bluuebunny/crossref_metadata_2025_split huggingface dataset:
NRT1.1-centered nitrate signaling in plants
Authors: Maghiaoui Amel , Gojon Alain , Bach Liên 
Published: August 2020

Abstract
Plants need efficient nitrate (NO3–) sensing systems and sophisticated signaling pathways to develop a wide range of adaptive responses to external fluctuations of NO3– supply. In Arabidopsis thaliana, numerous molecular regulators have been identified to participate in signaling pathways that respond specifically to NO3–. In contrast, only a single NO3– sensing system has been described to date, relying on the NRT1.1 (NPF6.3/CHL1) NO3– transceptor. NRT1.1 governs a wide range of responses to NO3–, from fast reprogramming of genome expression (the primary nitrate response) to longer-term developmental changes (effects on lateral root development). NRT1.1 appears to be at the center of a complex network of signaling pathways, involving numerous molecular players acting downstream and/or upstream of it. Interestingly, some of these regulators are involved in crosstalk with the signaling pathways of other nutrients, such as inorganic phosphate or potassium. Although NRT1.1-mediated NO3– sensing and signaling has mostly been documented in Arabidopsis, recent evidence indicates that similar mechanisms involving NRT1.1 orthologues are operative in rice. This review aims to delineate how the NRT1.1 sensing system and the downstream/upstream transduction cascades are integrated to control both the expression of NO3–-responsive genes and the induced plasticity of root development.
The SEDIGISM survey: First Data Release and overview of the Galactic structure
Authors: Schuller F , Urquhart J S , Csengeri T , Colombo D , Duarte-Cabral A , Mattern M , Ginsburg A , Pettitt A R , Wyrowski F , Anderson L , Azagra F , Barnes P , Beltran M , Beuther H , Billington S , Bronfman L , Cesaroni R , Dobbs C , Eden D , Lee M-Y , Medina S-N X , Menten K M , Moore T , Montenegro-Montes F M , Ragan S , Rigby A , Riener M , Russeil D , Schisano E , Sanchez-Monge A , Traficante A , Zavagno A , Agurto C , Bontemps S , Finger R , Giannetti A , Gonzalez E , Hernandez A K , Henning T , Kainulainen J , Kauffmann J , Leurini S , Lopez S , Mac-Auliffe F , Mazumdar P , Molinari S , Motte F , Muller E , Nguyen-Luong Q , Parra R , Perez-Beaupuits J-P , Schilke P , Schneider N , Suri S , Testi L , Torstensson K , Veena V S , Venegas P , Wang K , Wienen M 
Published: August 2020

ABSTRACT
The SEDIGISM (Structure, Excitation and Dynamics of the Inner Galactic Interstellar Medium) survey used the APEX telescope to map 84 deg2 of the Galactic plane between ℓ = −60° and +31° in several molecular transitions, including 13CO (2 – 1) and C18O (2 – 1), thus probing the moderately dense (∼103 cm−3) component of the interstellar medium. With an angular resolution of 30 arcsec and a typical 1σ sensitivity of 0.8–1.0 K at 0.25 km s−1 velocity resolution, it gives access to a wide range of structures, from individual star-forming clumps to giant molecular clouds and complexes. The coverage includes a good fraction of the first and fourth Galactic quadrants, allowing us to constrain the large-scale distribution of cold molecular gas in the inner Galaxy. In this paper, we provide an updated overview of the full survey and the data reduction procedures used. We also assess the quality of these data and describe the data products that are being made publicly available as part of this First Data Release (DR1). We present integrated maps and position–velocity maps of the molecular gas and use these to investigate the correlation between the molecular gas and the large-scale structural features of the Milky Way such as the spiral arms, Galactic bar and Galactic Centre. We find that approximately 60 per cent of the molecular gas is associated with the spiral arms and these appear as strong intensity peaks in the derived Galactocentric distribution. We also find strong peaks in intensity at specific longitudes that correspond to the Galactic Centre and well-known star-forming complexes, revealing that the 13CO emission is concentrated in a small number of complexes rather than evenly distributed along spiral arms.
Chemical evolution of the Milky Way: constraints on the formation of the thick and thin discs
Authors: Palla M , Matteucci F , Spitoni E , Vincenzo F , Grisoni V 
Published: August 2020

