bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies
Authors: Islam Shahidul , Rahaman Md Mahfuzur , Zhang Shaojie 
Published: February 2021

Abstract
Understanding the 3D structural properties of RNAs will play a critical role in identifying their functional characteristics and designing new RNAs for RNA-based therapeutics and nanotechnology. While several existing computational methods can help in the analysis of RNA properties by recognizing structural motifs, they do not provide the means to compare and contrast those motifs extensively. We have developed a new method, RNAMotifContrast, which focuses on analyzing the similarities and variations of RNA structural motif characteristics. In this method, a graph is formed to represent the similarities among motifs, and a new traversal algorithm is applied to generate visualizations of their structural properties. Analyzing the structural features among motifs, we have recognized and generalized the concept of motif subfamilies. To asses its effectiveness, we have applied RNAMotifContrast on a dataset of known RNA structural motif families. From the results, we observed that the derived subfamilies possess unique structural variations while holding standard features of the families. Overall, the visualization approach of this method presents a new perspective to observe the relation among motifs more closely, and the discovered subfamilies provide opportunities to achieve valuable insights into RNA’s diverse roles.
Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter
Authors: Dion Moïra B , Plante Pier-Luc , Zufferey Edwige , Shah Shiraz A , Corbeil Jacques , Moineau Sylvain 
Published: February 2021

Abstract
Thousands of new phages have recently been discovered thanks to viral metagenomics. These phages are extremely diverse and their genome sequences often do not resemble any known phages. To appreciate their ecological impact, it is important to determine their bacterial hosts. CRISPR spacers can be used to predict hosts of unknown phages, as spacers represent biological records of past phage–bacteria interactions. However, no guidelines have been established to standardize host prediction based on CRISPR spacers. Additionally, there are no tools that use spacers to perform host predictions on large viral datasets. Here, we developed a set of tools that includes all the necessary steps for predicting the hosts of uncharacterized phages. We created a database of &gt;11 million spacers and a program to execute host predictions on large viral datasets. Our host prediction approach uses biological criteria inspired by how CRISPR–Cas naturally work as adaptive immune systems, which make the results easy to interpret. We evaluated the performance using 9484 phages with known hosts and obtained a recall of 49% and a precision of 69%. We also found that this host prediction method yielded higher performance for phages that infect gut-associated bacteria, suggesting it is well suited for gut-virome characterization.
An in vitro reconstituted U1 snRNP allows the study of the disordered regions of the particle and the interactions with proteins and ligands
Authors: Campagne Sébastien , de Vries Tebbe , Malard Florian , Afanasyev Pavel , Dorn Georg , Dedic Emil , Kohlbrecher Joachim , Boehringer Daniel , Cléry Antoine , Allain Frédéric H-T 
Published: February 2021

Abstract
U1 small nuclear ribonucleoparticle (U1 snRNP) plays a central role during RNA processing. Previous structures of U1 snRNP revealed how the ribonucleoparticle is organized and recognizes the pre-mRNA substrate at the exon–intron junction. As with many other ribonucleoparticles involved in RNA metabolism, U1 snRNP contains extensions made of low complexity sequences. Here, we developed a protocol to reconstitute U1 snRNP in vitro using mostly full-length components in order to perform liquid-state NMR spectroscopy. The accuracy of the reconstitution was validated by probing the shape and structure of the particle by SANS and cryo-EM. Using an NMR spectroscopy-based approach, we probed, for the first time, the U1 snRNP tails at atomic detail and our results confirm their high degree of flexibility. We also monitored the labile interaction between the splicing factor PTBP1 and U1 snRNP and validated the U1 snRNA stem loop 4 as a binding site for the splicing regulator on the ribonucleoparticle. Altogether, we developed a method to probe the intrinsically disordered regions of U1 snRNP and map the interactions controlling splicing regulation. This approach could be used to get insights into the molecular mechanisms of alternative splicing and screen for potential RNA therapeutics.
Roxadustat for anemia in patients with end-stage renal disease incident to dialysis
Authors: Provenzano Robert , Shutov Evgeny , Eremeeva Liubov , Korneyeva Svitlana , Poole Lona , Saha Gopal , Bradley Charles , Eyassu Meraf , Besarab Anatole , Leong Robert , Liu Cameron S , Neff Thomas B , Szczech Lynda , Yu Kin-Hung P 
Published: February 2021

Abstract

Background
We evaluated the efficacy and safety of roxadustat versus epoetin alfa for the treatment of chronic kidney disease-related anemia in patients new to dialysis.

