bluuebunny/crossref_metadata_2025_split huggingface dataset:
The post-Herschelview of intrinsic AGN emission: constructing templates for galaxy and AGN emission at IR wavelengths
Authors: Bernhard E , Tadhunter C , Mullaney J R , Grimmett L P , Rosario D J , Alexander D M 
Published: February 2021

ABSTRACTMeasuring the star-forming properties of active galactic nucleus (AGN) hosts is key to our understanding of galaxy formation and evolution. However, this topic remains debated, partly due to the difficulties in separating the infrared (i.e. 1–1000 ${\rm \mu m}$) emission into AGN and star-forming components. Taking advantage of archival far-infrared data from Herschel, we present a new set of AGN and galaxy infrared templates and introduce the spectral energy distribution fitting code iragnsep. Both can be used to measure infrared host galaxy properties, free of AGN contamination. To build these, we used a sample of 100 local (z &lt; 0.3), low-to-high luminosity AGNs (i.e. Lbol$\ \sim \ 10^{42-46}$ erg s−1), selected from the 105-month Swift–BAT X-ray survey, which have archival Spitzer–IRS spectra and Herschel photometry. We first built a set of seven galaxy templates using a sample of 55 star-forming galaxies selected via infrared diagnostics. Using these templates, combined with a flexible model for the AGN contribution, we extracted the intrinsic infrared emission of our AGN sample. We further demonstrate that we can reduce the diversity in the intrinsic shapes of AGN spectral energy distributions down to a set of three AGN templates, of which two represent AGN continuum, and one represents silicate emission. Our results indicate that, on average, the contribution of AGNs to the far-infrared (λ ≳ 50 ${\rm \mu m}$) is not as high as suggested by some recent work. We further show that the need for two infrared AGN continuum templates could be related to nuclear obscuration, where one of our templates appears dominated by the emission of the extended polar dust.
Very low-frequency oscillations from the 11 Hz pulsar in Terzan 5: frame dragging back on the table.
Authors: du Buisson L , Motta S , Fender R 
Published: February 2021

ABSTRACT
We present a re-analysis of 47 Rossi X-ray Timing Explorer observations of the 11 Hz accreting pulsar IGR J17480-2446 in Terzan 5 during its 2010 outburst. We studied the fast-time variability properties of the source and searched for quasi-periodic oscillations (QPOs) in a large-frequency range. General relativity predicts that frame dragging occurs in the vicinity of a spinning compact object and induces the precession of matter orbiting said object. The relativistic precession model predicts that this frame dragging can be observed as QPOs with a characteristic frequency in the light curves of accreting compact objects. Such QPOs have historically been classified as horizontal branch oscillations in neutron star (NS) systems, and for a NS spinning at 11 Hz, these oscillations are expected at frequencies below 1 Hz. However, previous studies of IGR J17480-2446 have classified QPOs at 35–50 Hz as horizontal branch oscillations, thus casting doubts on the frame-dragging nature of such QPOs. Here, we report the detection of seven very low-frequency QPOs, previously undetected, with centroid frequencies below 0.3 Hz, and which can be ascribed to frame dragging. We also discuss the possible nature of the QPOs detected at 35–50 Hz in this alternative scenario.
Complete minicircle genome ofLeptomonas pyrrhocorisreveals sources of its non-canonical mitochondrial RNA editing events
Authors: Gerasimov Evgeny S , Gasparyan Anna A , Afonin Dmitry A , Zimmer Sara L , Kraeva Natalya , Lukeš Julius , Yurchenko Vyacheslav , Kolesnikov Alexander 
Published: February 2021

