bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small molecules mediate cellular reprogramming across two kingdoms
Authors: Welsch Ralf , Touraev Alisher , Palme Klaus 
Published: November 2021

Abstract
The fertilized egg is the single totipotent cell from which multicellular organisms arise through the processes of cell division and differentiation. While animals typically lose their capacity to redifferentiate cells that are already fully differentiated, plant cells are thought to remain totipotent (Su et al., 2020). Every gardener knows well that plants can regenerate a full array of plant tissues from already differentiated organs. This also seems to be true for single plant cells such as protoplasts, which, under proper in vitro culture conditions, served as the initial source for generation of transgenic plants (Skoog and Miller, 1957; Birnbaum and Sánchez Alvarado, 2008). However, the mechanisms behind the totipotency of plant cells remain elusive, with the exception of the knowledge that the developmental fate of regenerating tissues can be directed by the ratio of two plant hormones, auxin and cytokinin (Skoog and Miller, 1957).
Nii: a Bayesian orbit retrieval code applied to differential astrometry
Authors: Jin Sheng , Ding Xiaojian , Wang Su , Dong Yao , Ji Jianghui 
Published: November 2021

ABSTRACTHere, we present an open source python-based Bayesian orbit retrieval code (Nii) that implements an automatic parallel tempering Markov chain Monte Carlo (APT-MCMC) strategy. Nii provides a module to simulate the observations of a space-based astrometry mission in the search for exoplanets, a signal extraction process for differential astrometric measurements using multiple reference stars, and an orbital parameter retrieval framework using APT-MCMC. We further verify the orbit retrieval ability of the code through two examples corresponding to a single-planet system and a dual-planet system. In both cases, efficient convergence on the posterior probability distribution can be achieved. Although this code specifically focuses on the orbital parameter retrieval problem of differential astrometry, Nii can also be widely used in other Bayesian analysis applications.
Too dense to go through: the role of low-mass clusters in the pre-processing of satellite galaxies
Authors: Pallero Diego , Gómez Facundo A , Padilla Nelson D , Bahé Yannick M , Vega-Martínez Cristian A , Torres-Flores S 
Published: November 2021

ABSTRACT
We study the evolution of satellite galaxies in clusters of the c-eagle simulations, a suite of 30 high-resolution cosmological hydrodynamical zoom-in simulations based on the eagle code. We find that the majority of galaxies that are quenched at z = 0 (≳80${{\ \rm per\ cent}}$) reached this state in a dense environment (log10M200[M⊙] ≥13.5). At low redshift, regardless of the final cluster mass, galaxies appear to reach their quenching state in low-mass clusters. Moreover, galaxies quenched inside the cluster that they reside in at z = 0 are the dominant population in low-mass clusters, while galaxies quenched in a different halo dominate in the most massive clusters. When looking at clusters at z &gt; 0.5, their in situ quenched population dominates at all cluster masses. This suggests that galaxies are quenched inside the first cluster they fall into. After galaxies cross the cluster’s r200 they rapidly become quenched (≲1 Gyr). Just a small fraction of galaxies ($\lesssim 15{{\ \rm per\ cent}}$) is capable of retaining their gas for a longer period of time, but after 4 Gyr, almost all galaxies are quenched. This phenomenon is related to ram pressure stripping and is produced when the density of the intracluster medium reaches a threshold of $\rho _{\rm ICM}\, \sim 3 \times 10 ^{-5}$ nH (cm−3). These results suggest that galaxies start a rapid-quenching phase shortly after their first infall inside r200 and that, by the time they reach r500, most of them are already quenched.
Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes
Authors: White Shannon M , Snyder Michael P , Yi Chunling 
Published: November 2021

Abstract
The term ‘super enhancers’ (SE) has been widely used to describe stretches of closely localized enhancers that are occupied collectively by large numbers of transcription factors (TFs) and co-factors, and control the transcription of highly-expressed genes. Through integrated analysis of &gt;600 DNase-seq, ChIP-seq, GRO-seq, STARR-seq, RNA-seq, Hi-C and ChIA-PET data in five human cancer cell lines, we identified a new class of autonomous SEs (aSEs) that are excluded from classic SE calls by the widely used Rank Ordering of Super-Enhancers (ROSE) method. TF footprint analysis revealed that compared to classic SEs and regular enhancers, aSEs are tightly bound by a dense array of master lineage TFs, which serve as anchors to recruit additional TFs and co-factors in trans. In addition, aSEs are preferentially enriched for Cohesins, which likely involve in stabilizing long-distance interactions between aSEs and their distal target genes. Finally, we showed that aSEs can be reliably predicted using a single DNase-seq data or combined with Mediator and/or P300 ChIP-seq. Overall, our study demonstrates that aSEs represent a unique class of functionally important enhancer elements that distally regulate the transcription of highly expressed genes.
Consensus core clinical data elements for meningiomas (v2021.1)
Authors: Nassiri Farshad , Wang Justin Z , Au Karolyn , Barnholtz-Sloan Jill , Jenkinson Michael D , Drummond Kate , Zhou Yueren , Snyder James M , Brastianos Priscilla , Santarius Thomas , Suppiah Suganth , Poisson Laila , Gaillard Francesco , Rosenthal Mark , Kaufmann Timothy , Tsang Derek S , Aldape Kenneth , Zadeh Gelareh 
Published: November 2021