Methods
HIMALAYAS was a Phase 3, open-label, epoetin alfa-controlled trial. Eligible adults were incident to hemodialysis/peritoneal dialysis for 2 weeks to ≤4 months prior to randomization and had mean hemoglobin (Hb) ≤10.0 g/dL. Primary endpoints were mean Hb (g/dL) change from baseline averaged over Weeks 28–52 regardless of rescue therapy [non-inferiority criterion: lower limit of 95% confidence interval (CI) for treatment difference &gt;−0.75] and percentage of patients achieving an Hb response between Weeks 1 and 24 censored for rescue therapy (non-inferiority margin for between-group difference −15%). Adverse events were monitored.

Results
The intent-to-treat population included patients randomized to roxadustat (n = 522) or epoetin alfa (n = 521). Mean (standard deviation) Hb changes from baseline averaged over Weeks 28–52 were 2.57 (1.27) and 2.36 (1.21) in the roxadustat and epoetin alfa groups. Roxadustat was non-inferior [least squares mean difference: 0.18 (95% CI 0.08, 0.29)] to epoetin alfa. Percentages of patients with an Hb response were 88.2% and 84.4% in the roxadustat and epoetin alfa groups, respectively. Roxadustat was non-inferior to epoetin alfa [treatment-group difference 3.5% (95% CI −0.7%, 7.7%)]. Adverse event rates were comparable between treatment groups.

Conclusions
Roxadustat was efficacious for correcting and maintaining Hb levels compared with epoetin alfa. Roxadustat had an acceptable safety profile.
The First Troll Prerequisite
Authors: Jamieson Kathleen Hall 
Published: February 2021

Abstract
Chapter 3 examines the first prerequisite required for social media or hacked content to influence the U.S. election: was it widespread and extensive enough to make a difference? The chapter first notes that 2016 election-related Russian propaganda was also disseminated overtly via Russia’s state-sponsored RT. Jamieson goes on to detail the extent and reach of the trolls’ covert social media messaging on platforms such as Facebook, Twitter, Instagram, YouTube, Tumblr, Reddit, 9GAG, and more. The chapter discusses the use of troll accounts to create and amplify content across platforms, including Russian-hacked Democratic content released on WikiLeaks, as well as the use of bots on these sites to skew the trending of content.
The Third Troll Prerequisite, Part 1
Authors: Jamieson Kathleen Hall 
Published: February 2021

Abstract
Chapter 5 examines the third prerequisite for Russian stolen or generated content to influence the U.S. election: did it address the interests of vital constituencies whose mobilization or demobilization was critical to a Trump Electoral College victory? The chapter details how troll messaging and the release of hacked content aimed to influence two key traditional Republican voting blocs that Trump needed in order to win: white Christians and veterans. Jamieson explores the trolls’ appeals to evangelical Protestants and conservative Catholics, including the use of a hacked exchange involving a Clinton communications director. In a similar fashion, the chapter shows how the trolls worked to mobilize veterans by attacking Clinton’s record on military affairs.
Lincoln Center
Authors: Robin William 
Published: February 2021

Abstract
When Bang on a Can first hosted their marathon concert and All-Stars recitals at Lincoln Center in 1994, critics and observers wrote about them with hyperbolic rhetoric, emphasizing how different the upstart festival was from the hallowed grounds of the Manhattan presenter. But under the direction of curator Jane Moss, Lincoln Center had begun to embrace contemporary music, representing a moment in which some of classical music’s most mainstream organizations looked to new work in the hopes of reaching new audiences. Bang on a Can, too, found new audiences at Lincoln Center; in partnering with the major institution, the organization prioritized their marketplace aims—their desire for expanding its reach—over the anti-establishment image that they had previously cultivated.
The Scientific Hypothesis Today
Authors: Alger Bradley E. 
Published: February 2021