AbstractUridine insertion/deletion (U-indel) editing of mitochondrial mRNA, unique to the protistan class Kinetoplastea, generates canonical as well as potentially non-productive editing events. While the molecular machinery and the role of the guide (g) RNAs that provide required information for U-indel editing are well understood, little is known about the forces underlying its apparently error-prone nature. Analysis of a gRNA:mRNA pair allows the dissection of editing events in a given position of a given mitochondrial transcript. A complete gRNA dataset, paired with a fully characterized mRNA population that includes non-canonically edited transcripts, would allow such an analysis to be performed globally across the mitochondrial transcriptome. To achieve this, we have assembled 67 minicircles of the insect parasite Leptomonas pyrrhocoris, with each minicircle typically encoding one gRNA located in one of two similar-sized units of different origin. From this relatively narrow set of annotated gRNAs, we have dissected all identified mitochondrial editing events in L. pyrrhocoris, the strains of which dramatically differ in the abundance of individual minicircle classes. Our results support a model in which a multitude of editing events are driven by a limited set of gRNAs, with individual gRNAs possessing an inherent ability to guide canonical and non-canonical editing.
Reactive astrocytes in ALS display diminished intron retention
Authors: Ziff Oliver J , Taha Doaa M , Crerar Hamish , Clarke Benjamin E , Chakrabarti Anob M , Kelly Gavin , Neeves Jacob , Tyzack Giulia E , Luscombe Nicholas M , Patani Rickie 
Published: February 2021

Abstract
Reactive astrocytes are implicated in amyotrophic lateral sclerosis (ALS), although the mechanisms controlling reactive transformation are unknown. We show that decreased intron retention (IR) is common to human-induced pluripotent stem cell (hiPSC)-derived astrocytes carrying ALS-causing mutations in VCP, SOD1 and C9orf72. Notably, transcripts with decreased IR and increased expression are overrepresented in reactivity processes including cell adhesion, stress response and immune activation. This was recapitulated in public-datasets for (i) hiPSC-derived astrocytes stimulated with cytokines to undergo reactive transformation and (ii) in vivo astrocytes following selective deletion of TDP-43. We also re-examined public translatome sequencing (TRAP-seq) of astrocytes from a SOD1 mouse model, which revealed that transcripts upregulated in translation significantly overlap with transcripts exhibiting decreased IR. Using nucleocytoplasmic fractionation of VCP mutant astrocytes coupled with mRNA sequencing and proteomics, we identify that decreased IR in nuclear transcripts is associated with enhanced nonsense mediated decay and increased cytoplasmic expression of transcripts and proteins regulating reactive transformation. These findings are consistent with a molecular model for reactive transformation in astrocytes whereby poised nuclear reactivity-related IR transcripts are spliced, undergo nuclear-to-cytoplasmic translocation and translation. Our study therefore provides new insights into the molecular regulation of reactive transformation in astrocytes.
Increased yields of duplex sequencing data by a series of quality control tools
Authors: Povysil Gundula , Heinzl Monika , Salazar Renato , Stoler Nicholas , Nekrutenko Anton , Tiemann-Boege Irene 
Published: February 2021

Abstract
Duplex sequencing is currently the most reliable method to identify ultra-low frequency DNA variants by grouping sequence reads derived from the same DNA molecule into families with information on the forward and reverse strand. However, only a small proportion of reads are assembled into duplex consensus sequences (DCS), and reads with potentially valuable information are discarded at different steps of the bioinformatics pipeline, especially reads without a family. We developed a bioinformatics toolset that analyses the tag and family composition with the purpose to understand data loss and implement modifications to maximize the data output for the variant calling. Specifically, our tools show that tags contain polymerase chain reaction and sequencing errors that contribute to data loss and lower DCS yields. Our tools also identified chimeras, which likely reflect barcode collisions. Finally, we also developed a tool that re-examines variant calls from raw reads and provides different summary data that categorizes the confidence level of a variant call by a tier-based system. With this tool, we can include reads without a family and check the reliability of the call, that increases substantially the sequencing depth for variant calling, a particular important advantage for low-input samples or low-coverage regions.
A prospective phase II randomized trial of proton radiotherapy vs intensity-modulated radiotherapy for patients with newly diagnosed glioblastoma
Authors: Brown Paul D , Chung Caroline , Liu Diane D , McAvoy Sarah , Grosshans David , Al Feghali Karine , Mahajan Anita , Li Jing , McGovern Susan L , McAleer Mary-Fran , Ghia Amol J , Sulman Erik P , Penas-Prado Marta , de Groot John F , Heimberger Amy B , Wang Jihong , Armstrong Terri S , Gilbert Mark R , Guha-Thakurta Nandita , Wefel Jeffrey S 
Published: February 2021

Abstract

Background
To determine if proton radiotherapy (PT), compared to intensity-modulated radiotherapy (IMRT), delayed time to cognitive failure in patients with newly diagnosed glioblastoma (GBM).

