AOSD patients were admitted to Peking Union Medical College Hospital from January 2015 to August 2019. The complete medical records were reviewed in this retrospective study. Clinical features of 14 AOSD patients with neurological involvement were collected and compared with those without.

Results
The prevalence of neurological involvement in AOSD inpatients was 7.5%. The median disease duration was 4.5 months, with a range of 1–15 months. The frequent symptoms were fever [14 (100%)], rash [13 (92.9%)], liver dysfunction [11 (78.6%)], arthralgia/arthritis [10 (71.4%)] and lymphadenopathy [10 (71.4%)]. Four (28.6%) patients had macrophage activation syndrome (MAS). Aseptic meningitis was the most common presentation (64.3%) when the nervous system was involved. Other rare manifestations included cranial nerve palsy, encephalitis and cerebral infarction. The rate of MAS, serum levels of lactate dehydrogenase and ferritin were significantly higher in AOSD patients with neurological involvement than in those without. All patients received high-dose corticosteroid therapy and immunosuppressive agents and two were given tocilizumab. Clinical remission was achieved in all 14 AOSD patients with neurological involvement.

Conclusion
Neurological involvement, particularly aseptic meningitis, is not a rare complication of AOSD. It is frequently complicated by MAS. There may be a potential relationship between the neurological damage of AOSD and MAS.
Barriers and facilitators to the implementation of a novel web-based sleep apnea management platform
Authors: Chang Yoon Hee A , Folmer Robert L , Shasha Becky , Shea Judy A , Sarmiento Kathleen , Stepnowsky Carl J , Lim Diane , Pack Allan , Kuna Samuel T 
Published: December 2020

Abstract

Study Objective
Obstructive sleep apnea (OSA) is a highly prevalent yet underdiagnosed disorder affecting US military Veterans. The Remote Veterans Apnea Management Platform (REVAMP) is a web-based OSA management program created to improve access to care. REVAMP was launched within the Veterans Health Administration (VHA) in July 2017, with variable patient recruitment rates (from 0 to 573 patients per site) at the first 10 Veterans Affairs (VA) medical centers (Wave-1 sites). This study aimed to examine the contextual circumstances surrounding the implementation of REVAMP from the provider perspective to inform strategies to increase its uptake at future rollout sites.

Methods
A purposive sample of REVAMP site leaders from the Wave-1 sites was recruited with additional staff members being solicited as well. Semi-structured interviews were conducted. Two independent coders reviewed individual transcripts using content analysis to identify emerging themes.

Results
Fifteen individuals from Wave-1 sites were interviewed. Implementation of REVAMP was facilitated by the presence of leadership support, staff, and time dedicated to REVAMP, and perceived usefulness of REVAMP by staff as well as positive feedback from the Veterans using REVAMP. The difficulty of supporting Veteran creation of login credentials to the program and integrating REVAMP into the existing workflow were major barriers to its implementation.

Conclusion
Improving leadership engagement, simplifying the enrollment process, and enhancing the medical staff experience through shared best practice alerts were identified as actions needed to improve the penetration of REVAMP at future rollout sites.