Abstract
Chapter 2 begins by reviewing the concept of the Scientific Method, as well as many outdated definitions of “hypothesis.” The discussion leads to the modern definition of the hypothesis as a conjectural explanation for a phenomenon; it is testable and falsifiable. The hypothesis serves as a blueprint and a summary of an investigation. Certain criticisms of the hypothesis and hypothesis-driven research are based on the older definitions of the term, and the book returns to them later. This chapter identifies and defines, with simple, nontechnical examples, concepts associated with the hypothesis, such as prediction and direct and indirect measurements. The philosophical programs of Karl Popper and John Platt, Critical Rationalism and Strong Inference, respectively, form a major focus of the chapter. The chapter explores the complexities of the concepts of falsification and corroboration and the importance of having multiple hypotheses. The chapter introduces the idea of the implicit hypothesis and ends with the presentation and discussion of key features of a good hypothesis.
Equal Footing
Authors: Ablavsky Gregory 
Published: February 2021

Abstract
In 1796, the Southwest Territory became the first U.S. territory to become a state, joining the union as Tennessee. This new state promptly used its newfound status as a sovereign on “equal footing” with existing states to challenge the persistence of federal authority, especially over land and Indian affairs. A series of collisions followed: over ownership of the public domain; over William Blount’s odd scheme to use his supposed influence in Indian country to challenge federal power; and, above all, over the federal government’s attempt to survey the boundary of the Cherokee Nation, which threatened to dispossess white land claimants. Ultimately, the federal government preserved its formal authority even as it gave Tennessee what it wanted—a seemingly Pyrrhic victory that had important precedential consequences. In particular, when part of the Northwest Territory sought to become the new state of Ohio in 1802, the federal government sought to protect its authority. Most importantly, it decided for the first time to attach conditions to the new state’s admission that guaranteed federal land ownership, a practice that quickly became a constitutional norm; the new state also tacitly accepted continued federal authority over the state’s Native peoples. The result was that the federal government’s power to adjudicate property and jurisdictional conflicts survived despite state challenge; in the process, the federal government ironically became the most visible defender of the earlier, multipolar order against these states’ assaults.
Epilogue
Authors: Ablavsky Gregory 
Published: February 2021

Abstract
Three federal systems coalesced from the ad hoc practices of governance in the Northwest and Southwest Territories—over land, Indian affairs, and the territories themselves. The foundations for the federal land system laid in these early struggles persisted and survived through the Civil War and beyond, as federal adjudication of land rights expanded. The federal government also codified its earlier experiments in compensation, formalizing its payments to Natives and whites even as it also continued to pay for brutal, even genocidal violence against Native peoples from the federal treasury. Finally, even Congress continued to use conditional admission to try to control newly admitted states, the territorial system entrenched the expectation that the plural sovereignty and ownership of the borderlands was temporary; statehood represented the moment when these preexisting claims supposedly passed away. Statehood also helped doom the flawed vision that the federal government would serve as a neutral arbiter between Natives and whites. Rather, statehood gave the former territories perhaps the most effective way yet to make claims on the federal government. As these new states increasingly became the federal government—in Congress, in the cabinet, and in the presidency—they turned their goals into federal law. This result occurred within the federal lands, where states successfully bent federal land policy to serve their expansionist aims, and in Indian affairs, where state representatives successfully persuaded the federal government to back their assertions of sovereignty against the compelling sovereignty claims of the Cherokee and Native Nations in the struggle known as Removal. This effectiveness at exploiting federal power allowed these former territories to rapidly remake these former borderlands to satisfy their long-standing settler colonial aspirations.
A First Example: The “Particle in a Box“ and Quantized Translational Motion
Authors: Autschbach Jochen 
Published: February 2021