Methods
Eligible patients were randomized unblinded to PT vs IMRT. The primary endpoint was time to cognitive failure. Secondary endpoints included overall survival (OS), intracranial progression-free survival (PFS), toxicity, and patient-reported outcomes (PROs).

Results
A total of 90 patients were enrolled and 67 were evaluable with median follow-up of 48.7 months (range 7.1-66.7). There was no significant difference in time to cognitive failure between treatment arms (HR, 0.88; 95% CI, 0.45-1.75; P = .74). PT was associated with a lower rate of fatigue (24% vs 58%, P = .05), but otherwise, there were no significant differences in PROs at 6 months. There was no difference in PFS (HR, 0.74; 95% CI, 0.44-1.23; P = .24) or OS (HR, 0.86; 95% CI, 0.49-1.50; P = .60). However, PT significantly reduced the radiation dose for nearly all structures analyzed. The average number of grade 2 or higher toxicities was significantly higher in patients who received IMRT (mean 1.15, range 0-6) compared to PT (mean 0.35, range 0-3; P = .02).

Conclusions
In this signal-seeking phase II trial, PT was not associated with a delay in time to cognitive failure but did reduce toxicity and patient-reported fatigue. Larger randomized trials are needed to determine the potential of PT such as dose escalation for GBM and cognitive preservation in patients with lower-grade gliomas with a longer survival time.
Parental Anti-Smoking Encouragement as a Longitudinal Predictor of Young Adult Cigarette and E-cigarette Use in a US National Study
Authors: Broun Aaron , Haynie Denise , Choi Kelvin 
Published: February 2021

Abstract

Introduction
Young adulthood is a critical period for the adoption of risk behaviors like tobacco use. Protective factors in adolescence may promote a tobacco-free transition to young adulthood. We examine associations between the frequency of parental anti-smoking encouragement in adolescence and cigarette and e-cigarette use in young adulthood.

Aims and Methods
We analyzed data from Waves 1 (2009–2010, 10th grade, mean age = 16.2 years) and 5 (2013–2014 mean age = 20.3 years) of the US nationally representative NEXT Generation Health Study (n = 1718). At Wave 1, participants reported how often their parents or guardians encourage them to not smoke cigarettes (1 = Rarely or Never, 7 = Frequently). We used separate weighted multiple logistic regression models to model Wave 5 past 30-day cigarette and e-cigarette use as functions of the frequency of parental anti-smoking encouragement at Wave 1, adjusting for sociodemographic and parenting factors, initial substance use, and peer tobacco use.

Results
The average frequency of parental encouragement to not smoke cigarettes was fairly high (mean = 5.35). At Wave 5, 24.7% and 14.2% of respondents reported cigarette and e-cigarette use in the past 30 days, respectively. Greater frequency of parental anti-smoking encouragement was associated with lower odds of subsequent cigarette smoking (adjusted odds ratio 0.91, 95% confidence interval 0.83, 0.99) but its association with e-cigarette use was not significant (adjusted odds ratio 0.93, 95% confidence interval 0.84, 1.04).

Conclusions
The longitudinal negative association between anti-smoking encouragement and cigarette use suggests that parental anti-tobacco communication could be a long-term protective factor against young adult tobacco use. Our findings may also suggest the importance of product-specific messages in the evolving tobacco use landscape.

Implications
This study builds upon prior investigations of parenting in adolescence as a protective factor against young adult risk behavior. We isolate the frequency of anti-smoking encouragement during adolescence as an actionable factor distinct from other parenting variables. Our findings also suggest that message specificity may be an important factor in parental anti-tobacco communication as youth and young adult tobacco use becomes increasingly dominated by e-cigarettes.
Association Between the Mode of Delivery and Infant Gut Microbiota Composition Up to 6 Months of Age: A Systematic Literature Review Considering the Role of Breastfeeding
Authors: Princisval Luciana , Rebelo Fernanda , Williams Brent L , Coimbra Anna Carolina , Crovesy Louise , Ferreira Ana Lorena , Kac Gilberto 
Published: February 2021

Abstract

Context
Cesarean section (CS), breastfeeding, and geographic location can influence the infant microbiota.

