bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rising Islamism and the Struggle for Islamic Authority in Post-Reformasi Indonesia
Authors: Arifianto Alexander R. 
Published: September 2019

AbstractThe successful ‘Defending Islam’ rallies of 2016–2017 provide clear evidence that Islamism is on the rise in contemporary Indonesia. Mainstream Islamic authorities, including groups such as Nahdlatul Ulama and Muhammadiyah, are increasingly losing their authority to newer, more conservative Islamic preachers and groups. What explains this phenomenon – and what does it mean for the moderate perspectives that many predicted would dominate Islam in Indonesia in the post-Reformasi era?This article argues that three main mechanisms can explain the rise of Islamism in Indonesia: 1) the creation of a ‘marketplace of ideas’ in post-Reformasi Indonesia and the way in which this marketplace has contributed to the rise of Islamism and the breakdown of Islamic authority; 2) the ascent of new Islamic authority figures, who propagate their views using new methods, ranging from social media to campus da'wa organisations and community-based activities (majelis taklim); and 3) the growing influence of new Islamic groups and preachers, who are building alliances with established religious elites and politicians. Such alliances strengthen the influence of new Islamic authorities, while further marginalising religious minorities, such as Ahmadi and Shi'a Muslims.
Separating Content and Structure in Humor Appreciation
Authors: Heintz Sonja 
Published: September 2019

Abstract. The present study empirically tests a bimodal model of humor appreciation. In this model, individual differences in evaluating jokes and cartoons are attributed to their contents (sexual and aggressive) and structures (incongruity-resolution and nonsense). A total of 225 participants (64% women, Mage = 32.37 years) rated 50 jokes and cartoons on funniness, offensiveness, and boringness. They also completed a standard humor appreciation measure (the 3 WD). Using structural equation modeling, the bimodal model was found to be superior to alternative models. Regressions predicting the 3 WD categories supported the convergent and discriminant validity of the content and structure factors. In line with previous research, gender differences were found for the content factors, but not for the structure factors. Overall, this study is the first to show the viability of bimodal models of humor appreciation. They allow capturing the sources of individual differences in humor appreciation more adequately than previous models, thus providing a basis for future theories, research, and applications.
Historical Changes in Lower Columbia River and Estuary Floods: A Numerical Study
Authors: Helaire Lumas T. , Talke Stefan A. , Jay David A. , Mahedy Drew 
Published: September 2019

AbstractOver the past 150 years, the Lower Columbia River Estuary controlling depth has approximately doubled, the majority of historical wetlands and floodplain have been reclaimed, numerous infrastructure projects have altered and confined flow pathways, and significant natural and anthropogenic changes to the discharge hydrograph have occurred. To investigate the effect of these changes on tides, river slope, and flood water levels, we construct and validate numerical models that simulate flow over late nineteenth‐century and present‐day bathymetry. The models are validated using archival (1853–1877) and modern tide measurements throughout the Lower Columbia River Estuary and river stage measurements from the tidal river (1876–present). Historical flood plain roughness and levee heights are validated iteratively by requiring simulations to match the observed roll off in the river stage rating curve during floods. Measurements and model results show that environmental change has amplified tidal constituents, with peak change about 60 km from the coast. By contrast, increased depth has reduced river slope for low and moderate river discharge. For rarely observed extreme floods of 30 × 103m3/s, simulated modern water levels exceed historical in Portland (OR). These observations highlight competing hydrodynamic effects, which are investigated by scaling the St. Venant equations for a simulated 25 × 103‐m3/s flood: While larger modern depth reduces frictional effects and decreases surface slope, reduced floodplain access confines modern flow into channels, increasing velocity, bed stress, and water levels. However, the highly frictional historical floodplain conveyed little flow, limiting the effect of floodplain to storage effects; hence, most simulated historical floods exceed modern levels.
Kinetic Energy of Eddy‐Like Features From Sea Surface Altimetry
Authors: Martínez‐Moreno Josué , Hogg Andrew McC. , Kiss Andrew E. , Constantinou Navid C. , Morrison Adele K. 
Published: September 2019

