bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous TESS and NGTS transit observations of WASP-166 b
Authors: Bryant Edward M , Bayliss Daniel , McCormac James , Wheatley Peter J , Acton Jack S , Anderson David R , Armstrong David J , Bouchy François , Belardi Claudia , Burleigh Matthew R , Tilbrook Rosie H , Casewell Sarah L , Cooke Benjamin F , Gill Samuel , Goad Michael R , Jenkins James S , Lendl Monika , Pollacco Don , Queloz Didier , Raynard Liam , Smith Alexis M S , Vines Jose I , West Richard G , Udry Stephane 
Published: April 2020

ABSTRACT
We observed a transit of WASP-166 b using nine Next Generation Transit Survey (NGTS) telescopes simultaneously with the Transiting Exoplanet Survey Satellite (TESS) observations of the same transit. We achieved a photometric precision of 152 ppm per 30 min with the nine NGTS telescopes combined, matching the precision reached by TESS for the transit event around this bright (T = 8.87) star. The individual NGTS light-curve noise is found to be dominated by scintillation noise and appears free from any time-correlated noise or any correlation between telescope systems. We fit the NGTS data for TC and Rp/R*. We find TC to be consistent to within 0.25σ of the result from the TESS data, and the difference between the TESS and NGTS measured Rp/R* values is 0.9σ. This experiment shows that multitelescope NGTS photometry can match the precision of TESS for bright stars, and will be a valuable tool in refining the radii and ephemerides for bright TESS candidates and planets. The transit timing achieved will also enable NGTS to measure significant transit timing variations in multiplanet systems.
Performing Highly Efficient Genome Scans for Local Adaptation with R Package pcadapt Version 4
Authors: Privé Florian , Luu Keurcien , Vilhjálmsson Bjarni J , Blum Michael G B 
Published: April 2020

Abstract
R package pcadapt is a user-friendly R package for performing genome scans for local adaptation. Here, we present version 4 of pcadapt which substantially improves computational efficiency while providing similar results. This improvement is made possible by using a different format for storing genotypes and a different algorithm for computing principal components of the genotype matrix, which is the most computationally demanding step in method pcadapt. These changes are seamlessly integrated into the existing pcadapt package, and users will experience a large reduction in computation time (by a factor of 20–60 in our analyses) as compared with previous versions.
Alternative proteins are functional regulators in cell reprogramming by PKA activation
Authors: Cardon Tristan , Franck Julien , Coyaud Etienne , Laurent Estelle M N , Damato Marina , Maffia Michele , Vergara Daniele , Fournier Isabelle , Salzet Michel 
Published: April 2020

AbstractIt has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial–mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies.
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems
Authors: Kern Fabian , Fehlmann Tobias , Solomon Jeffrey , Schwed Louisa , Grammes Nadja , Backes Christina , Van Keuren-Jensen Kendall , Craig David Wesley , Meese Eckart , Keller Andreas 
Published: April 2020

AbstractGene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from ten frequently investigated organisms. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miRBase miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualizations such as heatmaps and running sum curves with background distributions. We demonstrate the new features with case studies for human kidney cancer, a biomarker study on Parkinson’s disease from the PPMI cohort, and a mouse model for breast cancer. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.
miRSwitch: detecting microRNA arm shift and switch events
Authors: Kern Fabian , Amand Jeremy , Senatorov Ilya , Isakova Alina , Backes Christina , Meese Eckart , Keller Andreas , Fehlmann Tobias 
Published: April 2020

Abstract
Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30 521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customized arm switch analyses along with comprehensive visualizations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts
Authors: Gobeill Julien , Caucheteur Déborah , Michel Pierre-André , Mottin Luc , Pasche Emilie , Ruch Patrick 
Published: April 2020

