bluuebunny/crossref_metadata_2025_split huggingface dataset:
A statistical evaluation of ballistic backmapping for the slow solar wind: The interplay of solar wind acceleration and corotation
Authors: Macneil Allan R , Owens Mathew J , Finley Adam J , Matt Sean P 
Published: October 2021

Abstract
Mapping solar wind plasma back to its source is often achieved using the ‘two-step ballistic backmapping’ method. Solar wind observations are mapped through the heliosphere to the edge of a PFSS model, by assuming a constant speed, radial, plasma flow. Tracing field lines through the model gives the source location at 1 R⊙ The heliospheric mapping component hinges upon the argument that two known sources of error, stemming from solar wind acceleration and non-radial flow, effectively cancel. This assumption has not been tested statistically. In this study, we evaluate the heliospheric portion of two-step backmapping, in addition to mapping using models with explicit radial acceleration, and azimuthal velocity, vφ, derived from angular momentum conservation. We estimate longitudinal mapping offsets, Δφ, between 326 Earth-observed crossings of the heliospheric current sheet (HCS), and corresponding crossings at 2.5 R⊙ from PFSS models. While the detailed solar wind models can be optimised to produce Δφ in good average agreement with HCS crossing data, the ballistic mapping performs almost as well, although all residuals have a sizeable standard deviation σ ∼ 16○. We conclude that the proposed error cancellation likely contributes to the good performance of ballistic mapping. However, interplanetary acceleration and the height of effective solar wind corotation are both smaller than previously assumed. Our results further suggest that early Parker Solar Probe observations of large vφ around 36 R⊙ do not represent the overall solar wind, due to the requirement for it to be balanced by increased acceleration.
SN 2008iy circumstellar interaction: bright and lesser light effects
Authors: Chugai N N 
Published: October 2021

ABSTRACT
Optical photometry and spectra of the luminous type IIn supernova SN 2008iy are analysed in detail with implications for cosmic ray acceleration and the radio emission. The light curve and expansion velocities indicate ejecta with the kinetic energy of 3 × 1051 erg to collide with the ∼10 M⊙ circumstellar envelope. The luminous  H α is explained as originated primarily from circumstellar clouds interacting with the forward shock. For the first time the fluorescent O i 8446 Å emission is used to demonstrate that the cloud fragmentation cascade spans a scale range &gt;2.3 dex. The narrow circumstellar  H α permitted us to estimate the acceleration efficiency of cosmic rays. The found value is close to the efficiency inferred in the same way for other two SNe IIn, SN 1997eg and SN 2002ic. The efficiency of cosmic ray acceleration is utilized to reproduce the radio flux from SN 2008iy for the amplified magnetic field consistent with the saturated turbulent magnetic field in the diffusive shock acceleration mechanism.
Panpsychism and the Inner-Outer Gap Problem
Authors: Albahari Miri 
Published: October 2021

AbstractPanpsychism is viewed by its advocates as resolving the main sticking points for materialism and dualism. While sympathetic to this approach, I locate two prevalent assumptions within modern panpsychism which I think are problematic: first, that fundamental consciousness belongs to a perspectival subject (whether microlevel or cosmic) and second, that the physical world, despite being backed by conscious subject(s), is observer-independent. I re-introduce an argument I’d made elsewhere against the first assumption: that it lies behind the well-known combination and decombination problems. I then propose a new argument against the second assumption: that it leads to an equally pernicious difficulty I call the “Inner-Outer Gap Problem.” The variant of panpsychism I continue to develop and defend, Perennial Idealism, avoids these assumptions and their problems, allowing real progress on the mind-body problem. Perennial Idealism is a type of panpsychist idealism rather than panpsychist materialism.
Cosmic Consciousness
Authors: Ganeri Jonardon 
Published: October 2021

