bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cycle of metals in the infalling elliptical galaxy NGC 1404
Authors: Mernier F , Werner N , Su Y , Pinto C , Grossová R , Simionescu A , Iodice E , Sarzi M , Görgei A 
Published: January 2022

ABSTRACT
Hot atmospheres pervading galaxy clusters, groups, and early-type galaxies are rich in metals, produced during epochs and diffused via processes that are still to be determined. While this enrichment has been routinely investigated in clusters, metals in lower mass systems are more challenging to probe with standard X-ray exposures and spectroscopy. In this paper, we focus on very deep XMM–Newton (∼350 ks) observations of NGC 1404, a massive elliptical galaxy experiencing ram-pressure stripping of its hot atmosphere while infalling towards the centre of the Fornax cluster, with the aim to derive abundances through its hot gas extent. Importantly, we report the existence of a new fitting bias – the ‘double Fe bias’ – leading to an underestimate of the Fe abundance when two thermal components cannot realistically model the complex temperature structure present in the outer atmosphere of the galaxy. Contrasting with the ‘metal conundrum’ seen in clusters, the Fe and Mg masses of NGC 1404 are measured 1–2 orders of magnitude below what stars and supernovae could have reasonably produced and released. In addition, we note the remarkable Solar abundance ratios of the galaxy’s halo, different from its stellar counterpart but similar to the chemical composition of the ICM of rich clusters. Completing the clusters regime, all these findings provide additional support towards a scenario of early enrichment, at play over two orders of magnitude in mass. A few peculiar and intriguing features, such as a possible double metal peak as well as an apparent ring of enhanced Si near the galaxy core, are also discussed.
Effect of evolving physical constants on type Ia supernova luminosity
Authors: Gupta Rajendra P 
Published: January 2022

ABSTRACT
Type Ia supernovae, SNeIa, are used as standard candles in cosmology to determine the distances of the galaxies harbouring them. We show that the luminosity of an SNIa depends on its distance from us when physical constants (the speed of light c, the gravitational constant G, and the Planck constant h) are permitted to evolve. It is because the Chandrasekhar mass of the white dwarf that explodes to create SNIa depends on the values of the constants at the epoch the SNIa is formed. We show that the SNeIa luminosities could be about four times higher in the past than they are now. Thus, the luminosity distance estimation of the earliest SNeIa could be off by up to a factor of 2. Cosmological parameters, determined with this correction applied to the redshift versus distance modulus data base (Pantheon SNeIa), are not very different from those from the standard ΛCDM model without this correction, except for the dark-energy density and the curvature energy density; the latter increases at the cost of the former. Variations of the constants are given by $\dot{G}/G = \ 3.90 \ ( { \pm 0.04} ) \times {10^{ - 10}}\ {\rm y{r^{ - 1}}}$and $\dot{c}/c = \dot{h}/h\ = \ 1.30\ ( { \pm 0.01} ) \times {10^{ - 10}}\ {\rm y{r^{ - 1}}}$ at present. These variations are valid only when $G,\ c,\ $and$\ h$ are permitted to vary concurrently rather than individually.
Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes
Authors: Ha Doyeon , Kim Donghyo , Kim Inhae , Oh Youngchul , Kong JungHo , Han Seong Kyu , Kim Sanguk 
Published: January 2022

AbstractMouse models have been engineered to reveal the biological mechanisms of human diseases based on an assumption. The assumption is that orthologous genes underlie conserved phenotypes across species. However, genetically modified mouse orthologs of human genes do not often recapitulate human disease phenotypes which might be due to the molecular evolution of phenotypic differences across species from the time of the last common ancestor. Here, we systematically investigated the evolutionary divergence of regulatory relationships between transcription factors (TFs) and target genes in functional modules, and found that the rewiring of gene regulatory networks (GRNs) contributes to the phenotypic discrepancies that occur between humans and mice. We confirmed that the rewired regulatory networks of orthologous genes contain a higher proportion of species-specific regulatory elements. Additionally, we verified that the divergence of target gene expression levels, which was triggered by network rewiring, could lead to phenotypic differences. Taken together, a careful consideration of evolutionary divergence in regulatory networks could be a novel strategy to understand the failure or success of mouse models to mimic human diseases. To help interpret mouse phenotypes in human disease studies, we provide quantitative comparisons of gene expression profiles on our website (http://sbi.postech.ac.kr/w/RN).
Usage of the H3 variants during the S-phase of the cell cycle in Physarum polycephalum
Authors: Thiriet Christophe 
Published: January 2022