ABSTRACT
We study the evolution of Milky Way thick and thin discs in the light of the most recent observational data. In particular, we analyse abundance gradients of O, N, Fe, and Mg along the thin disc as well as the [Mg/Fe] versus [Fe/H] relations and the metallicity distribution functions at different Galactocentric distances. We run several models starting from the two-infall paradigm, assuming that the thick and thin discs formed by means of two different infall episodes, and we explore several physical parameters, such as radial gas flows, variable efficiency of star formation, different times for the maximum infall on to the disc, different distributions of the total surface mass density of the thick disc, and enriched gas infall. Our best model suggests that radial gas flows and variable efficiency of star formation should be acting together with the inside-out mechanism for the thin disc formation. The time-scale for maximum infall on to the thin disc, which determines the gap between the formation of the two discs, should be tmax ≃ 3.25 Gyr. The thick disc should have an exponential, small-scale length density profile and gas infall on the inner thin disc should be enriched. We also compute the evolution of Gaia–Enceladus system and study the effects of possible interactions with the thick and thin discs. We conclude that the gas lost by Enceladus or even part of it could have been responsible for the formation of the thick disc but not the thin disc.
The host galaxies of 106 rapidly evolving transients discovered by the Dark Energy Survey
Authors: Wiseman P , Pursiainen M , Childress M , Swann E , Smith M , Galbany L , Lidman C , Davis T M , Gutiérrez C P , Möller A , Thomas B P , Frohmaier C , Foley R J , Hinton S R , Kelsey L , Kessler R , Lewis G F , Sako M , Scolnic D , Sullivan M , Vincenzi M , Abbott T M C , Aguena M , Allam S , Annis J , Bertin E , Bhargava S , Brooks D , Burke D L , Carnero Rosell A , Carollo D , Carrasco Kind M , Carretero J , Costanzi M , da Costa L N , Diehl H T , Doel P , Everett S , Fosalba P , Frieman J , García-Bellido J , Gaztanaga E , Glazebrook K , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hollowood D L , Honscheid K , James D J , Kuehn K , Kuropatkin N , Lima M , Maia M A G , Marshall J L , Martini P , Menanteau F , Miquel R , Palmese A , Paz-Chinchón F , Plazas A A , Romer A K , Sanchez E , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Sommer N E , Suchyta E , Swanson M E C , Tarle G , Tucker B E , Tucker D L , Varga T N , Walker A R ,   (DES Collaboration)
Published: August 2020

ABSTRACT
Rapidly evolving transients (RETs), also termed fast blue optical transients, are a recently discovered group of astrophysical events that display rapid luminosity evolution. RETs typically rise to peak in less than 10 d and fade within 30, a time-scale unlikely to be compatible with the decay of Nickel-56 that drives conventional supernovae (SNe). Their peak luminosity spans a range of −15 &lt; Mg &lt; −22.5, with some events observed at redshifts greater than 1. Their evolution on fast time-scales has hindered high-quality follow-up observations, and thus their origin and explosion/emission mechanism remains unexplained. In this paper, we present the largest sample of RETs to date, comprising 106 objects discovered by the Dark Energy Survey, and perform the most comprehensive analysis of RET host galaxies. Using deep-stacked photometry and emission lines from OzDES spectroscopy, we derive stellar masses and star formation rates (SFRs) for 49 host galaxies, and metallicities ([O/H]) for 37. We find that RETs explode exclusively in star-forming galaxies and are thus likely associated with massive stars. Comparing RET hosts to samples of host galaxies of other explosive transients as well as field galaxies, we find that RETs prefer galaxies with high specific SFRs (〈log (sSFR)〉 ∼ −9.6), indicating a link to young stellar populations, similar to stripped-envelope SNe. RET hosts appear to show a lack of chemical enrichment, their metallicities akin to long-duration gamma-ray bursts and superluminous SN host galaxies (〈12 + log (O/H)〉 ∼ 9.4). There are no clear relationships between mass or SFR of the host galaxies and the peak magnitudes or decline rates of the transients themselves.
A census of ultraluminous X-ray sources in the local Universe
Authors: Kovlakas K , Zezas A , Andrews J J , Basu-Zych A , Fragos T , Hornschemeier A , Lehmer B , Ptak A 
Published: August 2020

