bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reimagining Democracy: The Socialist Origins of the Initiative and Referendum in the United States
Authors: Ellis Richard J. 
Published: May 2023

AbstractThe initiative and referendum are commonly characterized as quintessentially Populist or Progressive reforms, but transatlantic socialism deserves pride of place in the intellectual history of direct legislation in the United States. A decade and a half before the People’s Party famously commended the idea of direct legislation at its 1892 nominating convention in Omaha, Nebraska, the Socialist Labor Party (SLP) made the demand for direct legislation a plank in its first party platform. That demand was shaped by the 1875 Gotha Program formulated by the Socialist Workers Party of Germany and informed by socialist debates during the First International and the pioneering work of Moritz Rittinghausen. The diffusion of these ideas among Gilded Age labor radicals is a crucial and underappreciated part of the story of the origins of the initiative and referendum in the United States. That socialists’ pioneering role in the origins of the initiative and referendum in the United States has largely been slighted is particularly ironic since the individual arguably most responsible for securing the direct legislation resolution at Omaha was among the nation’s most successful radical labor organizers and a committed socialist, Joseph R. Buchanan.
Climatic Control on Mean Annual Groundwater Evapotranspiration in a Three‐Stage Precipitation Partitioning Framework
Authors: Zhang Yu , Yao Lili , Geurink Jeffrey S. , Parajuli Kshitij , Wang Dingbao 
Published: May 2023

AbstractA three‐stage precipitation partitioning framework is proposed to study the climate controls on mean annual groundwater evapotranspiration (GWET) for 33 gauged watersheds in west‐central Florida. Daily GWET, total evapotranspiration (ET), groundwater recharge, base flow, and total runoff are simulated by the Integrated Hydrologic Model, which dynamically couples a surface water model (HSPF) and a groundwater flow model (MODFLOW). The roles of GWET on long‐term water balance are quantified by four ratios. The ratios of GWET to total available water, watershed wetting, ET, and recharge decrease exponentially with watershed aridity index (WAI), which is defined as the ratio of potential evapotranspiration to total available water. In the one‐stage precipitation partitioning framework, the contribution of GWET to the ratio between total ET and available water for ET (i.e., the y‐axis of Budyko curve) decreases with WAI. In the two‐stage precipitation partitioning framework, the contribution of GWET to the ratio between total ET and watershed wetting (i.e., Horton index) decreases with WAI. The changes in GWET caused by intra‐monthly (IM) climate variability are the highest among the temporal scales of climate variability investigated to understand controls on GWET. The inter‐annual, intra‐annual, and IM climate variabilities lead to increase of GWET; but the sub‐daily climate variability results in decrease of GWET. For the third stage of partitioning, given the same ratio of potential GWET to available water for GWET, higher percentage of forest and wetland and lower percentage of impervious land contribute to higher ratio of GWET to available water for GWET.
Moho Geometry Estimation Beneath the Gulf of Guinea From Satellite Gravity Data Based on a Regularized Non‐Linear Gravity Inversion
Authors: Kamto Paul Gautier , Lemotio Willy , Kamguia Joseph 
Published: May 2023

AbstractIn this work, we present a new gravimetric Moho model over the Gulf of Guinea computed from the inversion of the global gravity EIGEN‐6C4 model. The computation procedure contains a regularized non‐linear inversion algorithm. Before applying the inversion algorithm, the gravity data from the EIGEN‐6C4 model have been corrected from gravimetric effects of topography, bathymetry, and sediments. To calculate these corrections, a forward modeling has been applied using tesseroids to take into account the earth curvature, and via the Legendre Quadrature integration technique. The inversion procedure of the Bouguer disturbances integrates the use of hyperparameters in particular the regularization parameter, the anomalous Moho density contrast and the reference Moho depth. This regularized non‐linear inversion method has been tested on synthetic data contaminated by a normally distributed noise. Through this test, the inversion method showed its effectiveness in estimating a Moho model. The application of this method on the Gulf of Guinea has produced a high‐resolution gravimetric model, whose depths vary between 7.75 and 44.50 km. The greatest depths (greater than 40 km) are located along the eastern part of the study area. The comparison of our gravimetric model with the isostatic Airy, GEMMA (GOCE Exploitation for Moho Modeling and Applications) and CRUST1.0 Moho models, globally shows good similarities. The comparison of our gravimetric Moho model to the GEMMA gravimetric model exhibits large residuals around the continental margin, thus reflecting the limit of the inversion method for areas with great Moho depth gradients. The differences observed between our gravimetric model and the CRUST1.0 model in certain regions such as southern Nigeria show the impact of the neglect of anomalous crustal and mantle sources in the accuracy of the solutions obtained after inversion. However, our gravimetric model yields an improved and high‐resolution representation of the Moho undulations over the Gulf of Guinea compared to previous gravimetric Moho models.
Rapidly Changing East Asian Marine Heatwaves Under a Warming Climate
Authors: Lee S. , Park M. S. , Kwon M. , Park Y. G. , Kim Y. H. , Choi N. 
Published: May 2023

