bluuebunny/crossref_metadata_2025_split huggingface dataset:
SCUBA-2 overdensities associated with candidate protoclusters selected from Planck data
Authors: Cheng T , Clements D L , Greenslade J , Cairns J , Andreani P , Bremer M , Conversi L , Cooray A , Dannerbauer H , De Zotti G , Eales S , González-Nuevo J , Ibar E , Leeuw L , Ma J , Michałowski M J , Nayyeri H , Riechers D A , Scott D , Temi P , Vaccari M , Valtchanov I , van Kampen E , Wang L 
Published: April 2020

ABSTRACT
We measure the 850-μm source densities of 46 candidate protoclusters selected from the Planck high-z catalogue (PHz) and the Planck Catalogue of Compact Sources (PCCS) that were followed up with Herschel-SPIRE and SCUBA-2. This paper aims to search for overdensities of 850-μm sources in order to select the fields that are most likely to be genuine protoclusters. Of the 46 candidate protoclusters, 25 have significant overdensities (&gt;5 times the field counts), 11 have intermediate overdensities (3–5 times the field counts), and 10 have no overdensity (&lt;3 times the field counts) of 850-μm sources. We find that the enhanced number densities are unlikely to be the result of sample variance. Compared with the number counts of another sample selected from Planck’s compact source catalogues, this [PHz + PCCS]-selected sample has a higher fraction of candidate protoclusters with significant overdensities, though both samples show overdensities of 850-μm sources above intermediate level. Based on the estimated star formation rate densities (SFRDs), we suggest that both samples can efficiently select protoclusters with starbursting galaxies near the redshift at which the global field SFRD peaks (2 &lt; z &lt; 3). Based on the confirmation of overdensities found here, future follow-up observations on other PHz targets may greatly increase the number of genuine dusty star-forming galaxy-rich clusters/protoclusters.
Optical turbulence at Ali, China – results from the first year of lunar scintillometer observations
Authors: Hickson Paul , Feng Lu , Hellemeier Joschua A , Shen Zhixia , Xue Suijian , Yao Yongqiang , Ma Bin , Chen Hualin , Yang Rui 
Published: April 2020

ABSTRACT
The location of an astronomical observatory is a key factor that affects its scientific productivity. The best astronomical sites are generally those found at high altitudes. Several such sites in western China and the Tibetan plateau are presently under development for astronomy. One of these is Ali, which, at over 5000 m, is one of the highest astronomical sites in the world. In order to further investigate the astronomical potential of Ali, we have installed a lunar scintillometer, for the primary purpose of profiling atmospheric turbulence. This paper describes the instrument and technique, and reports results from the first year of observations. We find that ground layer (GL) turbulence at Ali is remarkably weak and relatively thin. The median seeing, from turbulence in the range 11–500 m above ground, is 0.34 arcsec, with seeing better than 0.26 arcsec occurring 25 per cent of the time. Under median conditions, half of the GL turbulence lies below a height of 62 m. These initial results, and the high altitude and relatively low temperatures, suggest that Ali could prove to be an outstanding site for ground-based astronomy.
A Magnetic Snapshot Survey of F-Type Stars
Authors: Seach J M , Marsden S C , Carter B D , Neiner C , Folsom C P , Mengel M W , Oksala M E , Buysschaert B 
Published: April 2020

Abstract
We present a spectropolarimetric magnetic snapshot survey of 55 stars which includes 53 F-type stars ranging from spectral types F0 to F9 plus 2 chemically peculiar stars β CrB, and δ Cap. We look for magnetic fields in stars spanning a range of effective temperatures where the transition from fossil to dynamo magnetic fields is believed to occur. High-resolution spectropolarimetry using circularly polarized spectra is used to look for a magnetic detection in the Stokes V profile, determine the mean longitudinal magnetic field (Bl), and to look for correlations with stellar parameters. Surface magnetic fields are detected on 14 F-stars, and present in every spectral class from F3V-F9V ranging in strength from 0.3 ± 0.1 G (36 UMa, F8V) to 8.3 ± 0.9 G (h Dra, F8V). Thus we find photospheric magnetic fields are present in stars as early as spectral type F3V with an outer convection zone thickness less than a few per cent of the stellar radius.
Ultradiffuse galaxies in the IC 1459 group from the VEGAS survey
Authors: Forbes Duncan A , Dullo Bililign T , Gannon Jonah , Couch Warrick J , Iodice Enrichetta , Spavone Marilena , Cantiello Michele , Schipani Pietro 
Published: April 2020