Abstract
DNA replication occurring in S-phase is critical for the maintenance of the cell fate from one generation to the next, and requires the duplication of epigenetic information. The integrity of the epigenome is, in part, insured by the recycling of parental histones and de novo deposition of newly synthesized histones. While the histone variants have revealed important functions in epigenetic regulations, the deposition in chromatin during S-phase of newly synthesized histone variants remains unclear. The identification of histone variants of H3 and unique features of Physarum polycephalum provides a powerful system for investigating de novo deposition of newly synthesized histones by tracking the incorporation of exogenous histones within cells. The analyses revealed that the rate of deposition of H3.1 and H3.3 is anticorrelated as S-phase progresses, H3.3 is predominately produced and utilized in early S and dropped throughout S-phase, while H3.1 behaved in the opposite way. Disturbing the expression of H3 variants by siRNAs revealed mutual compensation of histone transcripts. Interestingly, the incorporation of pre-formed constrained histone complexes showed that tetramers of H3/H4 are more efficiently utilized by the cell than dimers. These results support the model whereby the histone variant distribution is established upon replication and new histone deposition.
High mobility group AT-hook 1 (HMGA1) is an important positive regulator of hepatitis B virus (HBV) that is reciprocally upregulated by HBV X protein
Authors: Shen Zhongliang , Wu Jingwen , Gao Zixiang , Zhang Shenyan , Chen Jingwen , He Jingjing , Guo Yifei , Deng Qiang , Xie Youhua , Liu Jing , Zhang Jiming 
Published: January 2022

Abstract
Chronic infection with hepatitis B virus (HBV) is associated with liver cirrhosis and hepatocellular carcinoma. Upon infection of hepatocytes, HBV covalently closed circular DNA (cccDNA) exists as histone-bound mini-chromosome, subjected to transcriptional regulation similar to chromosomal DNA. Here we identify high mobility group AT-hook 1 (HMGA1) protein as a positive regulator of HBV transcription that binds to a conserved ATTGG site within enhancer II/core promoter (EII/Cp) and recruits transcription factors FOXO3α and PGC1α. HMGA1-mediated upregulation of EII/Cp results in enhanced viral gene expression and genome replication. Notably, expression of endogenous HMGA1 was also demonstrated to be upregulated by HBV, which involves HBV X protein (HBx) interacting with SP1 transcription factor to activate HMGA1 promoter. Consistent with these in vitro results, chronic hepatitis B patients in immune tolerant phase display both higher intrahepatic HMGA1 protein levels and higher serum HBV markers compared to patients in inactive carrier phase. Finally, using a mouse model of HBV persistence, we show that targeting endogenous HMGA1 through RNA interference facilitated HBV clearance. These data establish HMGA1 as an important positive regulator of HBV that is reciprocally upregulated by HBV via HBx and also suggest the HMGA1-HBV positive feedback loop as a potential therapeutic target.
Structural characterization of the ANTAR antiterminator domain bound to RNA
Authors: Walshe James L , Siddiquee Rezwan , Patel Karishma , Ataide Sandro F 
Published: January 2022