Abstract
The simple ‘particle in a box’ (Piab) is introduced in this chapter so that the reader can get familiar with applying the quantum recipe and atomic units. The PiaB is introduced in its one, two, and three dimensional variants, which demonstrates the use of the separation of variables technique as a strategy to solve the Schrodinger equation for a particle with two or three degrees of freedom. It is shown that the confinement of the particle causes the energy to be quantized. The one-dimensional PiaB is then applied to treat the electronic spectra of cyanine dyes and their absorption colors. The chapter then introduces more general setups with finite potential wells, in order to introduce the phenomenon of quantum tunnelling and to discuss more generally with the unintuitive ‘quantum behavior’ of particles such as electrons. Scanning tunnelling and atomic force microscopes are also discussed briefly.
Hydrogen-like Atomic Wavefunctions: A First Sketch
Authors: Autschbach Jochen 
Published: February 2021

Abstract
This chapter reiterates the quantum numbers for atomic orbitals, known from general chemistry, and places them into the context developed so far. It is sketched how the Schrodinger equation (SE) for the hydrogen atom hydrogen-like systems (one electron plus a nucleus of charge Z) is set up. When the nucleus is treated as a fixed point charge, the SE is only for the electron. The solutions of the SE can be obtained by switching to spherical polar coordinates, such that the variables are separable in terms of the electron distance from the nucleus, r, and two angles. The kinetic energy of the electron then has a radial component, and an angular component. The latter is associated with the angular momentum quantum number, which is codified by the letters s, p, d, f, and so forth. A step by step solution of the SE is provided later, in chapter 19.
Particle in a Cylinder, in a Sphere, and on a Helix
Authors: Autschbach Jochen 
Published: February 2021

Abstract
The particle in a box from an earlier chapter is useful as a model to treat the electron motion in linear molecular ‘wires’, rectangular surfaces, and cuboid nano-particles. In this chapter, similar models are developed for spherical and cylindrical nano-particles, and helical nano-wires. Applications of these models that have been reported in the literature are discussed. For example, the particle in a cylinder model has been applied to treat the absorption spectra of silver nano-rods. The particle in a sphere model can be used tom rationalize the occurrence of sodium nano-clusters with certain ‘magic’ numbers of Na atoms. The model also explains the behaviour of potassium under high pressure, where the element starts to behave like a transition metal. The particle on a helix has been used to rationalize the optical activity of helical pi-conjugated molecules.
The One-electron Quantum Hamiltonian in the Presence of EM Fields
Authors: Autschbach Jochen 
Published: February 2021

Abstract
The interaction between atoms or molecules and electromagnetic (EM) fields underlies all spectroscopic techniques and a great variety of desirable molecular properties. EM fields and EM waves are introduced via the famous Maxwell equations. The scalar and vector potential are defined, and the gauge freedom is outlined. The Coulomb gauge is adopted. The classical Hamiltonian for a charged particle in an EM field is derived, and from this the ‘minimal substitution’ rules for incorporating the fields in the quantum Hamiltonian are obtained. The operators describing the interaction of an electron with static electric and magnetic fields, including the magnetic fields from nuclear spins, are derived, followed by the derivation of the interaction between an electron and an EM wave.
Goodbye to All That: Escape Stories
Authors: Woldoff Rachael A. , Litchfield Robert C. 
Published: February 2021

Abstract
Place matters—so much so that some successful people are willing to abandon their established lives to change it. Creative class professionals who leave behind their conventional lives and employment report that life in creative class cities is expensive and demanding. Moreover, their so-called creative jobs are often routine and disappointing, failing to offer a career track or promise of wage growth that will outpace the rising cost of living in these prime locations. This chapter examines digital nomads’ narratives of the push factors that drove them from their home countries into the digital nomad lifestyle abroad, detailing the factors that triggered their decisions to flee unfulfilling jobs, unsatisfying relationships, and unsustainable lifestyles. It explains why people with initiative and skills are increasingly considering new paths that allow them to retain control over their location, lifestyle, and employment options.
Epistemological Issues
Authors: Van Nieuwenhove Rik 
Published: February 2021

