bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Their New Jerusalem”: Representations of Jewish Immigrants in the American Popular Press, 1880–1903
Authors: Varat Deborah 
Published: April 2021

AbstractMillions of immigrants arrived in the United States during the Gilded Age, drastically altering the ethnic character of the American citizenry. This dramatic social change was met with mixed reactions from the native-born population that were vividly communicated in the popular press. Cartoonists for newspapers and magazines across the country developed a language of caricature to identify and distinguish among ethnic groups and mocked new arrivals in imagery that ranged from mild to malicious. One might assume that the masses of Eastern European Jews flooding into the country (poor, Yiddish-speaking, shtetl-bred) would have been singled out for anti-Semitic attack, just as they were in Europe at the time. However, Jews were not the primary victims of visual insults in America, nor were the Jewish caricatures wholly negative. Further, the broader scope of popular imagery, which, in addition to cartoons, includes a plethora of illustrations as well as photographs, presents a generally positive attitude toward Jewish immigrants. This attitude aligned with political rhetoric, literature, newspaper editorials, and financial opportunity. This article will propose a better alignment of the visual evidence with the scholarly understanding of the essentially providential experience of Jews in America during this period.
From Native Sovereignty to an Oilman’s State: Land, Race, and Petroleum in Indian Territory and Oklahoma
Authors: Boxell Mark 
Published: April 2021

AbstractDuring the first two decades of the twentieth century, Indian Territory and the State of Oklahoma experienced one of the world’s largest petroleum booms, with much of the oil extracted from the territory and state produced on land owned by Indigenous, Black, and mixed-race peoples. White settlers, backed by governing institutions and cultures rooted in settler colonialism, anti-Black racism, and anti-monopolism, struggled to seize control of oil-rich land amid the allotment of Native-owned property. These latter elements insisted that non-whites could not grasp the value of petroleum nor be trusted with the control of such a vital resource, especially in the shadow of ever-looming oil monopolies. Settlers and wildcat prospectors built a white-supremacist oil-field politics that elevated the rights of small-scale, proprietary "independent" oilmen and worked to ensure that the latter controlled flows of crude vis-à-vis non-white property holders and “outside” corporations. For white settlers in Indian Territory and Oklahoma, oil rose to the top of collective imaginaries about race, property, and wealth, encouraging the creation of both legal and often violent extralegal strategies for dispossessing unworthy landowners of their hydrocarbon inheritance.
Publish the Picture at Your Peril: Visual Ideas and the Commercial Apparatus of Life Magazine
Authors: Schwartz Joshua S. 
Published: April 2021

AbstractIn the early years of the twentieth century, Life magazine had only approximately one hundred thousand subscribers, yet its illustrated images (like the Gibson Girl) significantly influenced fashion trends and social behaviors nationally. Its outsized influence can be explained by examining the magazine’s business practices, particularly the novel ways in which it treated and conceptualized its images as intellectual property. While other magazines relied on their circulation and advertising revenue to attain profitability, Life used its page space to sell not only ads, but also its own creative components—principally illustrations—to manufacturers of consumer goods, advertisers, and consumers themselves. In so doing, Life’s publishers relied on a developing legal conception of intellectual property and copyright, one that was not always amenable to their designs. By looking at a quasi-litigious disagreement in which a candy manufacturing company attempted to copy one of the magazine’s images, this article explores the mechanisms behind the commodification and distribution of mass-circulated images.
Fractures in Low‐Permeability Rocks: Can Poroelastic Effects Associated With Damage Zones Enhance Their Seismic Visibility?
Authors: Sotelo Edith , Rubino J. Germán , Solazzi Santiago G. , Barbosa Nicolás D. , Holliger Klaus 
Published: April 2021