Abstract
Regulated transcription termination provides an efficient and responsive means to control gene expression. In bacteria, rho-independent termination occurs through the formation of an intrinsic RNA terminator loop, which disrupts the RNA polymerase elongation complex, resulting in its dissociation from the DNA template. Bacteria have a number of pathways for overriding termination, one of which is the formation of mutually exclusive RNA motifs. ANTAR domains are a class of antiterminator that bind and stabilize dual hexaloop RNA motifs within the nascent RNA chain to prevent terminator loop formation. We have determined the structures of the dimeric ANTAR domain protein EutV, from Enterococcus faecialis, in the absence of and in complex with the dual hexaloop RNA target. The structures illustrate conformational changes that occur upon RNA binding and reveal that the molecular interactions between the ANTAR domains and RNA are restricted to a single hexaloop of the motif. An ANTAR domain dimer must contact each hexaloop of the dual hexaloop motif individually to prevent termination in eubacteria. Our findings thereby redefine the minimal ANTAR domain binding motif to a single hexaloop and revise the current model for ANTAR-mediated antitermination. These insights will inform and facilitate the discovery of novel ANTAR domain RNA targets.
Nicotine Patch Alters Patterns of Cigarette Smoking-Induced Dopamine Release: Patterns Relate to Biomarkers Associated With Treatment Response
Authors: Zakiniaeiz Yasmin , Liu Heather , Gao Hong , Najafzadeh Soheila , Ropchan Jim , Nabulsi Nabeel , Huang Yiyun , Matuskey David , Chen Ming-Kai , Cosgrove Kelly P , Morris Evan D 
Published: January 2022

Abstract

Introduction
Tobacco smoking is a major public health burden. The first-line pharmacological treatment for tobacco smoking is nicotine replacement therapy (eg, the nicotine patch (NIC)). Nicotine acts on nicotinic-acetylcholine receptors on dopamine terminals to release dopamine in the ventral and dorsal striatum encoding reward and habit formation, respectively.

Aims and Methods
To better understand treatment efficacy, a naturalistic experimental design combined with a kinetic model designed to characterize smoking-induced dopamine release in vivo was used. Thirty-five tobacco smokers (16 female) wore a NIC (21 mg, daily) for 1-week and a placebo patch (PBO) for 1-week in a randomized, counter-balanced order. Following 1-week under NIC and then overnight abstinence, smokers participated in a 90-minute [11C]raclopride positron emission tomography scan and smoked a cigarette while in the scanner. Identical procedures were followed for the PBO scan. A time-varying kinetic model was used at the voxel level to model transient dopamine release peaking instantaneously at the start of the stimulus and decaying exponentially. Magnitude and spatial extent of dopamine release were estimated. Smokers were subcategorized by nicotine dependence level and nicotine metabolism rate.

Results
Dopamine release magnitude was enhanced by NIC in ventral striatum and diminished by NIC in dorsal striatum. More-dependent smokers activated more voxels than the less-dependent smokers under both conditions. Under PBO, fast metabolizers activated more voxels in ventral striatum and fewer voxels in dorsal striatum compared to slow metabolizers.

Conclusions
These findings demonstrate that the model captured a pattern of transient dopamine responses to cigarette smoking which may be different across smoker subgroup categorizations.

Implications
This is the first study to show that NIC alters highly localized patterns of cigarette smoking-induced dopamine release and that levels of nicotine dependence and nicotine clearance rate contribute to these alterations. This current work included a homogeneous subject sample with regards to demographic and smoking variables, as well as a highly sensitive model capable of detecting significant acute dopamine transients. The findings of this study add support to the recent identification of biomarkers for predicting the effect of nicotine replacement therapies on dopamine function which could help refine clinical practice for smoking cessation.
Pembrolizumab and Trastuzumab in High Tumor Mutational Burden and POLE-Mutated HER2-Positive Refractory Breast Cancer
Authors: Zhang Li , Chen Yimeng , Lv Yao , Jiao Shunchang , Zhao Weihong 
Published: January 2022

Abstract
Metastatic breast cancer (mBC) is an incurable disease, and it is not sensitive to immunotherapy due to its low immunogenicity. Recently, inactivated DNA polymerase epsilon (POLE) mutations have been found to be associated with high tumor mutational burden (TMB), which is an effective immuno-oncology biomarker. Patients with POLE mutations with different types of cancer have properly responded to immunotherapy. We aimed to report the first case of programmed death-ligand 1 (PD-L1)-negative mBC presenting with high TMB and POLE mutations, in which a complete response to 5 cycles of chemotherapy and 1 year of pembrolizumab and trastuzumab was noted after failing several lines of HER2-targeted therapies. Our findings also suggest that biomarker-driven patient selection is highly significant for further clinical development of combination therapies via anti-HER2 plus immune-checkpoint inhibitors for HER2+ BC patients.
Urban Climate Adaptation
Authors: Chu Eric , Shi Linda 
Published: January 2022