ABSTRACT
Using deep g, r, i imaging from the VST Early-type GAlaxy Survey (VEGAS), we have searched for ultradiffuse galaxies (UDGs) in the IC 1459 group. Assuming they are group members, we identify nine galaxies with physical sizes and surface brightnesses that match the UDG criteria within our measurement uncertainties. They have mean colours of g − i = 0.6 and stellar masses of ∼108 M⊙. Several galaxies appear to have associated systems of compact objects, e.g. globular clusters. Two UDGs contain a central bright nucleus, with a third UDG revealing a remarkable double nucleus. This appears to be the first reported detection of a double nucleus in a UDG – its origin is currently unclear.
One star, two stars, or both? Investigating metallicity-dependent models for gamma-ray burst progenitors with the IllustrisTNG simulation
Authors: Metha Benjamin , Trenti Michele 
Published: April 2020

ABSTRACT
The rate of long-duration gamma-ray bursts (GRBs) has been identified as a potential proxy for the star formation rate (SFR) across redshift, but the exact relationship depends on GRB progenitor models (single versus binary). The single-progenitor collapsar model accounts for the preference towards low-metallicity GRB progenitors, but is in apparent tension with some high-metallicity GRB host galaxy measurements. As a possible solution, we consider the scenario where high-metallicity GRB hosts harbour low-metallicity regions in which GRB progenitors form. For this, we use the IllustrisTNG cosmological hydrodynamical simulation to investigate the internal metallicity distribution of GRB hosts, implementing in post-processing different GRB formation models. Predictions (GRB rate, host metallicities, and stellar masses) are compared to the high-completeness GRB legacy surveys BAT6 and SHOALS and a sample of high-redshift GRB-DLA metallicities, allowing us to compute their relative likelihoods. When the internal metallicity distribution of galaxies is ignored, the best-fitting model requires a metallicity-independent channel, as previously proposed by Trenti, Perna, & Jimenez. However, when the internal metallicity distribution is considered, a basic metallicity bias model with a cutoff at $Z_{\rm max}=0.35\, \mathrm{\it Z}_\odot$ is the best-fitting one. Current data are insufficient to discriminate among more realistic metallicity bias models, such as weak metallicity dependence of massive binaries versus stronger metallicity bias of collapsars. An increased sample of objects, and direct measurements of host stellar masses at redshift z &gt; 2 would allow to further constrain the origin of long GRBs.
Q wind code release: a non-hydrodynamical approach to modelling line-driven winds in active galactic nuclei
Authors: Quera-Bofarull Arnau , Done Chris , Lacey Cedric , McDowell Jonathan C , Risaliti Guido , Elvis Martin 
Published: April 2020

ABSTRACT
Ultraviolet (UV) line-driven winds may be an important part of the active galactic nucleus (AGN) feedback process, but understanding their impact is hindered by the complex nature of the radiation hydrodynamics. Instead, we have taken the approach pioneered by Risaliti & Elvis, calculating only ballistic trajectories from radiation forces and gravity but neglecting gas pressure. We have completely rewritten their Qwind code using more robust algorithms and can now quickly model the acceleration phase of these winds for any AGN spectral energy distribution spanning UV and X-ray wavebands. We demonstrate the code using an AGN with black hole mass $10^8\, \text{M}_\odot$ emitting at half the Eddington rate and show that this can effectively eject a wind with velocities ${\simeq}(0.1-0.2)\, c$. The mass loss rates can be up to ≃0.3M⊙ per year, consistent with more computationally expensive hydrodynamical simulations, though we highlight the importance of future improvements in radiation transfer along the multiple different lines of sight illuminating the wind. The code is fully public and can be used to quickly explore the conditions under which AGN feedback can be dominated by accretion disc winds.
Particle acceleration at colliding shock waves
Authors: Vieu T , Gabici S , Tatischeff V 
Published: April 2020