AbstractFluid pressure diffusion (FPD) between a fracture and a porous permeable background can increase the normal compliance of the fracture and, thus, its reflectivity. However, many fractured environments of interest are associated with background rocks that can be regarded as largely impermeable for the the typical frequencies employed in seismic surveys. Nonetheless, there is evidence to suggest that the seemingly ubiquitous presence of damaged zones (DZs) associated with fractures may provide the necessary hydraulic communication between fractures and their immediate surroundings for FPD to occur. Here, we assess the pertinence of this phenomenon. To this end, we consider a 1D elastic‐poroelastic model, which comprises a poroelastic system consisting of a fracture embedded in adjacent DZ layers. This system is enclosed in an impermeable background represented by two elastic half‐spaces. We calculate the frequency‐dependent P‐wave reflectivity at normal incidence at the background‐DZ interface for different permeabilities, thicknesses, and porosities of the DZ. We also evaluate the corresponding normal fracture compliance. Our results show that, when accounting for the presence of a DZ surrounding an individual fracture, FPD effects between these regions induce a higher seismic reflectivity and a higher normal compliance compared to that of a hydraulically isolated fracture. This, in turn, implies that, even in largely impermeable environments, the seismic visibility of fractures can be enhanced through FPD enabled by the presence of DZs.
Survey of Transverse Range Fire Scars in 10 Years of UAVSAR Polarimetry
Authors: Parker Jay , Donnellan Andrea , Glasscoe Margaret 
Published: April 2021

AbstractBecause cross‐polarized radar returns are highly associated with volume scatter, radar polarimetry returns tend to show strong evidence of wildfire scars and recovery in forest and chaparral. We focus on the polarimetry images from UAVSAR (PolSAR) line SanAnd_08525, which covers a roughly 20 km wide swath over the Transverse Range including parts of the Santa Monica, San Gabriel and San Bernardino Mountains. We select images from four acquisition dates from October 2009 to September 2020, very roughly 4 years apart. These are compared to fire perimeters from the national Geospatial Multi‐Agency Coordination and NIFC databases for years 2003–2020, which shows the areas affected by the major fires (west to east) Springs2013, Woolsey2018, Topanga2005, LaTuna2017, Station2009, BlueCut2016, Pilot2016, Slide2007, Butler2007, and many smaller fires. PolSAR images are shown to be helpful in identifying types and boundaries of fire, 50‐meter scale details of vegetation loss, and variability of vegetation recovery in post‐fire years.
SHR/NCrl rats as a model of ADHD can be discriminated from controls based on their brain, blood, or urine metabolomes
Authors: Dupuy Camille , Castelnau Pierre , Mavel Sylvie , Lefevre Antoine , Nadal-Desbarats Lydie , Bodard Sylvie , Busson Julie , Dufour-Rainfray Diane , Blasco Helene , Emond Patrick , Galineau Laurent 
Published: April 2021

AbstractAttention-Deficit Hyperactivity Disorder (ADHD) is one of the most common neurodevelopmental disorder characterized by inattention, impulsivity, and hyperactivity. The neurobiological mechanisms underlying ADHD are still poorly understood, and its diagnosis remains difficult due to its heterogeneity. Metabolomics is a recent strategy for the holistic exploration of metabolism and is well suited for investigating the pathophysiology of diseases and finding molecular biomarkers. A few clinical metabolomic studies have been performed on peripheral samples from ADHD patients but are limited by their access to the brain. Here, we investigated the brain, blood, and urine metabolomes of SHR/NCrl vs WKY/NHsd rats to better understand the neurobiology and to find potential peripheral biomarkers underlying the ADHD-like phenotype of this animal model. We showed that SHR/NCrl rats can be differentiated from controls based on their brain, blood, and urine metabolomes. In the brain, SHR/NCrl rats displayed modifications in metabolic pathways related to energy metabolism and oxidative stress further supporting their importance in the pathophysiology of ADHD bringing news arguments in favor of the Neuroenergetic theory of ADHD. Besides, the peripheral metabolome of SHR/NCrl rats also shared more than half of these differences further supporting the importance of looking at multiple matrices to characterize a pathophysiological condition of an individual. This also stresses out the importance of investigating the peripheral energy and oxidative stress metabolic pathways in the search of biomarkers of ADHD.
BDNF haploinsufficiency induces behavioral endophenotypes of schizophrenia in male mice that are rescued by enriched environment
Authors: Harb Mahmoud , Jagusch Justina , Durairaja Archana , Endres Thomas , Leßmann Volkmar , Fendt Markus 
Published: April 2021