Objective
In this systematic review, evidence of the association between mode of delivery and infant gut microbiota up to 6 months of age was evaluated, as was the role of breastfeeding in this association, according to PRISMA guidelines.

Data Source
The Pubmed, Web of Science, Scopus, Embase, Medical Database, and Open Grey databases were searched.

Data Extraction
A total of 31 observational studies with ≥2 infant stool collections up to the sixth month of age and a comparison of gut microbiota between CS and vaginal delivery (VD) were included.

Data Analysis
Infants born by CS had a lower abundance of Bifidobacterium and Bacteroides spp. at almost all points up to age 6 months. Populations of Lactobacillus, Bifidobacterium longum, Bifidobacterium catenulatum, and Escherichia coli were reduced in infants delivered by CS. Infants born by CS and exclusively breastfed had greater similarity with the microbiota of infants born by VD.

Conclusions
Species of Bifidobacterium and Bacteroides are potentially reduced in infants born by CS. Geographic location influenced bacterial colonization.

Systematic Review Registration
PROSPERO registration no. 42017071285
The Farm Lobby and Agricultural Policy in Japan
Authors: Maclachlan Patricia L. , Shimizu Kay 
Published: February 2021

Abstract
Japanese agricultural policymaking has been changing over the past generation. For much of the postwar era, policy formulation fell under the purview of the powerful “farm lobby”—an iron triangle consisting of farm bureaucrats, conservative politicians, and Japan Agricultural Cooperatives (JA), a nationwide network of agricultural cooperative organizations. For the most part, the lobby prioritized the heavy subsidization of farm household incomes and other market-distorting redistributive measures. But by the end of the twentieth century, severe demographic and economic challenges in the countryside combined with new electoral rules to weaken the relative powers of the farm lobby and generate a gradual shift toward structural reform in the farm sector. In tracing these policy-related developments, which reached new heights during the second administration of Shinzō Abe, this chapter illuminates the significance of the organized farm vote, the empowerment of prime ministerial leadership, and the changing fortunes of agriculture in Japan.
The Bank of Japan
Authors: Park Gene 
Published: February 2021

Abstract
In April 1998, the Bank of Japan (BOJ) gained legal independence. While the primary theoretical justification was to enhance the central bank’s inflation-fighting credibility, the newly independent BOJ immediately confronted a different and unexpected problem: a long and persistent deflation. As the government battled economic stagnation, debates over the extent to which the BOJ should prioritize overcoming deflation and the policies that should be employed to this end led to a profound politicization of monetary policy. This culminated in the Prime Minister Abe’s landslide electoral victory at the end of 2012 in which he campaigned on overcoming deflation, and then, once in power, effectively took over control of a previously intransigent BOJ Policy Board to reflate the economy. The democratic electoral process paved the way for a reassertion of control over the still legally independent central bank. From a wider perspective, these developments reflect broader changes in Japanese democracy: the greater influence of electoral incentives on policy and the centralization of executive power.
Japan-EU Relations
Authors: Söderberg Marie 
Published: February 2021

Abstract
Japan and the European Union have recently made several agreements aiming to deepen their cooperation. An example of this is the “Partnership on Sustainable Connectivity and Quality Infrastructure between the European Union and Japan,” by which both EU and Japan agreed to “promote free, open, rules-based, fair, non-discriminatory and predictable regional and international trade and investment, transparent procurement practices, the ensuring of debt sustainability and the high standards of economic, fiscal, financial, social and environmental sustainability.” This is just the latest part in an effort by both to revive multilateral cooperation in the face of US withdrawal from international agreements and the rise of a more assertive China. Japan and EUs Strategic Partnership Agreement provides a legally binding framework for further cooperation in the field of politics, security, and development. Underpinning it are shared values and principles of democracy, the rule of law, human rights, and fundamental freedoms. For the protection of democracy and the liberal world order, Japan and the EU seem like ideal partners. The question is whether ongoing shifts in the power balance, geopolitics, crises of liberalism, domestic politics, and legal and technological changes will lead to broader and deeper cooperation. This chapter provides a historical background to Japan-European relations from WWII until today. The relation started with a heavy emphasis on trade and business. It is only recently that the two have broadened their cooperation and now stand up as two of the strongest defenders of a liberal rule-based world order.
Music Festival Capitalism
Authors: Anderton Chris 
Published: February 2021