AbstractThe phrase “cosmic consciousness” has a surprising and fascinating history. I will show how it first enters into circulation in the writings of the remarkable Englishman Edward Carpenter (1844–1929), a socialist, philosopher, and prescient activist for gay rights and prison reform. Carpenter made a trip to India and Sri Lanka in 1890, where he spent two months sitting at the feet of Ramaswami, an Indian sage and disciple of Tilleinathan Swami. Carpenter invents the phrase in order to paraphrase Ramaswami’s teaching, which was itself a commonplace among the Advaita-inspired sages of the period, that there is in human beings the possibility of an all-encompassing consciousness (the Sanskrit phrase jñāna-ākāśa would later be offered as a translation of Carpenter’s phrase). Later still, in the writings of William James and others, the phrase acquires a new and different meaning in the idea that the cosmos itself exhibits a form of consciousness. James, indeed, uses just this phrase in his early formulation of cosmopsychism.
Analytic Panpsychism and the Metaphysics of Rāmānuja’s Viśiṣṭādvaita Vedānta
Authors: Vaidya Anand Jayprakash 
Published: October 2021

AbstractAnalytic Panpsychism has been brought into contact with Indian philosophy primarily through an examination of the Advaita Vedānta tradition and the Yogācāra tradition. In this work I explore the relation between Rāmānuja, the 12th century father of the Viśiṣṭādvaita Vedānta tradition, and analytic panpsychism. I argue that Rāmānuja’s philosophy inspires a more world affirming form of cosmopsychism where there are different kinds of reality, rather than one fundamental reality of pure consciousness and an ordinary wrold that is illusory from the perspective of fundamental reality.
In vivo architecture of the telomerase RNA catalytic core in Trypanosoma brucei
Authors: Dey Abhishek , Monroy-Eklund Anais , Klotz Kaitlin , Saha Arpita , Davis Justin , Li Bibo , Laederach Alain , Chakrabarti Kausik 
Published: October 2021

Abstract
Telomerase is a unique ribonucleoprotein (RNP) reverse transcriptase that utilizes its cognate RNA molecule as a template for telomere DNA repeat synthesis. Telomerase contains the reverse transcriptase protein, TERT and the template RNA, TR, as its core components. The 5’-half of TR forms a highly conserved catalytic core comprising of the template region and adjacent domains necessary for telomere synthesis. However, how telomerase RNA folding takes place in vivo has not been fully understood due to low abundance of the native RNP. Here, using unicellular pathogen Trypanosoma brucei as a model, we reveal important regional folding information of the native telomerase RNA core domains, i.e. TR template, template boundary element, template proximal helix and Helix IV (eCR4-CR5) domain. For this purpose, we uniquely combined in-cell probing with targeted high-throughput RNA sequencing and mutational mapping under three conditions: in vivo (in WT and TERT−/− cells), in an immunopurified catalytically active telomerase RNP complex and ex vivo (deproteinized). We discover that TR forms at least two different conformers with distinct folding topologies in the insect and mammalian developmental stages of T. brucei. Also, TERT does not significantly affect the RNA folding in vivo, suggesting that the telomerase RNA in T. brucei exists in a conformationally preorganized stable structure. Our observed differences in RNA (TR) folding at two distinct developmental stages of T. brucei suggest that important conformational changes are a key component of T. brucei development.
The carbohydrate-active enzyme database: functions and literature
Authors: Drula Elodie , Garron Marie-Line , Dogan Suzan , Lombard Vincent , Henrissat Bernard , Terrapon Nicolas 
Published: October 2021

Abstract
Thirty years have elapsed since the emergence of the classification of carbohydrate-active enzymes in sequence-based families that became the CAZy database over 20 years ago, freely available for browsing and download at www.cazy.org. In the era of large scale sequencing and high-throughput Biology, it is important to examine the position of this specialist database that is deeply rooted in human curation. The three primary tasks of the CAZy curators are (i) to maintain and update the family classification of this class of enzymes, (ii) to classify sequences newly released by GenBank and the Protein Data Bank and (iii) to capture and present functional information for each family. The CAZy website is updated once a month. Here we briefly summarize the increase in novel families and the annotations conducted during the last 8 years. We present several important changes that facilitate taxonomic navigation, and allow to download the entirety of the annotations. Most importantly we highlight the considerable amount of work that accompanies the analysis and report of biochemical data from the literature.
BioSamples database: FAIRer samples metadata to accelerate research data management
Authors: Courtot Mélanie , Gupta Dipayan , Liyanage Isuru , Xu Fuqi , Burdett Tony 
Published: October 2021

