bluuebunny/crossref_metadata_2025_split huggingface dataset:
Partnership as Experimentation
Authors: Artunç Cihan , Guinnane Timothy W 
Published: May 2019

Abstract
Recent research disputes the view that the joint-stock corporation played a crucial role in historical economic development, but retains the idea that the costless firm dissolution implicit in non-corporate forms deterred investment. A multi-armed bandit model demonstrates the benefits of costless dissolution in an environment where potential business partners are not fully informed. Experimentation creates a spike in dissolution rates early in firms’ lives, as less productive matches break down and agents look for better matches. Many of the better matches adopt the corporate form, whose higher dissolution cost functions as a commitment device. We test the model’s predictions using firm-level data on 12,000 enterprises established in Egypt between 1910 and 1949. The partnership reflected a trade-off between committing to a partner and sorting into potentially better matches, fostering the formation of more productive enterprises (JEL D21, D22, L26, N15, O16).
Supergiant Fast X-ray Transients uncovered by the EXTraS project: flares reveal the development of magnetospheric instability in accreting neutron stars
Authors: Sidoli Lara , Postnov Konstantin A , Belfiore Andrea , Marelli Martino , Salvetti David , Salvaterra Ruben , De Luca Andrea , Esposito Paolo 
Published: May 2019

ABSTRACT
The low luminosity, X-ray flaring activity, of the sub-class of high-mass X-ray binaries called Supergiant Fast X-ray Transients, has been investigated using XMM–Newton public observations, taking advantage of the products made publicly available by the EXTraS project. One of the goals of EXTraS was to extract from the XMM–Newton public archive information on the aperiodic variability of all sources observed in the soft X-ray range with EPIC (0.2–12 keV). Adopting a Bayesian block decomposition of the X-ray light curves of a sample of SFXTs, we picked out 144 X-ray flares, covering a large range of soft X-ray luminosities (1032–1036 erg s−1). We measured temporal quantities, like the rise time to and the decay time from the peak of the flares, their duration and the time interval between adjacent flares. We also estimated the peak luminosity, average accretion rate, and energy release in the flares. The observed soft X-ray properties of low-luminosity flaring activity from SFXTs is in qualitative agreement with what is expected by the application of the Rayleigh–Taylor instability model in accreting plasma near the neutron star magnetosphere. In the case of rapidly rotating neutron stars, sporadic accretion from temporary discs cannot be excluded.
On the detectability of transiting planets orbiting white dwarfs using LSST
Authors: Cortés Jorge , Kipping David 
Published: May 2019

ABSTRACT
White dwarfs are one of the few types of stellar object for which we have yet to confirm the existence of companion planets. Recent evidence for metal contaminated atmospheres, circumstellar debris discs, and transiting planetary debris all indicates that planets may be likely. However, white dwarf transit surveys are challenging due to the intrinsic faintness of such objects, the short time-scale of the transits, and the low transit probabilities due to their compact radii. The Large Synoptic Survey Telescope (LSST) offers a remedy to these problems as a deep, half-sky survey with fast exposures encompassing approximately 10 million white dwarfs with r &lt; 24.5 apparent magnitude (mr). We simulate LSST photometric observations of 3.5 million white dwarfs over a 10 yr period and calculate the detectability of companion planets with P &lt; 10 d via transits. We find typical detection rates in the range of 5 × 10−6 to 4 × 10−4 for Ceres-sized bodies to Earth-sized worlds, yielding ∼50–$4000$ detections for a 100 per cent occurrence rate of each. For terrestrial planets in the continuously habitable zone, we find detection rates of ∼10−3 indicating that LSST would reveal hundreds of such worlds for occurrence rates in the range of 1–10 per cent.
RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants
Authors: Schwarz Jana Marie , Hombach Daniela , Köhler Sebastian , Cooper David N , Schuelke Markus , Seelow Dominik 
Published: May 2019