Abstract
Despite early optimism in cities’ leadership on climate adaptation planning, critics increasingly find that prevailing adaptation interventions are financially speculative, economically exclusive, and socially discriminatory. In this chapter, the authors discuss how emerging adaptation plans have taken on characteristics of climate urbanism by privileging the epistemologies, operations, and normative values of cities in the Global North, which in turn has shaped the scope, scale, strategies, and empirical evidence of adaptation actions on the ground. Dominant global imaginaries of climate-resilient futures prioritize technological fixes, decentralized and individual responsibility, consumption-led economic growth, and the securitization of upper-middle class values, experiences, and lifestyles. Adaptation planning practice has yet to recognize the long history of alternative epistemologies, everyday strategies, and normative socio-cultural values that tackle the drivers of systemic environmental, racial, and economic injustices in cities. Socio-political instability, even under currently observed warming trends, suggests that effective and just adaptation moving forward must be more political, relational, and anticipatory not only to biophysical changes but also to responses from the market, state, community, and social movements. Adaptation plans must therefore engage with epistemologies heretofore sidelined in the field, including critical political economy, embodied knowledge, postcolonial, anti-racist, and feminist studies. This chapter charts a way to comparatively view these alternative perspectives from “off the map” that are essential in pursuit of more just, equitable, and sustainable cities.
Illegal Wildlife Trade in the Mekong
Authors: Nillasithanukroh Songkhun , Patel Ekta , Malesky Edmund , Weinthal Erika 
Published: January 2022

Abstract
This chapter examines the illegal wildlife trade (IWT) in the Mekong, with particular attention to how political economic factors and legal structures shape actors’ interests and incentives. The current literature on wildlife trafficking mainly attributes wildlife protection failures to weak enforcement. However, this literature has paid little attention to the underlying factors that contribute to the weak enforcement of wildlife laws. This chapter applies a political economy analysis to better understand the role of each actor from the point of wildlife sourcing to end consumption. It also explains why effectively enforcing wildlife laws is difficult and is often not in the interest of wildlife officials. This chapter thus examines why actors along IWT supply chains engage in illegal activities and do not abide by conservation laws. With rising demand for wildlife products, particularly because of increasing economic prosperity, the survival of many endangered species is under threat. Despite growing calls for total bans of wildlife trade or trade regulations to prevent overharvesting, these frequently fail to achieve conservation goals if they do not consider the local political economy context. This chapter focuses on the global IWT hotspots of Vietnam, Laos, and Cambodia, analyzing how legal frameworks shape local political economies and showing why IWT is a pervasive problem in the region.
US Efforts to Promote Peace in the Nineteenth Century
Authors: Minardi Margot 
Published: January 2022

Abstract
Fueled by both religious and secular ideals, an organized peace movement emerged in the United States in the aftermath of the War of 1812 and the Napoleonic Wars. Rather than protesting a particular war, peace reformers in this period sought to rout out warfare entirely. Some nineteenth-century American advocates of peace promoted alternative forms of conflict resolution, such as a congress of nations or arbitration agreements, to the governments of the world. Others sought to make peace from the bottom up, coupling the pacifist cause with calls for democratization, workers’ rights, and the abolition of slavery. These two approaches, while occasionally intersecting, stemmed from different understandings of the problem of war: was war to be understood primarily as the product of conflict between nation-states, or was it a manifestation of a social system rooted in inequality and inhumanity? The tensions within the movement were particularly evident at key moments in the nineteenth century, including the rise of abolitionism in the 1830s, the midcentury international peace congresses in Europe, and the period outbreak of war (particularly the Civil War within the United States). This chapter argues that debates over the relationship between peace and social reform permeated nineteenth-century American advocacy for peace, as peace reformers grappled with explaining how social and political transformation could happen in the absence of war.
Analysis of exocyst function in endodermis reveals its widespread contribution and specificity of action
Authors: Hématy Kian , De Bellis Damien , Wang Xin , Mähönen Ari Pekka , Geldner Niko 
Published: January 2022