AbstractThe mesoscale eddy field plays a key role in the mixing and transport of physical and biological properties and redistribution of energy in the ocean. Eddy kinetic energy is commonly defined as the kinetic energy of the time‐varying component of the velocity field. However, this definition contains all processes that vary in time, including coherent mesoscale eddies, jets, waves, and large‐scale motions. The focus of this paper is on the eddy kinetic energy contained in coherent mesoscale eddies. We present a new method to decompose eddy kinetic energy into oceanic processes. The proposed method uses a new eddy identification algorithm (TrackEddy). This algorithm is based on the premise that the sea level signature of a coherent eddy can be approximated as a Gaussian feature. The eddy Gaussian signature then allows for the calculation of kinetic energy of the eddy field through the geostrophic approximation. TrackEddy has been validated using synthetic sea surface height data and then used to investigate trends of eddy kinetic energy in the Southern Ocean using satellite sea surface height anomaly (AVISO+). We detect an increasing trend of eddy kinetic energy associated with mesoscale eddies in the Southern Ocean. This trend is correlated with an increase in the coherent eddy amplitude and the strengthening of wind stress over the last two decades.
Collision Chronology Along the İzmir‐Ankara‐Erzincan Suture Zone: Insights From the Sarıcakaya Basin, Western Anatolia
Authors: Mueller M. A. , Licht A. , Campbell C. , Ocakoğlu F. , Taylor M. H. , Burch L. , Ugrai T. , Kaya M. , Kurtoğlu B. , Coster P. M. C. , Métais G. , Beard K. C. 
Published: September 2019

AbstractDebate persists concerning the timing and geodynamics of intercontinental collision, style of syncollisional deformation, and development of topography and fold‐and‐thrust belts along the >1,700‐km‐long İzmir‐Ankara‐Erzincan suture zone (İAESZ) in Turkey. Resolving this debate is a necessary precursor to evaluating the integrity of convergent margin models and kinematic, topographic, and biogeographic reconstructions of the Mediterranean domain. Geodynamic models argue either for a synchronous or diachronous collision during either the Late Cretaceous and/or Eocene, followed by Eocene slab breakoff and postcollisional magmatism.We investigate the collision chronology in western Anatolia as recorded in the sedimentary archives of the 90‐km‐long Sarıcakaya Basin perched at shallow structural levels along the İAESZ. Based on new zircon U‐Pb geochronology and depositional environment and sedimentary provenance results, we demonstrate that the Sarıcakaya Basin is an Eocene sedimentary basin with sediment sourced from both the İAESZ and Söğüt Thrust fault to the south and north, respectively, and formed primarily by flexural loading from north‐south shortening along the syncollisional Söğüt Thrust. Our results refine the timing of collision between the Anatolides and Pontide terranes in western Anatolia to Maastrichtian‐Middle Paleocene and Early Eocene crustal shortening and basin formation. Furthermore, we demonstrate contemporaneous collision, deformation, and magmatism across the İAESZ, supporting synchronous collision models. We show that regional postcollisional magmatism can be explained by renewed underthrusting instead of slab breakoff. This new İAESZ chronology provides additional constraints for kinematic, geodynamic, and biogeographic reconstructions of the Mediterranean domain.
Indole-3-propionic acid inhibits gut dysbiosis and endotoxin leakage to attenuate steatohepatitis in rats
Authors: Zhao Ze-Hua , Xin Feng-Zhi , Xue Yaqian , Hu Zhimin , Han Yamei , Ma Fengguang , Zhou Da , Liu Xiao-Lin , Cui Aoyuan , Liu Zhengshuai , Liu Yuxiao , Gao Jing , Pan Qin , Li Yu , Fan Jian-Gao 
Published: September 2019