AbstractBrain-derived neurotrophic factor (BDNF) is implicated in a number of processes that are crucial for healthy functioning of the brain. Schizophrenia is associated with low BDNF levels in the brain and blood, however, not much is known about BDNF’s role in the different symptoms of schizophrenia. Here, we used BDNF-haploinsufficient (BDNF+/−) mice to investigate the role of BDNF in different mouse behavioral endophenotypes of schizophrenia. Furthermore, we assessed if an enriched environment can prevent the observed changes. In this study, male mature adult wild-type and BDNF+/− mice were tested in mouse paradigms for cognitive flexibility (attentional set shifting), sensorimotor gating (prepulse inhibition), and associative emotional learning (safety and fear conditioning). Before these tests, half of the mice had a 2-month exposure to an enriched environment, including running wheels. After the tests, BDNF brain levels were quantified. BDNF+/− mice had general deficits in the attentional set-shifting task, increased startle magnitudes, and prepulse inhibition deficits. Contextual fear learning was not affected but safety learning was absent. Enriched environment housing completely prevented the observed behavioral deficits in BDNF+/− mice. Notably, the behavioral performance of the mice was negatively correlated with BDNF protein levels. These novel findings strongly suggest that decreased BDNF levels are associated with several behavioral endophenotypes of schizophrenia. Furthermore, an enriched environment increases BDNF protein to wild-type levels and is thereby able to rescue these behavioral endophenotypes.
Improving cell-free glycoprotein synthesis by characterizing and enriching native membrane vesicles
Authors: Hershewe Jasmine M. , Warfel Katherine F. , Iyer Shaelyn M. , Peruzzi Justin A. , Sullivan Claretta J. , Roth Eric W. , DeLisa Matthew P. , Kamat Neha P. , Jewett Michael C. 
Published: April 2021

AbstractCell-free gene expression (CFE) systems from crude cellular extracts have attracted much attention for biomanufacturing and synthetic biology. However, activating membrane-dependent functionality of cell-derived vesicles in bacterial CFE systems has been limited. Here, we address this limitation by characterizing native membrane vesicles in Escherichia coli-based CFE extracts and describing methods to enrich vesicles with heterologous, membrane-bound machinery. As a model, we focus on bacterial glycoengineering. We first use multiple, orthogonal techniques to characterize vesicles and show how extract processing methods can be used to increase concentrations of membrane vesicles in CFE systems. Then, we show that extracts enriched in vesicle number also display enhanced concentrations of heterologous membrane protein cargo. Finally, we apply our methods to enrich membrane-bound oligosaccharyltransferases and lipid-linked oligosaccharides for improving cell-free N-linked and O-linked glycoprotein synthesis. We anticipate that these methods will facilitate on-demand glycoprotein production and enable new CFE systems with membrane-associated activities.
Blood n-3 fatty acid levels and total and cause-specific mortality from 17 prospective studies
Authors: Harris William S. , Tintle Nathan L. , Imamura Fumiaki , Qian Frank , Korat Andres V. Ardisson , Marklund Matti , Djoussé Luc , Bassett Julie K. , Carmichael Pierre-Hugues , Chen Yun-Yu , Hirakawa Yoichiro , Küpers Leanne K. , Laguzzi Federica , Lankinen Maria , Murphy Rachel A. , Samieri Cécilia , Senn Mackenzie K. , Shi Peilin , Virtanen Jyrki K. , Brouwer Ingeborg A. , Chien Kuo-Liong , Eiriksdottir Gudny , Forouhi Nita G. , Geleijnse Johanna M. , Giles Graham G. , Gudnason Vilmundur , Helmer Catherine , Hodge Allison , Jackson Rebecca , Khaw Kay-Tee , Laakso Markku , Lai Heidi , Laurin Danielle , Leander Karin , Lindsay Joan , Micha Renata , Mursu Jaako , Ninomiya Toshiharu , Post Wendy , Psaty Bruce M. , Risérus Ulf , Robinson Jennifer G. , Shadyab Aladdin H. , Snetselaar Linda , Sala-Vila Aleix , Sun Yangbo , Steffen Lyn M. , Tsai Michael Y. , Wareham Nicholas J. , Wood Alexis C. , Wu Jason H. Y. , Hu Frank , Sun Qi , Siscovick David S. , Lemaitre Rozenn N. , Mozaffarian Dariush ,   The Fatty Acids and Outcomes Research Consortium (FORCE)
Published: April 2021