Abstract
Thanks to recent efforts by the text mining community, biocurators have now access to plenty of good tools and Web interfaces for identifying and visualizing biomedical entities in literature. Yet, many of these systems start with a PubMed query, which is limited by strong Boolean constraints. Some semantic search engines exploit entities for Information Retrieval, and/or deliver relevance-based ranked results. Yet, they are not designed for supporting a specific curation workflow, and allow very limited control on the search process. The Swiss Institute of Bioinformatics Literature Services (SIBiLS) provide personalized Information Retrieval in the biological literature. Indeed, SIBiLS allow fully customizable search in semantically enriched contents, based on keywords and/or mapped biomedical entities from a growing set of standardized and legacy vocabularies. The services have been used and favourably evaluated to assist the curation of genes and gene products, by delivering customized literature triage engines to different curation teams. SIBiLS (https://candy.hesge.ch/SIBiLS) are freely accessible via REST APIs and are ready to empower any curation workflow, built on modern technologies scalable with big data: MongoDB and Elasticsearch. They cover MEDLINE and PubMed Central Open Access enriched by nearly 2 billion of mapped biomedical entities, and are daily updated.
AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations
Authors: Tan Zhen Wah , Guarnera Enrico , Tee Wei-Ven , Berezovsky Igor N 
Published: April 2020

Abstract
The AlloSigMA 2 server provides an interactive platform for exploring the allosteric signaling caused by ligand binding and/or mutations, for analyzing the allosteric effects of mutations and for detecting potential cancer drivers and pathogenic nsSNPs. It can also be used for searching latent allosteric sites and for computationally designing allosteric effectors for these sites with required agonist/antagonist activity. The server is based on the implementation of the Structure-Based Statistical Mechanical Model of Allostery (SBSMMA), which allows one to evaluate the allosteric free energy as a result of the perturbation at per-residue resolution. The Allosteric Signaling Map (ASM) providing a comprehensive residue-by-residue allosteric control over the protein activity can be obtained for any structure of interest. The Allosteric Probing Map (APM), in turn, allows one to perform the fragment-based-like computational design experiment aimed at finding leads for potential allosteric effectors. The server can be instrumental in elucidating of allosteric mechanisms and actions of allosteric mutations, and in the efforts on design of new elements of allosteric control. The server is freely available at: http://allosigma.bii.a-star.edu.sg
Construction of hollow mesoporous silica nanoreactors for enhanced photo-oxidations over Au-Pt catalysts
Authors: Tian Hao , Zhao Jinhui , Wang Xinyao , Wang Lizhuo , Liu Hao , Wang Guoxiu , Huang Jun , Liu Jian , Lu G Q (Max) 
Published: April 2020

Abstract
It is highly desirable to design hollow structures with multi-scale functions by mimicking cells for the construction of micro/nanoreactors. Herein, we report the construction of hollow-structured submicrometer-photoreactors with bimetallic catalysts loaded within mesoporous silicas. The synthesis parameters are optimized to study the evolution of hollow structure through hydrothermal treatment and an ‘adhesive-contraction’ formation mechanism is proposed. AuPt@HMZS catalysts exhibited a broader absorbance region under visible light and the adsorption edge displayed a red-shift, indicating the strong metal–metal interactions at the alloy interface. The reaction performance of the coupled Au-Pt catalysts can be tuned to achieve excellent catalytic activity in cinnamyl alcohol oxidation to cinnamic acid for 3.1 mmol g−1 with 99% selectivity. The proposed strategy to build hollow structures as multifunctional micro/nanoreactors is promising for the design of high-performance and sustainable catalysts for chemical synthesis.
Equatorial aurora: the aurora-like airglow in the negative magnetic anomaly
Authors: He Fei , Wei Yong , Wan Weixing 
Published: April 2020

Abstract
The most fantastic optical phenomena in the Earth's upper atmosphere are the auroras. They are highly informative indicators of solar activity, geomagnetic activity, upper atmospheric structures and dynamics, and magnetospheric energetic particles. An area where the geomagnetic field differs significantly from the expected symmetric dipole, such as at the South Atlantic Anomaly, where the magnetic field intensity is low, gives rise to stronger precipitation of energetic particles into the upper atmosphere. Impact excitation and the subsequent airglow emissions exhibit aurora-like dynamic signatures. Nomenclatures of nonpolar aurora or equatorial auroras are similar to those used with the polar auroras owing to their similar excitation mechanisms. This paper provides an overview of the knowledge and the challenges concerning auroral activity at the South Atlantic Anomaly, or more generally, at the negative magnetic anomaly. We emphasize systematic investigation of the equatorial auroras to reveal the temporal and spatial evolution of the magnetic anomaly and the behaviour of energetic particles in near-Earth space.
The Philosophy of Theater
Authors: Bennett Michael Y. 
Published: April 2020