AbstractMicrobial metabolites have emerged as critical components that mediate the metabolic effects of the gut microbiota. Here, we show that indole-3-propionic acid (IPA), a tryptophan metabolite produced by gut bacteria, is a potent anti-non-alcoholic steatohepatitis (NASH) microbial metabolite. Here, we demonstrate that administration of IPA modulates the microbiota composition in the gut and inhibits microbial dysbiosis in rats fed a high-fat diet. IPA induces the expression of tight junction proteins, such as ZO-1 and Occludin, and maintains intestinal epithelium homeostasis, leading to a reduction in plasma endotoxin levels. Interestingly, IPA inhibits NF-κB signaling and reduces the levels of proinflammatory cytokines, such as TNFα, IL-1β, and IL-6, in response to endotoxin in macrophages to repress hepatic inflammation and liver injury. Moreover, IPA is sufficient to inhibit the expression of fibrogenic and collagen genes and attenuate diet-induced NASH phenotypes. The beneficial effects of IPA on the liver are likely mediated through inhibiting the production of endotoxin in the gut. These findings suggest a protective role of IPA in the control of metabolism and uncover the gut microbiome and liver cross-talk in regulating the intestinal microenvironment and liver pathology via a novel dietary nutrient metabolite. IPA may provide a new therapeutic strategy for treating NASH.
High-fidelity optical diffraction tomography of multiple scattering samples
Authors: Lim Joowon , Ayoub Ahmed B. , Antoine Elizabeth E. , Psaltis Demetri 
Published: September 2019

AbstractWe propose an iterative reconstruction scheme for optical diffraction tomography that exploits the split-step non-paraxial (SSNP) method as the forward model in a learning tomography scheme. Compared with the beam propagation method (BPM) previously used in learning tomography (LT-BPM), the improved accuracy of SSNP maximizes the information retrieved from measurements, relying less on prior assumptions about the sample. A rigorous evaluation of learning tomography based on SSNP (LT-SSNP) using both synthetic and experimental measurements confirms its superior performance compared with that of the LT-BPM. Benefiting from the accuracy of SSNP, LT-SSNP can clearly resolve structures that are highly distorted in the LT-BPM. A serious limitation for quantifying the reconstruction accuracy for biological samples is that the ground truth is unknown. To overcome this limitation, we describe a novel method that allows us to compare the performances of different reconstruction schemes by using the discrete dipole approximation to generate synthetic measurements. Finally, we explore the capacity of learning approaches to enable data compression by reducing the number of scanning angles, which is of particular interest in minimizing the measurement time.
βarrestin-1 regulates DNA repair by acting as an E3-ubiquitin ligase adaptor for 53BP1
Authors: Nieto Ainhoa , Hara Makoto R. , Quereda Victor , Grant Wayne , Saunders Vanessa , Xiao Kunhong , McDonald Patricia H. , Duckett Derek R. 
Published: September 2019

AbstractCellular DNA is constantly under threat from internal and external insults, consequently multiple pathways have evolved to maintain chromosomal fidelity. Our previous studies revealed that chronic stress, mediated by continuous stimulation of the β2-adrenergic-βarrestin-1 signaling axis suppresses activity of the tumor suppressor p53 and impairs genomic integrity. In this pathway, βarrestin-1 (βarr1) acts as a molecular scaffold to promote the binding and degradation of p53 by the E3-ubiquitin ligase, MDM2. We sought to determine whether βarr1 plays additional roles in the repair of DNA damage. Here we demonstrate that in mice βarr1 interacts with p53-binding protein 1 (53BP1) with major consequences for the repair of DNA double-strand breaks. 53BP1 is a principle component of the DNA damage response, and when recruited to the site of double-strand breaks in DNA, 53BP1 plays an important role coordinating repair of these toxic lesions. Here, we report that βarr1 directs 53BP1 degradation by acting as a scaffold for the E3-ubiquitin ligase Rad18. Consequently, knockdown of βarr1 stabilizes 53BP1 augmenting the number of 53BP1 DNA damage repair foci following exposure to ionizing radiation. Accordingly, βarr1 loss leads to a marked increase in irradiation resistance both in cells and in vivo. Thus, βarr1 is an important regulator of double strand break repair, and disruption of the βarr1/53BP1 interaction offers an attractive strategy to protect cells against high levels of exposure to ionizing radiation.
Combining ERBB family and MET inhibitors is an effective therapeutic strategy in cutaneous malignant melanoma independent of BRAF/NRAS mutation status
Authors: Das Ishani , Wilhelm Margareta , Höiom Veronica , Franco Marquez Rodolfo , Costa Svedman Fernanda , Hansson Johan , Tuominen Rainer , Egyhàzi Brage Suzanne 
Published: September 2019