ABSTRACT
We model the diffusive shock acceleration of particles in a system of two colliding shock waves and present a method to solve the time-dependent problem analytically in the test-particle approximation and high energy limit. In particular, we show that in this limit the problem can be analysed with the help of a self-similar solution. While a number of recent works predict hard (E−1) spectra for the accelerated particles in the stationary limit, or the appearance of spectral breaks, we found instead that the spectrum of accelerated particles in a time-dependent collision follows quite closely the canonical E−2 prediction of diffusive shock acceleration at a single shock, except at the highest energy, where a hardening appears, originating a bumpy feature just before the exponential cut-off. We also investigated the effect of the reacceleration of pre-existing cosmic rays by a system of two shocks, and found that under certain conditions spectral features can appear in the cut-off region. Finally, the mathematical methods presented here are very general and could be easily applied to a variety of astrophysical situations, including for instance standing shocks in accretion flows, diverging shocks, backward collisions of a slow shock by a faster shock, and wind–wind or shock–wind collisions.
Dynamic regulation of chromatin organizer SATB1 via TCR-induced alternative promoter switch during T-cell development
Authors: Patta Indumathi , Madhok Ayush , Khare Satyajeet , Gottimukkala Kamalvishnu P , Verma Anjali , Giri Shilpi , Dandewad Vishal , Seshadri Vasudevan , Lal Girdhari , Misra-Sen Jyoti , Galande Sanjeev 
Published: April 2020

AbstractThe chromatin organizer SATB1 is highly enriched in thymocytes and is essential for T-cell development. Although SATB1 regulates a large number of genes important for T-cell development, the mechanism(s) regulating expression of SATB1 during this process remain elusive. Using chromatin immune precipitation-seq-based occupancy profiles of H3K4me3 and H3Kme1 at Satb1 gene locus, we predicted four different alternative promoters of Satb1 in mouse thymocytes and characterized them. The expression of Satb1 transcript variants with distinct 5′ UTRs occurs in a stage-specific manner during T-cell development and is dependent on TCR signaling. The observed discrepancy between the expression levels of SATB1 mRNA and protein in developing thymocytes can be explained by the differential translatability of Satb1 transcript variants as confirmed by polysome profiling and in vitro translation assay. We show that Satb1 alternative promoters exhibit lineage-specific chromatin accessibility during T-cell development from progenitors. Furthermore, TCF1 regulates the Satb1 P2 promoter switch during CD4SP development, via direct binding to the Satb1 P2 promoter. CD4SP T cells from TCF1 KO mice exhibit downregulation of P2 transcript variant expression as well as low levels of SATB1 protein. Collectively, these results provide unequivocal evidence toward alternative promoter switch-mediated developmental stage-specific regulation of SATB1 in thymocytes.
PaccMann: a web service for interpretable anticancer compound sensitivity prediction
Authors: Cadow Joris , Born Jannis , Manica Matteo , Oskooei Ali , Rodríguez Martínez María 
Published: April 2020

Abstract
The identification of new targeted and personalized therapies for cancer requires the fast and accurate assessment of the drug efficacy of potential compounds against a particular biomolecular sample. It has been suggested that the integration of complementary sources of information might strengthen the accuracy of a drug efficacy prediction model. Here, we present a web-based platform for the Prediction of AntiCancer Compound sensitivity with Multimodal Attention-based Neural Networks (PaccMann). PaccMann is trained on public transcriptomic cell line profiles, compound structure information and drug sensitivity screenings, and outperforms state-of-the-art methods on anticancer drug sensitivity prediction. On the open-access web service (https://ibm.biz/paccmann-aas), users can select a known drug compound or design their own compound structure in an interactive editor, perform in-silico drug testing and investigate compound efficacy on publicly available or user-provided transcriptomic profiles. PaccMann leverages methods for model interpretability and outputs confidence scores as well as attention heatmaps that highlight the genes and chemical sub-structures that were more important to make a prediction, hence facilitating the understanding of the model’s decision making and the involved biochemical processes. We hope to serve the community with a toolbox for fast and efficient validation in drug repositioning or lead compound identification regimes.
TeamTat: a collaborative text annotation tool
Authors: Islamaj Rezarta , Kwon Dongseop , Kim Sun , Lu Zhiyong 
Published: April 2020