Abstract
The BioSamples database at EMBL-EBI is the central institutional repository for sample metadata storage and connection to EMBL-EBI archives and other resources. The technical improvements to our infrastructure described in our last update have enabled us to scale and accommodate an increasing number of communities, resulting in a higher number of submissions and more heterogeneous data. The BioSamples database now has a valuable set of features and processes to improve data quality in BioSamples, and in particular enriching metadata content and following FAIR principles. In this manuscript, we describe how BioSamples in 2021 handles requirements from our community of users through exemplar use cases: increased findability of samples and improved data management practices support the goals of the ReSOLUTE project, how the plant community benefits from being able to link genotypic to phenotypic information, and we highlight how cumulatively those improvements contribute to more complex multi-omics data integration supporting COVID-19 research. Finally, we present underlying technical features used as pillars throughout those use cases and how they are reused for expanded engagement with communities such as FAIRplus and the Global Alliance for Genomics and Health. Availability: The BioSamples database is freely available at http://www.ebi.ac.uk/biosamples. Content is distributed under the EMBL-EBI Terms of Use available at https://www.ebi.ac.uk/about/terms-of-use. The BioSamples code is available at https://github.com/EBIBioSamples/biosamples-v4 and distributed under the Apache 2.0 license.
Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae
Authors: Singh Pragyan , Chaudhuri Anusha , Banerjea Mayukh , Marathe Neeraja , Das Biswadip 
Published: October 2021

Abstract
Nuclear degradation of aberrant mRNAs in Saccharomyces cerevisiae is accomplished by the nuclear exosome and its cofactors TRAMP/CTEXT. Evidence from this investigation establishes a universal role of the Nrd1p-Nab3p-Sen1p (NNS) complex in the nuclear decay of all categories of aberrant mRNAs. In agreement with this, both nrd1-1 and nrd1-2 mutations impaired the decay of all classes of aberrant messages. This phenotype is similar to that displayed by GAL::RRP41 and rrp6-Δ mutant yeast strains. Remarkably, however, nrd1ΔCID mutation (lacking the C-terminal domain required for interaction of Nrd1p with RNAPII) only diminished the decay of aberrant messages with defects occurring during the early stage of mRNP biogenesis, without affecting other messages with defects generated later in the process. Co-transcriptional recruitment of Nrd1p on the aberrant mRNAs was vital for their concomitant decay. Strikingly, this recruitment on to mRNAs defective in the early phases of biogenesis is solely dependent upon RNAPII. In contrast, Nrd1p recruitment onto export-defective transcripts with defects occurring in the later stage of biogenesis is independent of RNAPII and dependent on the CF1A component, Pcf11p, which explains the observed characteristic phenotype of nrd1ΔCID mutation. Consistently, pcf11-2 mutation displayed a selective impairment in the degradation of only the export-defective messages.
Bayesian theories of consciousness: a review in search for a minimal unifying model
Authors: Rorot Wiktor 
Published: October 2021

Abstract
The goal of the paper is to review existing work on consciousness within the frameworks of Predictive Processing, Active Inference, and Free Energy Principle. The emphasis is put on the role played by the precision and complexity of the internal generative model. In the light of those proposals, these two properties appear to be the minimal necessary components for the emergence of conscious experience—a Minimal Unifying Model of consciousness.
Human embryonic stem cell-derived neural crest model unveils CD55 as a cancer stem cell regulator for therapeutic targeting inMYCN-amplified neuroblastoma
Authors: Weng Zhihui , Lin Jiacheng , He Jiaozi , Gao Lin , Lin Sien , Tsang Lai Ling , Zhang Hang , He Xiaoyan , Wang Guang , Yang Xuesong , Zhou Hu , Zhao Hui , Li Gang , Zou Lin , Jiang Xiaohua 
Published: October 2021