ABSTRACTUsing the Chandra Source Catalog 2.0 and a newly compiled catalogue of galaxies in the local Universe, we deliver a census of ultraluminous X-ray source (ULX) populations in nearby galaxies. We find 629 ULX candidates in 309 galaxies with distance smaller than 40 Mpc. The foreground/background contamination is $\sim \! 20{{\ \rm per\ cent}}$. The ULX populations in bona fide star-forming galaxies scale on average with star formation rate and stellar mass (M⋆) such that the number of ULXs per galaxy is $0.45^{+0.06}_{-0.09}\times \frac{\rm SFR}{\rm M_\odot \, yr^{-1}}{+}3.3^{+3.8}_{-3.2}\times \frac{M_\star }{\rm M_\odot }$. The scaling depends strongly on the morphological type. This analysis shows that early spiral galaxies contain an additional population of ULXs that scales with M⋆. We also confirm the strong anticorrelation of the ULX rate with the host galaxy’s metallicity. In the case of early-type galaxies, we find that there is a non-linear dependence of the number of ULXs with M⋆, which is interpreted as the result of star formation history differences. Taking into account age and metallicity effects, we find that the predictions from X-ray binary population synthesis models are consistent with the observed ULX rates in early-type galaxies, as well as spiral/irregular galaxies.
Limitation of symmetry breaking by gravitational collapse: the revisit of Lin–Mestel–Shu instability
Authors: Worrakitpoonpon Tirawut 
Published: August 2020

ABSTRACT
We revisit the topic of shape evolution during the spherical collapse of an N-body system. Our main objective is to investigate the critical particle number below which, during a gravitational collapse, the amplification of triaxiality from initial fluctuations is effective, and above which it is ineffective. To this aim, we develop the Lin–Mestel–Shu theory for a system of particles initially with isotropic velocity dispersion and with a simple power-law density profile. We first determine, for an unstable cloud, two radii corresponding to the balance of two opposing forces and their fluctuations: such radii fix the sizes of the non-collapsing region and the triaxial seed from density fluctuations. We hypothesize that the triaxial degree of the final state depends on which radius is dominant prior to the collapse phase leading to a different scheme of the self-consistent shape evolution of the core and the rest of the system. The condition where the two radii are equal therefore identifies the critical particle number, which can be expressed as the function of the parameters of initial state. In numerical work, we can pinpoint such a critical number by comparing the virialized flattening with the initial flattening. The difference between these two quantities agrees with the theoretical predictions only for the power-law density profiles with an exponent in the range [0, 0.25]. For higher exponents, results suggest that the critical number is above the range of simulated N. We speculate that there is an additional mechanism, related to strong density gradients that increases further the flattening, requiring higher N to further weaken the initial fluctuations.
Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions
Authors: Hu Gongcheng , Dong Xiaotao , Gong Shixin , Song Yawei , Hutchins Andrew P , Yao Hongjie 
Published: August 2020

Abstract
CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators by co-localization analysis with CTCF. We screened all factors that had ChIP-seq data in humans by co-localization analysis with human super conserved CTCF (hscCTCF) binding sites, and identified many new factors that overlapped with hscCTCF binding sites. Combined with CTCF loop information, we observed that clustered factors could promote CTCF loops. After in-depth mining of each factor, we found that many factors might have the potential to promote CTCF loops. Our data further demonstrated that BHLHE40 affected CTCF loops by regulating CTCF binding. Together, this study revealed that many factors have the potential to participate in or regulate CTCF loops, and discovered a new role for BHLHE40 in modulating CTCF loop formation.
Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB
Authors: Lin Jianan , Chen Yang , Zhang Yuping , Ouyang Zhengqing 
Published: August 2020