Abstract
Epistemological issues addressed in this chapter include: How do we know? Can we know God? Which three operations of the intellect does Aquinas identify and what do they mean (apprehension, judgement, reasoning)? How does Aquinas conceive of contemplation in the strictly speculative sense and how does it relate to these three operations? It argues that Aquinas draws an emphatic distinction between discursive reason (ratio) and simple understanding (intellectus), describing the acme of the contemplative act in terms of intuitus simplex, a simple, non-discursive insight into truth. Aquinas draws on Christian Neoplatonic authors, not Aristotle, to explain this. It is argued that Aquinas wanted to give scope to a non-apodeictic notion of contemplation, which could accommodate the phenomenon of insight after speculative reasoning, as well as the connatural, intuitive insight of the ordinary Christian.
The Dominican Calling and the Relation between the Active and Contemplative Lives
Authors: Van Nieuwenhove Rik 
Published: February 2021

Abstract
This chapter discusses how Aquinas conceives of the relation between the active and contemplative lives in light of the mendicant controversy. Aquinas distinguishes between the two lives on the basis of the distinction between the practical and theoretical intellect. Hence, he does not explicitly adopt the terminology of the mixed life. From the beginning of his career Aquinas argued that the contemplative life is inherently more meaningful; but at times, given the needs of the present life, the active life deserves priority and may prove more useful. Aquinas proved unwavering on this issue but his argumentation subtly shifts: increasingly, he will appeal to the role of charity to argue that greatest love is manifested when, at times, we relinquish the delights of contemplation to engage in activities of the active life, especially those closely associated with, and nourished by, contemplation: contemplata aliis tradere.
Under the Banner of Islam
Authors: Türkmen Gülay 
Published: February 2021

Abstract
How do religious, ethnic, and national identities interact in religiously homogenous ethnic conflicts? Is it possible for religion to act as a resolution tool in such conflicts? Why? Why not? In search for answers to these questions, Under the Banner of Islam focuses on the ambivalent role Sunni Islam has played in Turkey’s Kurdish conflict—both as a conflict-resolution tool and as a tool of resistance—in the last two decades. Relying mainly on participant observation in Civil Friday Prayers and 62 interviews conducted in three different cities in Turkey (Istanbul and the majority-Kurdish Diyarbakir and Batman) between June 2012 and June 2013, it demonstrates that Sunni Islam has had a very limited impact as a conflict-resolution tool in Turkey. Blending interview data with a detailed historical institutional analysis that goes back as early as the nineteenth century, it argues that the strength of Turkish and Kurdish nationalisms, the symbiotic relationship between Turkey’s religious and political fields, religious elites’ varying conceptualizations of religious and ethnic identities, and the recent political developments in the region (particularly the establishment of an autonomous Kurdish region, Rojava, in Syria) have all contributed to this outcome. The resulting narrative is not only a record of religion, ethnicity, and nationalism in Turkey’s Kurdish conflict, but also an investigation of how ethnic and religious identities are negotiated in conflict resolution and how symbolic boundaries are drawn in ethnic conflict zones.
What Happened in 1950?
Authors: Kirchman David L. 
Published: February 2021

Abstract
This chapter discusses what happened around 1950 that led to the expansion of dead zones. For the Gulf of Mexico, there are many reasons to think the flow of the Mississippi River has changed since the days of Mark Twain, considering the construction of so many levees, dikes, floodways, spillways, weirs, and revetments. Rain-absorbing grasslands and forests have been replaced by asphalt, roof shingles, and other hydrophobic material that hasten rainwater to the Gulf. But the flow of the Mississippi has not changed enough to explain why the Gulf dead zone grew around 1950. As the chapter discusses, what did change was nutrients. It shows that concentrations doubled in the Mississippi River from the 1930s to the 1990s, which stimulated algal growth and production of organic material that eventually led to depletion of dissolved oxygen. In addition to creating dead zones, the increase in nutrients has stimulated harmful algal blooms, leading to fish kills and beach closings.