AbstractBackgroundNeuroblastoma (NB) is a common childhood malignant tumor of neural crest (NC) origin with remarkable heterogeneity in outcomes. Amplification of the oncogene MYCN is strongly associated with highly malignant behaviour and poor prognosis.MethodsThis study aims to use a human embryonic stem cell (hESC)-derived NC model to identify novel downstream effectors of MYCN that can be potentially used as prognostic marker and/or therapeutic target.ResultsWe show that MYCN-driven NB derived from human neural crest cells (hNCCs) recapitulate the pathological and molecular features of MYCN-amplified neuroblastoma (MNA-NB). By using this platform, we identify a group of 14 surface protein-encoding genes that are associated with MYCN expression level in MNA-NB. Among these genes, high CD55 expression is correlated with poor survival in MNA-NB but not in non-MNA-NB. Furthermore, CD55 promotes tumorigenesis, tumor growth, and cancer stemness in MNA-NB cell lines (MNA-NBL) through regulating the JNK pathway. Mechanistically, MYCN binds to both canonical and noncanonical E-boxes on the promoter of CD55 to regulate its transcriptional expression. Finally, neutralizing antibody targeting CD55 significantly attenuates cancer stemness, suppresses tumor growth, and improves survival exclusively in MNA-NBL-inoculated mice.ConclusionMYCN shapes CD55 into a cancer stem cell regulator which represents a prognostic marker and therapeutic target of MNA-NB. The hESC-derived NC model serves as a valuable platform for investigating NB initiation and progression and developing potential therapeutic targets.
New physics searches at the BESIII experiment
Authors: Chen Shenjian , Olsen Stephen Lars 
Published: October 2021

Abstract
The standard model (SM) of particle physics, comprised of the unified electroweak and quantum chromodynamic theories, accurately explains almost all experimental results related to the micro-world, and has made a number of predictions for previously unseen particles, most notably the Higgs scalar boson, that were subsequently discovered. As a result, the SM is currently universally accepted as the theory of the fundamental particles and their interactions. However, in spite of its numerous successes, the SM has a number of apparent shortcomings, including: many free parameters that must be supplied by experimental measurements; no mechanism to produce the dominance of matter over antimatter in the universe; and no explanations for gravity, the dark matter in the universe, neutrino masses, the number of particle generations, etc. Because of these shortcomings, there is considerable incentive to search for evidence for new, non-SM physics phenomena that might provide important clues about what a new, beyond the SM theory (BSM) might look like. Although the center-of-mass energies that BESIII can access are far below the energy frontier, searches for new, BSM physics are an important component of its research program. This report reviews some of the highlights from BESIII’s searches for signs of new, BSM physics by: measuring rates for processes that the SM predicts to be forbidden or very rare; searching for non-SM particles such as dark photons; performing precision tests of SM predictions; and looking for violations of the discrete symmetries C and CP in processes for which the SM expectations are immeasurably small.
Legislative Behaviour of MPs in the Czech Republic in Times of Covid-19 Pandemic
Authors: Hájek Lukáš 
Published: October 2021

AbstractThe COVID-19 (coronavirus disease 2019) pandemic has affected almost every aspect of our lives. While millions of people fought with the disease, economies, societies and institutions faced side-effects of government measures resisting the spread of the virus. This article describes the effects of the pandemic on the legislative behaviour of MPs in one of the worst-hit countries in the world, the Czech Republic. The results show that the number of bill proposals and roll calls substantially increased during the pandemic compared to pre-pandemic times. Since the start of the outbreak, a third of roll calls and a half of bill proposals concerned the pandemic. Nonetheless, the outbreak did not substantially affect the voting unity of parliamentary party groups nor the opposition became more supportive of the cabinet. Still, while the liberal Pirates became more cooperative during the pandemic than the pre-pandemic period, the rightist antisystem party Freedom and Direct Democracy receded from the rest of the parties on the pandemic issues.
Optical spectroscopic observations of a symbiotic star MWC 560 in the mass accumulation phase
Authors: Ando Kazuko , Fukuda Naoya , Sato Bunei , Maehara Hiroyuki , Izumiura Hideyuki 
Published: October 2021