AbstractRNA conformational alteration has significant impacts on cellular processes and phenotypic variations. An emerging genetic factor of RNA conformational alteration is a new class of single nucleotide variant (SNV) named riboSNitch. RiboSNitches have been demonstrated to be involved in many genetic diseases. However, identifying riboSNitches is notably difficult as the signals of RNA structural disruption are often subtle. Here, we introduce a novel computational framework–RIboSNitch Predictor based on Robust Analysis of Pairing probabilities (Riprap). Riprap identifies structurally disrupted regions around any given SNVs based on robust analysis of local structural configurations between wild-type and mutant RNA sequences. Compared to previous approaches, Riprap shows higher accuracy when assessed on hundreds of known riboSNitches captured by various experimental RNA structure probing methods including the parallel analysis of RNA structure (PARS) and the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). Further, Riprap detects the experimentally validated riboSNitch that regulates human catechol-O-methyltransferase haplotypes and outputs structurally disrupted regions precisely at base resolution. Riprap provides a new approach to interpreting disease-related genetic variants. In addition, we construct a database (RiboSNitchDB) that includes the annotation and visualization of all presented riboSNitches in this study as well as 24 629 predicted riboSNitches from human expression quantitative trait loci.
Experimental and computational technologies to dissect the kidney at the single-cell level
Authors: Kuppe Christoph , Perales-Patón Javier , Saez-Rodriguez Julio , Kramann Rafael 
Published: August 2020

Abstract
The field of single-cell technologies, in particular single-cell genomics with transcriptomics and epigenomics, and most recently single-cell proteomics, is rapidly growing and holds promise to advance our understanding of organ homoeostasis and disease, and facilitate the identification of novel therapeutic targets and biomarkers. This review offers an introduction to these technologies. In addition, as the size and complexity of the data require sophisticated computational methods for analysis and interpretation, we will also provide an overview of these methods and summarize the single-cell literature specifically pertaining to the kidney.
A novel fully automated MRI-based deep-learning method for classification of 1p/19q co-deletion status in brain gliomas
Authors: Yogananda Chandan Ganesh Bangalore , Shah Bhavya R , Yu Frank F , Pinho Marco C , Nalawade Sahil S , Murugesan Gowtham K , Wagner Benjamin C , Mickey Bruce , Patel Toral R , Fei Baowei , Madhuranthakam Ananth J , Maldjian Joseph A 
Published: August 2020

Abstract

Background
One of the most important recent discoveries in brain glioma biology has been the identification of the isocitrate dehydrogenase (IDH) mutation and 1p/19q co-deletion status as markers for therapy and prognosis. 1p/19q co-deletion is the defining genomic marker for oligodendrogliomas and confers a better prognosis and treatment response than gliomas without it. Our group has previously developed a highly accurate deep-learning network for determining IDH mutation status using T2-weighted (T2w) MRI only. The purpose of this study was to develop a similar 1p/19q deep-learning classification network.

Methods
Multiparametric brain MRI and corresponding genomic information were obtained for 368 subjects from The Cancer Imaging Archive and The Cancer Genome Atlas. 1p/19 co-deletions were present in 130 subjects. Two-hundred and thirty-eight subjects were non-co-deleted. A T2w image-only network (1p/19q-net) was developed to perform 1p/19q co-deletion status classification and simultaneous single-label tumor segmentation using 3D-Dense-UNets. Three-fold cross-validation was performed to generalize the network performance. Receiver operating characteristic analysis was also performed. Dice scores were computed to determine tumor segmentation accuracy.

Results
1p/19q-net demonstrated a mean cross-validation accuracy of 93.46% across the 3 folds (93.4%, 94.35%, and 92.62%, SD = 0.8) in predicting 1p/19q co-deletion status with a sensitivity and specificity of 0.90 ± 0.003 and 0.95 ± 0.01, respectively and a mean area under the curve of 0.95 ± 0.01. The whole tumor segmentation mean Dice score was 0.80 ± 0.007.