Abstract
RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of DNA variants located outside of protein-coding transcripts (extratranscriptic variants). It is designed for clinicians and researchers who wish to assess the potential impact of the considerable number of non-coding variants found in Whole Genome Sequencing runs. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Its dichotomous classifications, ‘functional’ or ‘non-functional’, and a human-readable presentation of the underlying evidence allow a biologically meaningful interpretation of the score. The output shows key aspects of every variant and allows rapid access to more detailed information about its possible role in gene regulation. RegulationSpotter can either analyse single variants or complete VCF files. Variants located within protein-coding transcripts are automatically assessed by MutationTaster as well as by RegulationSpotter to account for possible intragenic regulatory effects. RegulationSpotter offers the possibility of using phenotypic data to focus on known disease genes or genomic elements interacting with them. RegulationSpotter is freely available at https://www.regulationspotter.org.
Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes
Authors: Socol Marius , Wang Renjie , Jost Daniel , Carrivain Pascal , Vaillant Cédric , Le Cam Eric , Dahirel Vincent , Normand Christophe , Bystricky Kerstin , Victor Jean-Marc , Gadal Olivier , Bancaud Aurélien 
Published: May 2019

Abstract
DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of –0.3 to –0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in ‘theta’ conditions, in which they are poised for compartmentalization and phase separation.
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism
Authors: Aydınkal Rasim Murat , Serçinoğlu Onur , Ozbek Pemra 
Published: May 2019

AbstractProSNEx (Protein Structure Network Explorer) is a web service for construction and analysis of Protein Structure Networks (PSNs) alongside amino acid flexibility, sequence conservation and annotation features. ProSNEx constructs a PSN by adding nodes to represent residues and edges between these nodes using user-specified interaction distance cutoffs for either carbon-alpha, carbon-beta or atom-pair contact networks. Different types of weighted networks can also be constructed by using either (i) the residue-residue interaction energies in the format returned by gRINN, resulting in a Protein Energy Network (PEN); (ii) the dynamical cross correlations from a coarse-grained Normal Mode Analysis (NMA) of the protein structure; (iii) interaction strength. Upon construction of the network, common network metrics (such as node centralities) as well as shortest paths between nodes and k-cliques are calculated. Moreover, additional features of each residue in the form of conservation scores and mutation/natural variant information are included in the analysis. By this way, tool offers an enhanced and direct comparison of network-based residue metrics with other types of biological information. ProSNEx is free and open to all users without login requirement at http://prosnex-tool.com.
web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning
Authors: Röder Benedict , Kersten Nicolas , Herr Marius , Speicher Nora K , Pfeifer Nico 
Published: May 2019

Abstract
More and more affordable high-throughput techniques for measuring molecular features of biomedical samples have led to a huge increase in availability and size of different types of multi-omic datasets, containing, for example, genetic or histone modification data. Due to the multi-view characteristic of the data, established approaches for exploratory analysis are not directly applicable. Here we present web-rMKL, a web server that provides an integrative dimensionality reduction with subsequent clustering of samples based on data from multiple inputs. The underlying machine learning method rMKL-LPP performed best for clinical enrichment in a recent benchmark of state-of-the-art multi-view clustering algorithms. The method was introduced for a multi-omic cancer subtype discovery setting, however, it is not limited to this application scenario as exemplified by a presented use case for stem cell differentiation. web-rMKL offers an intuitive interface for uploading data and setting the parameters. rMKL-LPP runs on the back end and the user may receive notifications once the results are available. We also introduce a preprocessing tool for generating kernel matrices from tables containing numerical feature values. This program can be used to generate admissible input if no precomputed kernel matrices are available. The web server is freely available at web-rMKL.org.
PrankWeb: a web server for ligand binding site prediction and visualization
Authors: Jendele Lukas , Krivak Radoslav , Skoda Petr , Novotny Marian , Hoksza David 
Published: May 2019

AbstractPrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points with a high ligandability score are then clustered to form the resulting ligand binding sites. In addition, PrankWeb provides a web interface enabling users to easily carry out the prediction and visually inspect the predicted binding sites via an integrated sequence-structure view. Moreover, PrankWeb can determine sequence conservation for the input molecule and use this in both the prediction and result visualization steps. Alongside its online visualization options, PrankWeb also offers the possibility of exporting the results as a PyMOL script for offline visualization. The web frontend communicates with the server side via a REST API. In high-throughput scenarios, therefore, users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application. PrankWeb is available at http://prankweb.cz/, while the web application source code and the P2Rank method can be accessed at https://github.com/jendelel/PrankWebApp and https://github.com/rdk/p2rank, respectively.
ChEA3: transcription factor enrichment analysis by orthogonal omics integration
Authors: Keenan Alexandra B , Torre Denis , Lachmann Alexander , Leong Ariel K , Wojciechowicz Megan L , Utti Vivian , Jagodnik Kathleen M , Kropiwnicki Eryk , Wang Zichen , Ma’ayan Avi 
Published: May 2019

AbstractIdentifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step in understanding gene regulatory networks. ChIP-X Enrichment Analysis 3 (ChEA3) is a transcription factor enrichment analysis tool that ranks TFs associated with user-submitted gene sets. The ChEA3 background database contains a collection of gene set libraries generated from multiple sources including TF–gene co-expression from RNA-seq studies, TF–target associations from ChIP-seq experiments, and TF–gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate a composite rank that improves the prediction of the correct upstream TF compared to ranks produced by individual libraries. We compare ChEA3 with existing TF prediction tools and show that ChEA3 performs better. By integrating the ChEA3 libraries, we illuminate general transcription factor properties such as whether the TF behaves as an activator or a repressor. The ChEA3 web-server is available from https://amp.pharm.mssm.edu/ChEA3.
CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase
Authors: Jensen Drake , Manzano Ana Ruiz , Rammohan Jayan , Stallings Christina L , Galburt Eric A 
Published: May 2019

AbstractThe pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, enacts unique transcriptional regulatory mechanisms when subjected to host-derived stresses. Initiation of transcription by the Mycobacterial RNA polymerase (RNAP) has previously been shown to exhibit different open complex kinetics and stabilities relative to Escherichia coli (Eco) RNAP. However, transcription initiation rates also depend on the kinetics following open complex formation such as initial nucleotide incorporation and subsequent promoter escape. Here, using a real-time fluorescence assay, we present the first in-depth kinetic analysis of initial transcription and promoter escape for the Mtb RNAP. We show that in relation to Eco RNAP, Mtb displays slower initial nucleotide incorporation but faster overall promoter escape kinetics on the Mtb rrnAP3 promoter. Furthermore, in the context of the essential transcription factors CarD and RbpA, Mtb promoter escape is slowed via differential effects on initially transcribing complexes. Finally, based on their ability to increase the rate of open complex formation and decrease the rate of promoter escape, we suggest that CarD and RbpA are capable of activation or repression depending on the rate-limiting step of a given promoter's basal initiation kinetics.
Who Speaks for Porn?
Authors: Padgett Esra 
Published: May 2019

Abstract
This chapter opens with the question “Who speaks for porn?” as a way to interrogate historical discourses on pornography and to reposition academic approaches to the subject. Taking a linguistic anthropological lens to academic work on pornography, the chapter provides a close examination of the ways in which ideologies about porn are constructed, focusing in particular on the discursive circulation of the social figures central to pornography: performers, producers, and consumers. The concept of porn literacy is introduced to stress the importance of developing informed reading practices in future academic work on porn. To this end, a case study of a porn performer is offered to demonstrate how an ethnographically informed approach to semiotic processes of authentication, branding, and mediatization may lead to new understandings of the political economic structure of pornography and broaden our definitions of authenticity, desire, and subjectivity.
Inspired and Appreciated by the Group
Authors: Haslam S. Alexander , Adarves-Yorno Inmaculada , Steffens Niklas K. , Postmes Tom 
Published: May 2019

Abstract
The processes of creative production and creativity recognition are both understood to be central to the dynamics of creativity. Nevertheless, they are generally seen by creativity researchers as theoretically unrelated. In contrast, social identity theorizing suggests a model of creativity in which groups play a role both in inspiring creative acts and in determining the reception they receive. More specifically, this approach argues that shared social identity (or lack of it) motivates individuals to rise to particular creative challenges and provides a basis for certain forms of creativity to be recognized (or disregarded). This chapter explicates the logic underlying the social identity approach and summarizes some of the key evidence that supports it.
Including Islam
Authors: Leder Stefan 
Published: May 2019