AbstractThe health effects of omega-3 fatty acids have been controversial. Here we report the results of a de novo pooled analysis conducted with data from 17 prospective cohort studies examining the associations between blood omega-3 fatty acid levels and risk for all-cause mortality. Over a median of 16 years of follow-up, 15,720 deaths occurred among 42,466 individuals. We found that, after multivariable adjustment for relevant risk factors, risk for death from all causes was significantly lower (by 15–18%, at least p < 0.003) in the highest vs the lowest quintile for circulating long chain (20–22 carbon) omega-3 fatty acids (eicosapentaenoic, docosapentaenoic, and docosahexaenoic acids). Similar relationships were seen for death from cardiovascular disease, cancer and other causes. No associations were seen with the 18-carbon omega-3, alpha-linolenic acid. These findings suggest that higher circulating levels of marine n-3 PUFA are associated with a lower risk of premature death.
Hetero-site nucleation for growing twisted bilayer graphene with a wide range of twist angles
Authors: Sun Luzhao , Wang Zihao , Wang Yuechen , Zhao Liang , Li Yanglizhi , Chen Buhang , Huang Shenghong , Zhang Shishu , Wang Wendong , Pei Ding , Fang Hongwei , Zhong Shan , Liu Haiyang , Zhang Jincan , Tong Lianming , Chen Yulin , Li Zhenyu , Rümmeli Mark H. , Novoselov Kostya S. , Peng Hailin , Lin Li , Liu Zhongfan 
Published: April 2021

AbstractTwisted bilayer graphene (tBLG) has recently attracted growing interest due to its unique twist-angle-dependent electronic properties. The preparation of high-quality large-area bilayer graphene with rich rotation angles would be important for the investigation of angle-dependent physics and applications, which, however, is still challenging. Here, we demonstrate a chemical vapor deposition (CVD) approach for growing high-quality tBLG using a hetero-site nucleation strategy, which enables the nucleation of the second layer at a different site from that of the first layer. The fraction of tBLGs in bilayer graphene domains with twist angles ranging from 0° to 30° was found to be improved to 88%, which is significantly higher than those reported previously. The hetero-site nucleation behavior was carefully investigated using an isotope-labeling technique. Furthermore, the clear Moiré patterns and ultrahigh room-temperature carrier mobility of 68,000 cm2 V−1 s−1 confirmed the high crystalline quality of our tBLG. Our study opens an avenue for the controllable growth of tBLGs for both fundamental research and practical applications.
Machine learning guided aptamer refinement and discovery
Authors: Bashir Ali , Yang Qin , Wang Jinpeng , Hoyer Stephan , Chou Wenchuan , McLean Cory , Davis Geoff , Gong Qiang , Armstrong Zan , Jang Junghoon , Kang Hui , Pawlosky Annalisa , Scott Alexander , Dahl George E. , Berndl Marc , Dimon Michelle , Ferguson B. Scott 
Published: April 2021

AbstractAptamers are single-stranded nucleic acid ligands that bind to target molecules with high affinity and specificity. They are typically discovered by searching large libraries for sequences with desirable binding properties. These libraries, however, are practically constrained to a fraction of the theoretical sequence space. Machine learning provides an opportunity to intelligently navigate this space to identify high-performing aptamers. Here, we propose an approach that employs particle display (PD) to partition a library of aptamers by affinity, and uses such data to train machine learning models to predict affinity in silico. Our model predicted high-affinity DNA aptamers from experimental candidates at a rate 11-fold higher than random perturbation and generated novel, high-affinity aptamers at a greater rate than observed by PD alone. Our approach also facilitated the design of truncated aptamers 70% shorter and with higher binding affinity (1.5 nM) than the best experimental candidate. This work demonstrates how combining machine learning and physical approaches can be used to expedite the discovery of better diagnostic and therapeutic agents.
Crystal structures of an E1–E2–ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification
Authors: Yuan Lingmin , Lv Zongyang , Adams Melanie J. , Olsen Shaun K. 
Published: April 2021