Abstract
Manually annotated data is key to developing text-mining and information-extraction algorithms. However, human annotation requires considerable time, effort and expertise. Given the rapid growth of biomedical literature, it is paramount to build tools that facilitate speed and maintain expert quality. While existing text annotation tools may provide user-friendly interfaces to domain experts, limited support is available for figure display, project management, and multi-user team annotation. In response, we developed TeamTat (https://www.teamtat.org), a web-based annotation tool (local setup available), equipped to manage team annotation projects engagingly and efficiently. TeamTat is a novel tool for managing multi-user, multi-label document annotation, reflecting the entire production life cycle. Project managers can specify annotation schema for entities and relations and select annotator(s) and distribute documents anonymously to prevent bias. Document input format can be plain text, PDF or BioC (uploaded locally or automatically retrieved from PubMed/PMC), and output format is BioC with inline annotations. TeamTat displays figures from the full text for the annotator's convenience. Multiple users can work on the same document independently in their workspaces, and the team manager can track task completion. TeamTat provides corpus quality assessment via inter-annotator agreement statistics, and a user-friendly interface convenient for annotation review and inter-annotator disagreement resolution to improve corpus quality.
A Simple Flow Classification Parameter Can Discriminate Rupture Status in Intracranial Aneurysms
Authors: Asgharzadeh Hafez , Shahmohammadi Ali , Varble Nicole , Levy Elad I , Meng Hui , Borazjani Iman 
Published: April 2020

Abstract

BACKGROUND
A simple dimensionless aneurysm number (

), which depends on geometry and flow pulsatility, was previously shown to distinguish the flow mode in intracranial aneurysms (IA): vortex mode with a dynamic vortex formation/evolution if

, and cavity mode with a steady shear layer if

.

OBJECTIVE
To hypothesize that

can distinguish rupture status because vortex mode is associated with high oscillatory shear index, which, in turn, is statistically associated with rupture.

METHODS
The above hypothesis is tested on a retrospective, consecutively collected database of 204 patient-specific IAs. The first 119 cases are assigned to training and the remainder to testing dataset.

is calculated based on the pulsatility index (PI) approximated either from the literature or solving an optimization problem (denoted as

). Student's t-test and logistic regression (LR) are used for hypothesis testing and data fitting, respectively.

RESULTS

can significantly discriminate ruptured and unruptured status with 95% confidence level (P < .0001).

(using PI) and

(using

) significantly predict the ruptured IAs (for training dataset

AUC = 0.85,

AUC = 0.90, and for testing dataset

sensitivity = 94%, specificity = 33%,

sensitivity = 93.1%, specificity = 52.85%).

CONCLUSION

predicts ruptured status. Unlike traditional hemodynamic parameters such as wall shear stress and oscillatory shear index,

has a physical threshold of one (does not depend on statistical analysis) and does not require time-consuming flow simulations. Therefore,

is a simple, practical discriminator of IA rupture status.
An Update on Medications for Brain Arteriovenous Malformations
Authors: Raper Daniel M S , Winkler Ethan A , Rutledge W Caleb , Cooke Daniel L , Abla Adib A 
Published: April 2020