Conclusion
We demonstrate high 1p/19q co-deletion classification accuracy using only T2w MR images. This represents an important milestone toward using MRI to predict glioma histology, prognosis, and response to treatment.
Hierarchically structured porous materials: synthesis strategies and applications in energy storage
Authors: Wu Liang , Li Yu , Fu Zhengyi , Su Bao-Lian 
Published: August 2020

AbstractTo address the growing energy demands of sustainable development, it is crucial to develop new materials that can improve the efficiency of energy storage systems. Hierarchically structured porous materials have shown their great potential for energy storage applications owing to their large accessible space, high surface area, low density, excellent accommodation capability with volume and thermal variation, variable chemical compositions and well controlled and interconnected hierarchical porosity at different length scales. Porous hierarchy benefits electron and ion transport, and mass diffusion and exchange. The electrochemical behavior of hierarchically structured porous materials varies with different pore parameters. Understanding their relationship can lead to the defined and accurate design of highly efficient hierarchically structured porous materials to enhance further their energy storage performance. In this review, we take the characteristic parameters of the hierarchical pores as the survey object to summarize the recent progress on hierarchically structured porous materials for energy storage. This is the first of this kind exclusively to survey the performance of hierarchically structured porous materials from different porous characteristics. For those who are not familiar with hierarchically structured porous materials, a series of very significant synthesis strategies of hierarchically structured porous materials are firstly and briefly reviewed. This will be beneficial for those who want to quickly obtain useful reference information about the synthesis strategies of new hierarchically structured porous materials to improve their performance in energy storage. The effect of different organizational, structural and geometric parameters of porous hierarchy on their electrochemical behavior is then deeply discussed. We outline the existing problems and development challenges of hierarchically structured porous materials that need to be addressed in renewable energy applications. We hope that this review can stimulate strong intuition into the design and application of new hierarchically structured porous materials in energy storage and other fields.
Clinical and Patient-Reported Outcomes of Direct-Acting Antivirals for the Treatment of Chronic Hepatitis C Among Patients on Opioid Agonist Treatment: A Real-world Prospective Cohort Study
Authors: Schulte Bernd , Schmidt Christiane S , Manthey Jakob , Strada Lisa , Christensen Stefan , Cimander Konrad , Görne Herbert , Khaykin Pavel , Scherbaum Norbert , Walcher Stefan , Mauss Stefan , Schäfer Ingo , Verthein Uwe , Rehm Jürgen , Reimer Jens 
Published: August 2020

Abstract

Background
Patient-reported outcomes (PROs) can help to reduce uncertainties about hepatitis C virus (HCV) treatment with direct-acting antivirals (DAAs) among people who inject drugs and increase treatment uptake in this high-risk group. Besides clinical data, this study analyzed for the first time PROs in a real-world sample of patients on opioid agonist treatment (OAT) and HCV treatment with DAAs.

Methods
HCV treatment data including virological response, adherence, safety, and PROs of 328 German patients on OAT were analyzed in a pragmatic prospective cohort study conducted from 2016 to 2018. Clinical effectiveness was defined as sustained virological response (SVR) at week 12 after end of treatment and calculated in per-protocol (PP) and intention-to-treat (ITT) analyses. Changes over time in PROs on health-related quality of life, physical and mental health, functioning, medication tolerability, fatigue, concentration, and memory were analyzed by repeated-measures analyses of variances (ANOVAs).

Results
We found high adherence and treatment completion rates, a low number of mainly mild adverse events, and high SVR rates (PP: 97.5% [n = 285]; ITT: 84.5% [n = 328]). Missing SVR data in the ITT sample were mainly caused by patients lost to follow-up after treatment completion. Most PROs showed statistically significant but modest improvements over time, with more pronounced improvements in highly impaired patients.

Conclusions
This real-world study confirms that DAA treatment among OAT patients is feasible, safe, and effective. PROs show that all patients, but particularly those with higher somatic, mental, and social burden, benefit from DAA treatment.