Abstract
This chapter adds to a growing subfield of music festival studies by examining the business practices and cultures of the commercial outdoor sector, with a particular focus on rock, pop, and dance music events. The events of this sector require substantial financial and other capital in order to be staged and achieve success, yet the market is highly volatile, with relatively few festivals managing to attain longevity. It is argued that these events must balance their commercial needs with the socio-cultural expectations of their audiences for hedonistic, carnivalesque experiences that draw on countercultural understanding of festival culture (the countercultural carnivalesque). This balancing act has come into increased focus as corporate promoters, brand sponsors, and venture capitalists have sought to dominate the market in the neoliberal era of late capitalism. The chapter examines the riskiness and volatility of the sector before examining contemporary economic strategies for risk management and audience development, and critiques of these corporatizing and mainstreaming processes.
The Impact of Digitalization on Minority Music: Technological Change and Cultural Belonging among the Swedish-speaking Finns
Authors: Brusila Johannes 
Published: February 2021

Abstract
This chapter looks at the impact of digitalization on minority music. According to an often-recurring optimistic vision, digitalization has led to larger cultural diversification and democratization, whereas critical voices claim that social and industrial structures have not changed radically after all. From a cultural perspective, a key question is to what extent the technological changes have affected cultural belonging and the relationships between identity and music. These questions are discussed by applying theories related to identity and digitalization on the Swedish-speaking population of Finland. Based on the material, it appears that digitalization incorporates both opportunities and limits for preserving and developing cultural practices that are connected to the ethnicity. As a complex aesthetic practice, music also offers a variety of means of negotiating identity, tradition, and locality. Thus, it would be a simplification to expect any single one-way causal connection between digitalization and culture.
The Sunni Islamic Revival
Authors: Rock-Singer Aaron 
Published: February 2021

Abstract
Over the past century, waves of Sunni reformers from the Middle East to South Asia to central Asia have called for a return to Islam’s foundations by invoking well-established concepts in Islamic thought such as tajdid (renewal) and islah (reform). Yet, far from constituting a straightforward return to a well-established playbook, the revivalist movements of the 20th century have emerged at the intersection of longer Islamic theological and legal traditions, the ideological challenges of secular nationalism, and radical shifts in the nature of religious authority enabled by the linked spread of print and literacy. This chapter provides an overview of these movements, beginning in the late 19th century with the efforts of Jamal al-Din al-Afghani, Muhammad ‘Abduh, and Muhammad Rashid Rida, and then moving forward to varied revivalist trends, national and transnational, in the modern Middle East.
Excluded Generations in Non-Inclusive Nations
Authors: Fargues Philippe 
Published: February 2021

Abstract
This chapter offers an interpretation of the political link in Arab societies through the lens of demography. The first section shows how young generations today do not resemble those of earlier times. Rising education has raised expectations, and the reduction of fertility and postponement of childbearing have provided young adults with unprecedented individual freedom of movement. If expectations are not met by opportunities and young people have a feeling of exclusion, freedom of movement becomes a driver of emigration and rebellion. The second section of the chapter focuses on specific patterns of reproduction among Arab populations and the obstacles to building inclusive nations. On one side, the uniquely high prevalence of kinship endogamy means that marriage does not help unrelated population groups to integrate, so that blood bonds remain stronger than national bonds. On the other side, while the circulation of people is the most significant form of exchange between Arab countries, nationality laws based on exclusive jus sanguinis do not provide newcomers with pathways to full membership; and therefore, non-citizens have emerged as a category in Arab countries. Excluded generations in non-inclusive nations set the stage for prolonged political crises.