AbstractCurrent treatment modalities for disseminated cutaneous malignant melanoma (CMM) improve survival; however, relapses are common. A number of receptor tyrosine kinases (RTKs) including EGFR and MET have been reported to be involved in CMM metastasis and in the development of resistance to therapy, targeting the mitogen-activated protein kinase (MAPK pathway). IHC analysis showed that patients with higher MET protein expression had a significantly shorter overall survival. In addition, silencing of MET caused an upregulation of EGFR and p-AKT, which was abrogated by concomitant silencing of MET and EGFR in CMM cells resistant to MAPK-targeting drugs. We therefore explored novel treatment strategies using clinically approved drugs afatinib (ERBB family inhibitor) and crizotinib (MET inhibitor), to simultaneously block MET and ERBB family RTKs. The effects of the combination were assessed in cell culture and spheroid models using established CMM and patient-derived short-term cell lines, and an in vivo xenograft mouse model. The combination had a synergistic effect, promoting cell death, concomitant with a potent downregulation of migratory and invasive capacity independent of their BRAF/NRAS mutational status. Furthermore, the combination attenuated tumor growth rate, as ascertained by the significant reduction of Ki67 expression and induced DNA damage in vivo. Importantly, this combination therapy had minimal therapy-related toxicity in mice. Lastly, the cell cycle G2 checkpoint kinase WEE1 and the RTK IGF1R, non-canonical targets, were altered upon exposure to the combination. Knockdown of WEE1 abrogated the combination-mediated effects on cell migration and proliferation in BRAF mutant BRAF inhibitor-sensitive cells, whereas WEE1 silencing alone inhibited cell migration in NRAS mutant cells. In summary, our results show that afatinib and crizotinib in combination is a promising alternative targeted therapy option for CMM patients, irrespective of BRAF/NRAS mutational status, as well as for cases where resistance has developed towards BRAF inhibitors.
Structural insight into human N6amt1–Trm112 complex functioning as a protein methyltransferase
Authors: Li Wenjing , Shi Yu , Zhang Tianlong , Ye Jie , Ding Jianping 
Published: September 2019

AbstractDNA methylation is an important epigenetic modification in many organisms and can occur on cytosine or adenine. N6-methyladenine (6mA) exists widespreadly in bacterial genomes, which plays a vital role in the bacterial restriction-modification system. Recently, 6mA has also been reported to exist in the genomes of a variety of eukaryotes from unicellular organisms to metazoans. There were controversial reports on whether human N6amt1, which was originally reported as a glutamine MTase for eRF1, is a putative 6mA DNA MTase. We report here the crystal structure of human N6amt1–Trm112 in complex with cofactor SAM. Structural analysis shows that Trm112 binds to a hydrophobic surface of N6amt1 to stabilize its structure but does not directly contribute to substrate binding and catalysis. The active site and potential substrate-binding site of N6amt1 are dominantly negatively charged and thus are unsuitable for DNA binding. The biochemical data confirm that the complex cannot bind DNA and has no MTase activity for DNA, but exhibits activity for the methylation of Gln185 of eRF1. Our structural and biochemical data together demonstrate that N6amt1 is a bona fide protein MTase rather than a DNA MTase.
VcFT-induced mobile florigenic signals in transgenic and transgrafted blueberries
Authors: Song Guo-qing , Walworth Aaron , Lin Tianyi , Chen Qiuxia , Han Xiumei , Irina Zaharia L. , Zhong Gan-yuan 
Published: September 2019

Abstract
FLOWERING LOCUS T (FT) can promote early flowering in annual species, but such role has not been well demonstrated in woody species. We produced self and reciprocal grafts involving non-transgenic blueberry (NT) and transgenic blueberry (T) carrying a 35S-driven blueberry FT (VcFT-OX). We demonstrated that the transgenic VcFT-OX rootstock promoted flowering of non-transgenic blueberry scions in the NT (scion):T (rootstock) grafts. We further analyzed RNA-Seq profiles and six groups of phytohormones in both NT:T and NT:NT plants. We observed content changes of several hormone metabolites, in a descending order, in the transgenic NT:T, non-transgenic NT:T, and non-transgenic NT:NT leaves. By comparing differential expression transcripts (DETs) of these tissues in relative to their control, we found that the non-transgenic NT:T leaves had many DETs shared with the transgenic NT:T leaves, but very few with the transgenic NT:T roots. Interestingly, a number of these shared DETs belong to hormone pathway genes, concurring with the content changes of hormone metabolites in both transgenic and non-transgenic leaves of the NT:T plants. These results suggest that phytohormones induced by VcFT-OX in the transgenic leaves might serve as part of the signals that resulted in early flowering in both transgenic plants and the non-transgenic NT:T scions.
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
Authors: Andrio Pau , Hospital Adam , Conejero Javier , Jordá Luis , Del Pino Marc , Codo Laia , Soiland-Reyes Stian , Goble Carole , Lezzi Daniele , Badia Rosa M. , Orozco Modesto , Gelpi Josep Ll. 
Published: September 2019