AbstractE1 enzymes function as gatekeepers of ubiquitin (Ub) signaling by catalyzing activation and transfer of Ub to tens of cognate E2 conjugating enzymes in a process called E1–E2 transthioesterification. The molecular mechanisms of transthioesterification and the overall architecture of the E1–E2–Ub complex during catalysis are unknown. Here, we determine the structure of a covalently trapped E1–E2–ubiquitin thioester mimetic. Two distinct architectures of the complex are observed, one in which the Ub thioester (Ub(t)) contacts E1 in an open conformation and another in which Ub(t) instead contacts E2 in a drastically different, closed conformation. Altogether our structural and biochemical data suggest that these two conformational states represent snapshots of the E1–E2–Ub complex pre- and post-thioester transfer, and are consistent with a model in which catalysis is enhanced by a Ub(t)-mediated affinity switch that drives the reaction forward by promoting productive complex formation or product release depending on the conformational state.
The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation
Authors: Cui Zhaoxia , Liu Yuan , Yuan Jianbo , Zhang Xiaojun , Ventura Tomer , Ma Ka Yan , Sun Shuai , Song Chengwen , Zhan Dongliang , Yang Yanan , Liu Hourong , Fan Guangyi , Cai Qingle , Du Jing , Qin Jing , Shi Chengcheng , Hao Shijie , Fitzgibbon Quinn P. , Smith Gregory G. , Xiang Jianhai , Chan Tin-Yam , Hui Min , Bao Chenchang , Li Fuhua , Chu Ka Hou 
Published: April 2021

AbstractThe infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources. Here we report a chromosome-anchored reference genome and transcriptomes of the Chinese mitten crabEriocheir sinensis, a catadromous crab and invasive species with wide environmental tolerance, strong osmoregulatory capacity and high fertility. We show the expansion of specific gene families in the crab, including F-ATPase, which enhances our knowledge on the adaptive plasticity of this successful invasive species. Our analysis of spatio-temporal transcriptomes and the genome ofE. sinensisand other decapods shows that brachyurization development is associated with down-regulation of Hox genes at the megalopa stage when tail shortening occurs. A better understanding of the molecular mechanism regulating sexual development is achieved by integrated analysis of multiple omics. These genomic resources significantly expand the gene repertoire of Brachyura, and provide insights into the biology of this group, and Crustacea in general.
Loss of endothelial glucocorticoid receptor accelerates diabetic nephropathy
Authors: Srivastava Swayam Prakash , Zhou Han , Setia Ocean , Liu Bing , Kanasaki Keizo , Koya Daisuke , Dardik Alan , Fernandez-Hernando Carlos , Goodwin Julie 
Published: April 2021

AbstractEndothelial cells play a key role in the regulation of disease. Defective regulation of endothelial cell homeostasis may cause mesenchymal activation of other endothelial cells or neighboring cell types, and in both cases contributes to organ fibrosis. Regulatory control of endothelial cell homeostasis is not well studied. Diabetes accelerates renal fibrosis in mice lacking the endothelial glucocorticoid receptor (GR), compared to control mice. Hypercholesterolemia further enhances severe renal fibrosis. The fibrogenic phenotype in the kidneys of diabetic mice lacking endothelial GR is associated with aberrant cytokine and chemokine reprogramming, augmented Wnt signaling and suppression of fatty acid oxidation. Both neutralization of IL-6 and Wnt inhibition improve kidney fibrosis by mitigating mesenchymal transition. Conditioned media from endothelial cells from diabetic mice lacking endothelial GR stimulate Wnt signaling-dependent epithelial-to-mesenchymal transition in tubular epithelial cells from diabetic controls. These data demonstrate that endothelial GR is an essential antifibrotic molecule in diabetes.
Histone dynamics mediate DNA unwrapping and sliding in nucleosomes
Authors: Armeev Grigoriy A. , Kniazeva Anastasiia S. , Komarova Galina A. , Kirpichnikov Mikhail P. , Shaytan Alexey K. 
Published: April 2021

AbstractNucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly wrap ∼147 DNA base pairs around an octamer of histone proteins. How nucleosome structural dynamics affect genome functioning is not completely clear. Here we report all-atom molecular dynamics simulations of nucleosome core particles at a timescale of 15 microseconds. At this timescale, functional modes of nucleosome dynamics such as spontaneous nucleosomal DNA breathing, unwrapping, twisting, and sliding were observed. We identified atomistic mechanisms of these processes by analyzing the accompanying structural rearrangements of the histone octamer and histone-DNA contacts. Octamer dynamics and plasticity were found to enable DNA unwrapping and sliding. Through multi-scale modeling, we showed that nucleosomal DNA dynamics contribute to significant conformational variability of the chromatin fiber at the supranucleosomal level. Our study further supports mechanistic coupling between fine details of histone dynamics and chromatin functioning, provides a framework for understanding the effects of various chromatin modifications.