Theater—i.e., traditional text-based theater—is often considered the art form that most closely resembles lived life: real bodies in space play out a story through the passage of time. Because of this, theater (or theatre) has long been a laboratory of, and for, philosophical thought and reflection. The study of philosophy and theater has a history that dates back to, and flourished in, ancient Greece and Rome. While philosophers over the centuries have revisited the study of theater, the past four decades in particular have seen a noted and substantial increase of scholarship investigating this intersection between philosophy and theater. “Philosophy of theater” is, on one hand, a “field” that is just starting to take shape and is barely over a decade old; on another hand, it is a recognized subfield both of aesthetics and of theater and performance studies. And finally, it is also an amorphous concept, either not yet fleshed out, or intentionally amorphous and proudly organic. Philosophy of theater is also sometimes referred to—or is argued to be subsumed, more broadly, in—“performance philosophy,” which also refers to a network of academics and practitioners that publishes a book series and a journal of the same name. Regardless of what it is called or how it is classified, scholarship has coalesced around some fundamental preoccupations, which are not too dissimilar to questions that arise in other philosophies of. . . (e.g., art, film, dance, etc.). The debates in philosophy of theater mostly fall into three of the main branches of philosophy: metaphysics, epistemology, and aesthetics. The major metaphysical debates center on an ontological question: What is theater? Epistemological studies tend to focus on audience reception and/or how meaning is made and/or transmitted. Finally, studies in aesthetics focus on two main questions: (1) What is theater as an art form? (2) What is the relationship between dramatic text and theatrical performance? This article is intentionally narrow in its scope, focusing on philosophy and theater traditions that came out of Greek theater and philosophy, in order to ensure a sufficient amount of depth, not (merely) breadth.
Archaeology and Material Culture of Judah and the Judeans (ca. 1000–586 bce)
Authors: Mowry Tyler , Fulton Deirdre 
Published: April 2020

The kingdom of Judah was a small political state that arose in the southern Levantine hill country during the Iron Age and was eventually conquered by the Babylonian king Nebuchadnezzar in 586 bce. While the precise boundaries of the territory of Judah are difficult to define and likely fluctuated considerably, the traditional heartland of Judah in the Iron II extended from the southern mountain range that emerged from the Jezreel Valley in the north, to the Northern Negev, located in the south. At the beginning of the Iron II period (ca. 1000 bce), there began a steady increase in the small, unwalled settlements typical of that area in the Iron I period. The population of Judah remained relatively small throughout the 10th and early 9th centuries, but grew substantially during the late 9th century and especially the 8th century, as evinced by the proliferation of fortified settlements. At some point during this development, the political organization of these settlements coalesced into a monarchic state, but the precise nature and date of this transition is debated. Some scholars argue for the essential veracity of the biblical narratives concerning the foundation of the state under David and Solomon in the early 10th century bce, while others argue there is little definitive and undisputed archaeological evidence pointing to a strong centralized government until the 9th century. Indeed, this complicated relationship between the biblical text and the material culture has defined the practice and prerogatives of Judahite archaeology from its inception. Modern, stratigraphic excavation in Judah began under the guidance of biblical scholars in the early 20th century and continued in this fashion through the mid-century “Biblical Archaeology” movement. In recent decades, however, the archaeology of Judah (often included within the category of Syro-Palestinian archaeology) has gained some degree of independence from the field of Biblical Studies. Following wider trends in world archaeology, scholars studying ancient Judah have begun incorporating data from ethnographic studies and archaeometric methods into the primarily tell-based excavation process that characterized Judahite archaeology in the past. Still, the influence of the biblical traditions is undeniably present in the archaeology of the Levant, and as a result, studies of Judah are often combined with those of the kingdom of Israel to the north. Readers will note that combined form “Israel/Judah” is used when little or no distinction is made between the cultures of the two kingdoms.
Donatello
Authors: Bloch Amy R. 
Published: April 2020