AbstractBackgroundWith increasing molecular analyses of meningiomas, there is a need to harmonize language used to capture clinical data across centers to ensure that molecular alterations are appropriately linked to clinical variables of interest. Here the International Consortium on Meningiomas presents a set of core and supplemental meningioma-specific common data elements (CDEs) to facilitate comparative and pooled analyses.MethodsThe generation of CDEs followed the 4-phase process similar to other National Institute of Neurological Disorders and Stroke (NINDS) CDE projects: discovery, internal validation, external validation, and distribution.ResultsThe CDEs were organized into patient- and tumor-level modules. In total, 17 core CDEs (10 patient level and 7 tumor level) as well as 14 supplemental CDEs (7 patient level and 7 tumor level) were defined and described. These CDEs are now made publicly available for dissemination and adoption.ConclusionsCDEs provide a framework for discussion in the neuro-oncology community that will facilitate data-sharing for collaborative research projects and aid in developing a common language for comparative and pooled analyses. The meningioma-specific CDEs presented here are intended to be dynamic parameters that evolve with time and The Consortium welcomes international feedback for further refinement and implementation of these CDEs.
A metamaterial-free fluid-flow cloak
Authors: Tay Fuyang , Zhang Youming , Xu Hongyi , Goh Honghui , Luo Yu , Zhang Baile 
Published: November 2021

Abstract
The model of ideal fluid flow around a cylindrical obstacle exhibits a long-established physical picture, where originally straight streamlines are deflected over the whole space by the obstacle. Inspired by transformation optics and metamaterials, recent theories have proposed the concept of fluid cloaking, which is able to recover the straight streamlines, as if the obstacle did not exist. However, such a cloak, similar to all previous transformation-optics-based devices, relies on complex metamaterials with inhomogeneous parameters and is difficult to implement. Here we deploy the theory of scattering cancellation and report on the experimental realization of a fluid-flow cloak without metamaterials. This cloak is realized by engineering the geometry of the fluid channel, which effectively cancels the dipole-like scattering of the obstacle. The cloaking effect is demonstrated through the direct observation of recovered straight streamlines in the fluid flow. Our work sheds new light on conventional fluid control and may find application in microfluidic devices.
Prose Poetry
Authors: Desmarais Jane , Weir David 
Published: November 2021

Abstract
This chapter treats the prose poem as the decadent genre par excellence by focusing on Charles Baudelaire’s Le Spleen de Paris (Paris Spleen, 1869). The prose poem is well suited to the expression of decadent culture because of its formal subversion of conventional poetry, especially as adapted by Baudelaire to articulate “the bump and lurch” of urban experience. J. K. Huysmans certified the decadent credentials of the genre when he described it in À rebours (Against Nature, 1884) as “the osmazome of literature, the essential oil of art,” a literary distillation that makes it “an aesthetic treat to none but the most discerning.” The article analyzes “Any Where Out of the World” and other prose poems in relation to certain poems in Le Fleurs du mal (The Flowers of Evil, 1857), observing no loss of metaphorical power in the more “prosaic” medium despite Baudelaire’s secular and subversive treatment of many of the same poetic material given more elevated, spiritual treatment in the earlier collection.
Introduction to Gabriel García Márquez
Authors: Bell-Villada Gene H. , López-Calvo Ignacio 
Published: November 2021

Abstract
The publication in 1967 of his masterpiece Cien años de soledad, followed by the English-language translation in 1970, changed García Márquez’s personal and professional life forever and was arguably the main reason for his winning the 1982 Nobel Prize. Other masterworks would follow, notably The Autumn of the Patriarch, an experimental narrative about an aging Caribbean dictator that is also infused by magical realism while leaving behind the Macondo of One Hundred Years of Solitude. Also passed in review here are his short-story collections, his later novels of romantic love, and the highly praised novellas No One Writes to the Colonel and Chronicle of a Death Foretold. García Márquez’s literary success is placed within the context of the Cuban Revolution, the Latin American Boom, and the growing recognition received by previous Latin American authors (Cortázar, Fuentes, Vargas Llosa). In ensuing articles, García Márquez is examined via a broad array of perspectives, several of them unavoidable: biography, magical realism, and alchemy; local roots and world influence (especially in the Global South and Asia, as well as Spain); and issues of ethnicity, gender, myth, ecology, musical genres, left-wing politics, and anti-imperialism. Readings of individual works conclude our survey. Throughout these thirty-two essays, virtually all of García Márquez’s mature works—long and short, early and late, fictional, nonfictional, and even filmic—are expertly and subtly teased out for the benefit of his many devoted readers worldwide.
Sociological Perspectives on Disability
Authors: Mauldin Laura 
Published: November 2021