Abstract
The exocyst is the main plasma membrane vesicle-tethering complex in eukaryotes and is composed of eight different subunits. Yet, in plant genomes, many subunits display multiple copies, thought to reflect evolution of complex subtypes with divergent functions. In Arabidopsis thaliana root endodermal cells, the isoform EXO70A1 is required for positioning of CASP1 at the Casparian Strip Domain, but not for its non-targeted secretion to the plasma membrane. Here, we show that exo84b resembles exo70a1 mutants regarding CASP1 mistargeting and secretion of apoplastic proteins, but exo84b additionally affects secretion of other integral plasma membrane proteins. Moreover, conditional, cell-type-specific gene editing of the single-copy core component SEC6 allows visualization of secretion defects in plant cells with a complete lack of exocyst complex function. Our approach opens avenues for deciphering the complexity/diversity of exocyst functions in plant cells and enables analysis of central trafficking components with lethal phenotypes.
Consumers’ willingness to pay for pork produced with different levels of antibiotics
Authors: Paudel Bindu , Kolady Deepthi , Grebitus Carola , Roy Aniruddha , Ishaq Mariam 
Published: January 2022

Abstract
Compared with the EU, regulations on antibiotic use in livestock are less stringent in the USA. If consumers prefer non-antibiotic or minimal antibiotic-use meat, labeling different levels of antibiotic use in the USA could have the potential to mitigate the development of antibiotic-resistant livestock. This study used a survey of 660 US consumers to estimate willingness to pay (WTP) for pork chops from pigs raised with different levels of antibiotic use. Results show that WTP for antibiotic-free pork chops is higher compared with WTP for pork chops produced with minimal use of antibiotics for disease treatment and conventional use of antibiotics for growth promotion. These findings suggest that it could be beneficial to differentiate usage levels of antibiotics when labeling pork products rather than stating ‘use’ or ‘no use’.
‘Pericles’, ‘Reynard the Foxe’, Sidney’s ‘Arcadia’, Florio’s ‘Montaigne’ and More in Northwestern MS 67
Authors: Coatalen Guillaume 
Published: January 2022

Abstract
This paper offers an edition of 214 extracts contained in Northwestern MS 67, a manuscript completed no earlier than 1614, and a commentary on the compiler’s choices and practice. His identity is difficult to establish with any certainty but a lengthy letter in Latin by one Hugo Richardes to one William Yong dated 14 December 1583, and written at Basteldon (Basildon), is copied at the end of the commonplace book. The material ranges from playbooks (by Dekker, Marston and Shakespeare) to pastorals (Sidney’s ‘Arcadia’ and Tofte’s ‘Honours Academie’), through extracts from Plutarch’s ‘Lives’ in North’s translation. There are 28 translations of classical verse transcribed from Plutarch. Seven extracts from Montaigne’s ‘Essays’ in Florio’s translation also occur, but the most surprising source is probably Caxton’s 1550 ‘Reynard the Foxe’ which furnishes 50 quotations. In the beginning of the commonplace book, the compiler explains its purpose by using the well-known Senecan bee and honey trope: applying the extracts to discourse and life. All the extracts are adapted and kept in alphabetical order according to the first word of the extract. Most are proverbial in nature or copied to sound like sentences, and all point to an inspiration for moral and spiritual improvement. The extracts express humanistic concerns, like the power of eloquence and the treachery of public life, and Stoic principles such as constancy in the face of adversity. One central issue seems to be remaining virtuous in a sinful world.
Acquiring Innovation under Information Frictions
Authors: Celik Murat Alp , Tian Xu , Wang Wenyu 
Published: January 2022

Abstract
Acquiring innovation through M&A is subject to information frictions, as assessing the value of innovative targets is a challenging task. We find an inverted U-shaped relation between firm innovation and takeover exposure; equity usage increases with target innovation; and the deal completion rate drops with innovation. We develop and estimate a model of acquiring innovation under information frictions, featuring endogenous merger, innovation, and offer composition decisions. Our estimates suggest that acquirers’ due diligence reveals only 30$\%$ of private information possessed by targets. Eliminating information frictions increases capitalized merger gains by 59$\%$, stimulates innovation, and boosts productivity, business dynamism, and social welfare.