AbstractIn the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.
Interstitial cells in calcified aortic valves have reduced differentiation potential and stem cell-like properties
Authors: Bogdanova Maria , Zabirnyk Arsenii , Malashicheva Anna , Enayati Katarina Zihlavnikova , Karlsen Tommy Aleksander , Kaljusto Mari-Liis , Kvitting John-Peder Escobar , Dissen Erik , Sullivan Gareth John , Kostareva Anna , Stensløkken Kåre-Olav , Rutkovskiy Arkady , Vaage Jarle 
Published: September 2019

AbstractValve interstitial cells (VICs) are crucial in the development of calcific aortic valve disease. The purpose of the present investigation was to compare the phenotype, differentiation potential and stem cell-like properties of cells from calcified and healthy aortic valves. VICs were isolated from human healthy and calcified aortic valves. Calcification was induced with osteogenic medium. Unlike VICs from healthy valves, VICs from calcified valves cultured without osteogenic medium stained positively for calcium deposits with Alizarin Red confirming their calcific phenotype. Stimulation of VICs from calcified valves with osteogenic medium increased calcification (p = 0.02), but not significantly different from healthy VICs. When stimulated with myofibroblastic medium, VICs from calcified valves had lower expression of myofibroblastic markers, measured by flow cytometry and RT-qPCR, compared to healthy VICs. Contraction of collagen gel (a measure of myofibroblastic activity) was attenuated in cells from calcified valves (p = 0.04). Moreover, VICs from calcified valves, unlike cells from healthy valves had lower potential to differentiate into adipogenic pathway and lower expression of stem cell-associated markers CD106 (p = 0.04) and aldehyde dehydrogenase (p = 0.04). In conclusion, VICs from calcified aortic have reduced multipotency compared to cells from healthy valves, which should be considered when investigating possible medical treatments of aortic valve calcification.
Incidence of Intraocular Lens Exchange after Cataract Surgery
Authors: Abdalla Elsayed Maram E. A. , Ahmad Khabir , Al-Abdullah Abdulelah A. , Malik Rizwan , Khandekar Rajiv , Martinez-Osorio Hernan , Mura Marco , Schatz Patrik 
Published: September 2019

AbstractIntraocular lens (IOL) exchange after cataract surgery is unusual but may be associated with suboptimal visual outcome. The incidence of IOL exchange has not been consistently estimated. Such information is invaluable when counseling patients prior to cataract surgery. We examined the incidence of, and indications and risk factors for, IOL exchange after cataract surgery. We also assessed visual outcome of eyes that had an IOL exchange. A cohort design was used to estimate the incidence of IOL exchange and a case-control design to identify factors associated with it. All phacoemulsification surgeries with IOL (n = 17415 eyes) during 2010–2017 and those that had a subsequent IOL removal or replacement during the same time period were identified (n = 34 eyes). The incidence of IOL exchange was 2 per 1000 surgeries (95% confidence interval [CI] 1 to 3) over 8 years. Eyes that underwent subsequent IOL removal or replacement were compared with eyes that had cataract surgery only (n = 47) across demographic and clinical characteristics. In a binary logistic regression analysis, two factors were significantly associated with IOL exchange/removal: an adverse event during cataract surgery (adjusted odds ratio [aOR] 19.45; 95% CI 4.89–77.30, P < 0.001) and a pre-existing ocular comorbidity (aOR 10.70; 95% CI 1.69–67.63, P = 0.021). The effect of gender was marginally significant (P = 0.077). Eyes that underwent IOL exchange or explantation were nearly two and a half times more likely to have a final best-corrected visual acuity of <20/60 compared to those that had cataract surgery alone (adjusted RR 2.60 95% CI, 1.13–6.02; P = 0.025).