Abstract
This chapter outlines the roots of disability scholarship in sociology and how the sociology of disability subfield positions disability as an axis of inequality. The first part of the chapter argues that sociology is uniquely positioned to understand how disability as a social category is made through institutional structures, larger patterns of exclusion and inclusion, and emphasis on power and inequality. Yet it is often excluded in measurements and analyses in the discipline. The chapter then turns to the origins of disability scholarship in sociology, its influence on the interdisciplinary field of disability studies, and the emergent subfield of sociology of disability within the discipline. The remaining parts of the chapter survey how disability has been studied across subfields such as sociology of health and illness, sociology of body/embodiment, and feminist sociological scholarship. In discussing disability across these subfields, divergences between mainstream sociology and the sociology of disability are highlighted in an effort to map their departures and pinpoint why disability as a category or axis of inequality is persistently underresearched in sociology. The chapter concludes with thoughts about where new scholarship on disability might be going in sociology.
Irish song and the idea of tradition
Authors: Blankenhorn Virginia 
Published: November 2021

Abstract
Defining ‘tradition’ as something passed on within a community that provides a matrix for its understanding of past events and present choices, this essay discusses the evolution of Irish poetry and song since 1200. It explores the connections between vernacular poetry and various learned (literary) traditions, including bardic poetry (syllabic verse) and the later ‘poetic courts’ and ‘schools of poetry’, in terms of themes, verse structure, social context, and sung performance. It demonstrates that while some practices were bound to specific social contexts, the strand that most people today identify as ‘the Irish song tradition’ still employs centuries-old themes including panegyric and the Anglo-Norman ‘courtly love’ rhetoric, and displays prosodic features evidenced in Middle Irish bardic sources. Finally, we consider the emergence of ‘tradition’ as a concept, the impact since 1850 of song collecting and technology on repertoire and performance, and the implications of ‘authenticity’ for today’s definition of ‘tradition’.
The Public Music Theory of George Bernard Shaw
Authors: Biamonte Nicole 
Published: November 2021

Abstract
George Bernard Shaw is best known today for his plays, but he first exercised his incisive wit as a drama and music critic in London, intermittently from 1876, regularly from 1888 to 1894, and intermittently again to the end of his life. Shaw explicitly intended to make his reviews both educational and accessible to the general public, combining performance critiques with broader considerations, including aspects of music theory and music education, and avoiding technical terms to the extent possible. Thus, his music criticism serves as an example of public music theory. This chapter surveys Shaw’s music-theoretic comments through this lens, analyzing what they demonstrate about his own musical understanding and underlying ideologies, the educational purpose of his reviews, and the level of musical knowledge he assumed on the part of his late nineteenth-century London readership.
A CONCEPTUAL framework for combining brain mapping and brain stimulation
Authors: Karabanov Anke Ninija , Siebner Hartwig R. 
Published: November 2021

Abstract
Here, we introduce a conceptual framework for studies that combine non-invasive transcranial brain stimulation (NTBS) with neuroimaging. We outline the type of neuroscientific questions that can be addressed with a combined NTBS-neuroimaging approach and describe important experimental considerations. Neuroimaging methods differ with respect to their spatiotemporal resolution and reflect different neurobiological aspects of brain function, structure or metabolism. These characteristics need to be carefully considered in order to select the most appropriate neuroimaging modality. NTBS and neuroimaging can be combined concurrently (online) or sequentially (offline). The “online” approach applies neuroimaging while NTBS is delivered to the brain and thus, can reveal the immediate functional effects of NTBS on the targeted brain networks, but one has to deal with interfering effects of NTBS on brain mapping. The “offline” approach applies neuroimaging and NTBS in sequence: Offline neuroimaging can be performed BEFORE the stimulation session to inform NTBS parameter setting or AFTER the stimulation session to provide functional, metabolic or structural readouts of NTBS-effects. Since NTBS and neuroimaging can be separated in space and time, NTBS does not interfere with offline brain mapping. Finally, we discuss how NTBS and neuroimaging are gaining importance in clinical NTBS applications and how both techniques can be iteratively combined to create open-loop setups.
Computational neurostimulation
Authors: Johnstone Ainslie , Bonaiuto James J. , Bestmann Sven 
Published: November 2021