Abstract
Weber’s concept of Islam as a cultural configuration including religion, society, and political order was conceived against the backdrop of Europe’s supposed uniqueness and exemplary path to modernity. Yet his ambition of advancing transcultural understanding and exploring a plurality of developmental histories offers inspiration to this day also for the Islamic perspective. Repositioning his ideas about warrior Islam, Islamic beliefs, Islamic law, and patrimonialism in the context of contemporary postcolonial, postmodern, and global theory reveals details, correlations, and perspectives that Weber at the time ignored or omitted. Complementing theory with up-to-date historical research on the Middle East provides further corrections. A critical appraisal of Weber’s approach and the discussions it triggered allows recognition of the dynamics of Islamic history, such as the role of religion and religious authority in the evolution of state–society relations. It also assists in understanding Islamic features of modernity, including fundamentalism and the role of tradition, that inform the tension between moral values and politics. Going beyond the historical limitation of Weber’s assessment of prevalent features of Islam, the vitality of Islamic tradition and its particular pathway to modernity are recognizable in terms corresponding with the intention of Weber’s transcultural approach and its contemporary reinterpretations.
Money, Credit, and Finance in Capitalism
Authors: Ingham Geoffrey 
Published: May 2019

Abstract
The analysis of money was impaired by the disciplinary separation of economics and sociology following the Methodenstreit. Sociology abnegated responsibility for its study to economics, which treated it as a relatively unimportant “neutral veil” over the operation of the “real” economy. Weber worked to overcome the disciplinary balkanization, but ironically this has led to a neglect of his contributions to the analysis of money’s role in capitalism. For example, The Religion of China opens with an account of the underdeveloped monetary system and its inhibitory impact on the development of capitalism. Money is an essential element in the instrumental rationality in modern Western capitalism’s vast impersonal markets and rational capital accounting of profitability in the enterprise. Money prices which enable rational calculation can only be established when money is a “weapon in the struggle for economic existence” and not merely a “neutral” economic medium of exchange. Consequently, administered prices in command and socialist economies inhibit rationality and efficiency.
School District Boundaries
Authors: Frankenberg Erica , Siegel-Hawley Genevieve , Diem Sarah 
Published: May 2019

Abstract
This chapter focuses on district boundary lines, social science evidence, and litigation to consider how they shape student enrollment and segregation. Social science clearly shows that district boundaries continue to hamper school integration by race and income, perhaps more so now than in the past. When it comes to the courts, some decisions have recognized the damaging impact of school-related boundaries when it comes to school desegregation. Others have not. Over the past few decades, the ambiguity of the law has helped create differing boundary line arrangements across the country. The chapter reviews three different areas to understand the legal and political significance of boundaries. St. Louis, Missouri, shows us that interdistrict desegregation plans where district boundaries remain intact face uphill battles, with implications for state court cases in the highly fragmented Northeast. In Alabama, recent federal law suggests that the courts may be returning to their earlier understanding of how district boundaries work. In Tennessee, though, federal courts permitted a damaging proliferation of boundary lines. These cases illustrate what social science tells us about district boundaries—that they give shape to segregation. They show that boundary lines are not immutable and that the way they shift matters a great deal in shaping access to opportunity for students, particularly for black, Latino, and low-income students. Ultimately, the chapter argues that a renewed judicial and political understanding of the segregating impact of district boundaries is imperative and offer recommendations for how to mitigate their impact.
Race, Phenotype, and Nationality in Brazil and the United States
Authors: Joseph Tiffany D. 
Published: May 2019

AbstractIn recent decades, there have been substantial developments in the sociologies of the body and race. However, race has been understudied in sociology of the body at the same time that the sociology of race has not often explored the influence of phenotypical differences on individuals’ experiences and outcomes. Using ethnographic data from interviews with seventy-three Brazilians in Governador Valadares, this chapter illustrates how race and phenotype shape perceptions of Brazilian and American nationality and discrimination in Brazil and the United States. In so doing, the findings show that researchers cannot assess race in each context without incorporating the body. Thus, more theoretical leverage can be gained in each subfield by merging both literatures to better understand the crucial role that the body and race play in racialized societies.
Endogenous and Exogenous Election Timing
Authors: Schleiter Petra 
Published: May 2019

Abstract
This chapter examines the rules that govern election timing in democracies. It begins by distinguishing between constitutionally fixed (exogenous) and constitutionally flexible (endogenous) election timing, reviews which political actors can call early elections when endogenous election timing is permitted, and notes that early elections are heterogeneous and can be of two distinct types—either triggered by government failure or called for partisan advantage. Next, the chapter summarizes the current understanding of the consequences of election timing rules for four important political outcomes: gridlock resolution, the electoral performance of incumbents, the bargaining power of various political actors in negotiating governments and policy, and the rhythm of policy cycles. Together the findings reviewed in this chapter show that election timing rules are highly consequential: they shape election outcomes, accountability, and policy, with significant implications for governance and voter welfare.