Abstract
Despite a variety of treatment options for brain arteriovenous malformations (bAVMs), many lesions remain challenging to treat and present significant ongoing risk for hemorrhage. In Vitro investigations have recently led to a greater understanding of the formation, growth, and rupture of bAVMs. This has, in turn, led to the development of therapeutic targets for medications for bAVMs, some of which have begun testing in clinical trials in humans. These include bevacizumab, targeting the vascular endothelial growth factor driven angiogenic pathway; thalidomide or lenalidomide, targeting blood-brain barrier impairment; and doxycycline, targeting matrix metalloproteinase overexpression. A variety of other medications appear promising but either requires adaptation from other disease states or development from early bench studies into the clinical realm. This review aims to provide an overview of the current state of development of medications targeting bAVMs and to highlight their likely applications in the future.
Thermodynamic analysis and kinetic optimization of high-energy batteries based on multi-electron reactions
Authors: Huang Yong-Xin , Wu Feng , Chen Ren-Jie 
Published: April 2020

AbstractMulti-electron reaction can be regarded as an effective way of building high-energy systems (&gt;500 W h kg−1). However, some confusions hinder the development of multi-electron mechanisms, such as clear concept, complex reaction, material design and electrolyte optimization and full-cell fabrication. Therefore, this review discusses the basic theories and application bottlenecks of multi-electron mechanisms from the view of thermodynamic and dynamic principles. In future, high-energy batteries, metal anodes and multi-electron cathodes are promising electrode materials with high theoretical capacity and high output voltage. While the primary issue for the multi-electron transfer process is sluggish kinetics, which may be caused by multiple ionic migration, large ionic radius, high reaction energy barrier, low electron conductivity, poor structural stability, etc., it is urgent that feasible and versatile modification methods are summarized and new inspiration proposed in order to break through kinetic constraints. Finally, the remaining challenges and future research directions are revealed in detail, involving the search for high-energy systems, compatibility of full cells, cost control, etc.
Hierarchical structural complexity in atomically precise nanocluster frameworks
Authors: Wei Xiao , Kang Xi , Zuo Zewen , Song Fengqi , Wang Shuxin , Zhu Manzhou 
Published: April 2020

Abstract
The supramolecular chemistry of nanoclusters is a flourishing area of nano-research; however, the controllable assembly of cluster nano-building blocks in different arrays remains challenging. In this work, we report the hierarchical structural complexity of atomically precise nanoclusters in micrometric linear chains (1D array), grid networks (2D array) and superstructures (3D array). In the crystal lattice, the Ag29(SSR)12(PPh3)4 nanoclusters can be viewed as unassembled cluster dots (Ag29–0D). In the presence of Cs+ cations, the Ag29(SSR)12 nano-building blocks are selectively assembled into distinct arrays with different oxygen-carrying solvent molecules―Cs@Ag29(SSR)12(DMF)x as 1D linear chains (Ag29–1D), Cs@Ag29(SSR)12(NMP)x as 2D grid networks (Ag29–2D), and Cs@Ag29(SSR)12(TMS)x as 3D superstructures (Ag29–3D). Such self-assemblies of these Ag29(SSR)12 units have not only been observed in their crystalline state, but also in their amorphous state. Due to the diverse surface structures and crystalline packing modes, these Ag29-based assemblies manifest distinguishable optical absorptions and emissions in both solutions and crystallized films. Furthermore, the surface areas of the nanocluster crystals are evaluated, the maximum value of which occurs when the cluster nano-building blocks are assembled into 2D arrays (i.e. Ag29–2D). Overall, this work presents an exciting example of the hierarchical assembly of atomically precise nanoclusters by simply controlling the adsorbed molecules on the cluster surface.
RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG
Authors: Kajiya-Kanegae Hiromi , Takanashi Hideki , Fujimoto Masaru , Ishimori Motoyuki , Ohnishi Norikazu , Wacera W. Fiona , Omollo Everlyne A , Kobayashi Masaaki , Yano Kentaro , Nakano Michiharu , Kozuka Toshiaki , Kusaba Makoto , Iwata Hiroyoshi , Tsutsumi Nobuhiro , Sakamoto Wataru 
Published: April 2020

AbstractSorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a high-density linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.