Abstract
Computational neurostimulation is the use of biologically grounded computational models to investigate the mechanism of action of brain stimulation and predict the impact of transcranial magnetic stimulation (TMS) on behavior in health and disease. Computational models are now widespread, and their success is incontrovertible, yet they have left a rather small footprint on the field of TMS. We highlight and discuss recent advances in models of primary motor cortex TMS, the brain region for which most models have been developed. These models provide insight into the putative, but unobservable, mechanisms through which TMS influences physiology, and help predicting the effects of different TMS applications. We discuss how these advances in computational neurostimulation provide opportunities for mechanistically understanding and predicting the impact of TMS on behavior.
How Does Artificial Intelligence Pose an Existential Risk?
Authors: Vold Karina , Harris Daniel R. 
Published: November 2021

Abstract
Alan Turing, one of the fathers of computing, warned that artificial intelligence (AI) could one day pose an existential risk to humanity. Today, recent advancements in the field of AI have been accompanied by a renewed set of existential warnings. But what exactly constitutes an existential risk? And how exactly does AI pose such a threat? In this chapter, we aim to answer these questions. In particular, we will critically explore three commonly cited reasons for thinking that AI poses an existential threat to humanity: the control problem, the possibility of global disruption from an AI race dynamic, and the weaponization of AI.
Bypassing reproductive barriers in hybrid seeds using chemically induced epimutagenesis
Authors: Huc Jonathan , Dziasek Katarzyna , Pachamuthu Kannan , Woh Tristan , Köhler Claudia , Borges Filipe 
Published: November 2021

AbstractThe triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed genes (PEGs), which are upregulated in tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in the CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of “epimutagenized” plants, which may allow epialleles involved in the triploid block response to be identified in future studies. Finally, we demonstrate that chemically induced epimutagenesis facilitates hybridization between different Capsella species, thus potentially emerging as a strategy for producing triploids and interspecific hybrids with high agronomic interest.
AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes
Authors: Li Yang , Jiang Ning , Sun Yanni 
Published: November 2021

AbstractShort interspersed nuclear elements (SINEs) are a widespread type of small transposable element (TE). With increasing evidence for their impact on gene function and genome evolution in plants, accurate genome-scale SINE annotation becomes a fundamental step for studying the regulatory roles of SINEs and their relationship with other components in the genomes. Despite the overall promising progress made in TE annotation, SINE annotation remains a major challenge. Unlike some other TEs, SINEs are short and heterogeneous, and they usually lack well-conserved sequence or structural features. Thus, current SINE annotation tools have either low sensitivity or high false discovery rates. Given the demand and challenges, we aimed to provide a more accurate and efficient SINE annotation tool for plant genomes. The pipeline starts with maximizing the pool of SINE candidates via profile hidden Markov model-based homology search and de novo SINE search using structural features. Then, it excludes the false positives by integrating all known features of SINEs and the features of other types of TEs that can often be misannotated as SINEs. As a result, the pipeline substantially improves the tradeoff between sensitivity and accuracy, with both values close to or over 90%. We tested our tool in Arabidopsis thaliana and rice (Oryza sativa), and the results show that our tool competes favorably against existing SINE annotation tools. The simplicity and effectiveness of this tool would potentially be useful for generating more accurate SINE annotations for other plant species. The pipeline is freely available at https://github.com/yangli557/AnnoSINE.
Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles
Authors: Apelt Federico , Mavrothalassiti Eleni , Gupta Saurabh , Machin Frank , Olas Justyna Jadwiga , Annunziata Maria Grazia , Schindelasch Dana , Kragler Friedrich 
Published: November 2021

Abstract
Although several large-scale single-cell RNA sequencing (scRNAseq) studies addressing the root of Arabidopsis (Arabidopsis thaliana) have been published, there is still need for a de novo reference map for both root and especially above-ground cell types. As the plants’ transcriptome substantially changes throughout the day, shaped by the circadian clock, we performed scRNAseq on both Arabidopsis root and above-ground tissues at defined times of the day. For the root scRNAseq analysis, we used tissue-specific reporter lines grown on plates and harvested at the end of the day (ED). In addition, we submitted above-ground tissues from plants grown on soil at ED and end of the night to scRNAseq, which allowed us to identify common cell types/markers between root and shoot and uncover transcriptome changes to above-ground tissues depending on the time of the day. The dataset was also exploited beyond the traditional scRNAseq analysis to investigate non-annotated and di-cistronic transcripts. We experimentally confirmed the predicted presence of some of these transcripts and also addressed the potential function of a previously unidentified marker gene for dividing cells. In summary, this work provides insights into the spatial control of gene expression from nearly 70,000 cells of Arabidopsis for below- and whole above-ground tissue at single-cell resolution at defined time points.