Donatello, born Donato di Niccolò di Betto di Bardo (b. c. 1386–d. 1466) in Florence, was one of the most gifted and versatile sculptors working on the Italian peninsula during the Quattrocento. Reflecting his career, the scholarship on Donatello is vast and varied, and nearly all aspects of his life and works have received sustained attention. Though he trained in bronze casting and, apparently, in goldsmithery, his first documented works were in marble. From c. 1406 to 1440 he carved marble sculptures for Florence Cathedral and its Campanile. During the first three decades of the fifteenth century he fashioned statues for the exterior of the Florentine guild church of Orsanmichele (Sts. Mark, George, and Louis of Toulouse), as well as a variety of sculptures elsewhere. In the 1420s and 1430s he worked in Siena, carrying out a relief and statues for the font of the Baptistery and a tomb slab for Giovanni Pecci (Cathedral). Alongside Michelozzo, with whom he maintained a legal partnership (c. 1425–1434), he completed in the 1420s other tombs—one for Baldassare Cossa (the antipope John XXIII) in the Florence Baptistery and another for Rainaldo Brancacci in Sant’Angelo a Nilo in Naples—and, in the 1430s, a pulpit for Prato Cathedral. He spent two years in Rome—1432–1433—and made a number of sculptures there; he also worked for patrons in Mantua, Ferrara, and Modena. Though inspired by ancient and medieval art, Donatello was a relentlessly innovative sculptor whose approach was often experimental. He invented the schiacciato relief, demonstrating painterly effects in sculpture; he participated in the reinvention of the bronze statuette; and he was one of the first to fashion, after Antiquity, life-sized, freestanding statues. Examples include his extensively studied bronze David and Judith and Holofernes, both of which, along with relief sculptures at the church of San Lorenzo, he made for the Medici family, his enthusiastic patrons. From c. 1443 to 1453 he resided in Padua, where he made sculptures for the interior of the Basilica of Sant’Antonio, as well as the equestrian portrait of Gattamelata. He worked in Siena from 1457 to 1459 before returning to Florence, where he died. He utilized a wide range of media: stone of all types, metal (gilded and ungilded bronze), glass, fiber, wax, ceramic, polychromed wood (e.g., the St. John the Baptist in Venice; his haunting Mary Magdelene), terracotta, and stucco—the latter two used to craft inventive reliefs of the Virgin and Christ Child. He was especially attentive to the treatment of surface and often painted, carved, or scratched materials so they resembled other substances. Near-contemporary sources describe him as sarcastic, witty, and clever.
The Possibility of Striving Play
Authors: Nguyen C. Thi 
Published: April 2020

Abstract
There are two sorts of play. In achievement play, we play for the sake of winning. In striving play we take up a temporary interest in winning for the sake of the activity of the pursuit. Striving play is a motivational inversion of ordinary practical life. In striving play, we take on disposable ends—temporary ends that guide our actions for a time, and then are discarded. But a skeptic might doubt the possibility of striving play. This chapter addresses the skeptic and argues for the possibility of striving play, using Bernard Suits’s insights into the motivational structure of game playing. The chapter considers a wide variety of game-playing phenomena, including silly party games, long-term game-playing relationships among friends and family, and the joys of comic failure in games. We learn that we can inhabit our agency with considerably more nimbleness and fluidity than we might have thought.
The Economic Origins of the “War on Terror”
Authors: Bapat Navin A. 
Published: April 2020

Abstract
The U.S. was in a position of economic and military hegemony after World War II. However, by the early 1970s, the U.S. dollar depreciated following President Richard Nixon’s abandonment of the gold standard. To fight this problem, Nixon offered indefinite military protection from all of their enemies to all oil-producing states, if those states agreed to denominate their oil sales exclusively in U.S. dollars. This agreement reestablished the U.S. as the world’s sole superpower. At the turn of the millennium, U.S. dominance faced challenges from al Qaeda and Saddam Hussein’s decision to abandon the dollar in favor of the euro in oil sales. The war on terror began as an effort to eliminate each of these threats. Following the Iraq war, the U.S. seemed to establish control and alliances with all of the world’s key suppliers of energy, along with the states serving as transit routes.