Abstract
There are about a dozen symbiotic stars known to produce high-velocity jets during outbursts. MWC 560 (V694 Mon) is a symbiotic star that seems to show a permanent jet. After showing an unexpected brightening in 2018 November, it has continued to brighten until 2021 and is currently in the brightest state ever. We have been conducting long-term high-dispersion spectroscopic monitoring of this object since 2016 March. An emission wing with vFWHM ≈ 700 km s−1 in the hydrogen Balmer line at an unexpected brightening event in 2018 was reported by Ando et al. (2021, PASJ, 73, L1). In subsequent continuous observations, this emission wing was no longer seen on 2019 February 6. The absorption lines seen in the hydrogen Balmer lines are gradually deepening and spreading to the slower side of the velocity, and the outflow velocity is becoming slower. The expanding component generated by the outburst was initially observed in the emission wing just after the 2018 outburst, got gradually cooler, and was observed in the absorption line after 2019.
Flavonoid deficiency disrupts redox homeostasis and terpenoid biosynthesis in glandular trichomes of tomato
Authors: Sugimoto Koichi , Zager Jordan J , Aubin Brian St , Lange Bernd Markus , Howe Gregg A 
Published: October 2021

AbstractGlandular trichomes (GTs) are epidermal structures that provide the first line of chemical defense against arthropod herbivores and other biotic threats. The most conspicuous structure on leaves of cultivated tomato (Solanum lycopersicum) is the type-VI GT (tVI-GT), which accumulates both flavonoids and volatile terpenoids. Although these classes of specialized metabolites are derived from distinct metabolic pathways, previous studies with a chalcone isomerase 1 (CHI1)-deficient mutant called anthocyanin free (af) showed that flavonoids are required for terpenoid accumulation in tVI-GTs. Here, we combined global transcriptomic and proteomic analyses of isolated trichomes as a starting point to show that the lack of CHI1 is associated with reduced levels of terpenoid biosynthetic transcripts and enzymes. The flavonoid deficiency in af trichomes also resulted in the upregulation of abiotic stress-responsive genes associated with DNA damage and repair. Several lines of biochemical and genetic evidence indicate that the terpenoid defect in af mutants is specific for the tVI-GT and is associated with the absence of bulk flavonoids rather than loss of CHI1 per se. A newly developed genome-scale model of metabolism in tomato tVI-GTs helped identify metabolic imbalances caused by the loss of flavonoid production. We provide evidence that flavonoid deficiency in this cell type leads to increased production of reactive oxygen species (ROS), which may impair terpenoid biosynthesis. Collectively, our findings support a role for flavonoids as ROS-scavenging antioxidants in GTs.
Spontaneous scalarization in scalar–tensor theories with conformal symmetry as an attractor
Authors: Chiba Takeshi 
Published: October 2021

AbstractMotivated by constant-G theory, we introduce a one-parameter family of scalar–tensor theories as an extension of constant-G theory in which the conformal symmetry is a cosmological attractor. Since the model has the coupling function of negative curvature, we expect spontaneous scalarization to occur and that the parameter can be constrained by pulsar timing measurements. Modeling neutron stars with realistic equations of state, we study the structure of neutron stars and calculate the effective scalar coupling with the neutron star in these theories. We find that within the parameter region where the observational constraints are satisfied, the effective scalar coupling almost coincides with that derived using the quadratic model with the same curvature. This indicates that the constraints obtained by the quadratic model will be used to limit the curvature of the coupling function universally in the future.