AbstractThe East Asian marginal seas (EAMS) are one of the fastest‐warming ocean regions globally. This study presents the long‐term trends (1982–2020) of extreme ocean warming events called “marine heatwaves” over the EAMS and examines the relationships between marine heatwave trends and mean SST warming trends. We focus on five subregions with different influences from atmospheric perturbation and ocean currents: the northern East Sea (N‐ES), southern East Sea, Yellow Sea, Korea Strait (KS), and East China Sea (ECS). During the past four decades, marine heatwave duration and intensity in the EAMS have increased to approximately +4 days and +0.3°C per decade on average, respectively. In summer, the positive trend of marine heatwaves is the highest in the ECS, primarily due to the rapidly increasing mean sea surface temperature (SST). In winter, the N‐ES reveals remarkably rapid increases in marine heatwave properties in the last two decades, with increasing rates of approximately 6.2 (4.9) times longer total duration (stronger intensity) than the global average changes. Beyond the impact of the rapid increase in mean SST, the N‐ES marine heatwaves can be further extended due to the northward shift of the East Korea Warm Current. In general, mean SST changes are critical to the increasing trend in marine heatwave duration and intensity. This study further emphasizes that the changes in ocean circulation may expedite more rapid changes in extreme ocean events, which can produce more vulnerability in some places, such as the N‐ES, to marine heatwaves under continued global warming.
Modified Tracer Gas Injection for Measuring Stream Gas Exchange Velocity in the Presence of Significant Temperature Variation
Authors: Jensen Craig R. , Genereux David P. , Gilmore Troy E. , Solomon D. Kip 
Published: May 2023

AbstractGas exchange between streams and overlying air is an important physical‐chemical environmental process that is typically determined by injecting a tracer gas into a stream at a steady rate and sampling steady‐state tracer gas concentrations in the stream water. Previous modes of tracer gas injection allow gas‐water partitioning of the tracer gas, making the rate of gas injection and thus the measured gas transfer velocity potentially sensitive to temperature variation. Presented here is a modification to the tracer solution injection method in which a tracer gas solution was prepared in Tedlar® bags from which all headspace was removed before injecting the solution into the stream. Along with four other strategies to prevent a headspace from forming in the bags during tracer injection in the field, this zero‐headspace tracer solution method prevents gas‐water partitioning anywhere in the injection system, allowing a steady delivery of tracer gas to the stream even in the presence of variation in air and/or stream water temperature. A field test of the method in Nebraska yielded a gas transfer velocity of 4.1 m/day, within the range found in the literature for similarly‐sized streams.
Evaluation of Parameterization Schemes for Matric Potential in Frozen Soil in Land Surface Models: A Modeling Perspective
Authors: Zhao Yi , Nan Zhuotong , Cao Zetao , Ji Hailong , Hu Jianan 
Published: May 2023

AbstractSoil matric potential (SMP) is an important variable in land surface models (LSMs) for regulating soil hydrological processes and highly influenced by soil ice in frozen ground. In this study, four SMP parameterization schemes that incorporate different effects of soil pore ice were separately integrated into the Simultaneous Heat and Water (SHAW) model and evaluated for their ability to simulate heat and water transport at a permafrost monitoring site at the Tanggula Mountain Pass on the inner Qinghai‐Tibet Plateau based on the same data and model settings. The schemes differed in their treatment of pore ice effects, including effective porosity and cryosuction. An identifiability analysis of SMP‐related parameters for each scheme was performed, based on 1,000‐fold random parameter sampling. The scheme that considered both effects performed best, accurately simulating both soil moisture content and temperature in the active layer. The schemes that considered only one effect of pore ice showed limitations, with the effective porosity scheme underestimating unfrozen water content and the cryosuction scheme seriously overestimating it, and both schemes leading to large discrepancies in simulated soil temperature. The scheme that ignored both effects performed better than the partially considered schemes due to a compensating effect of reduced effective porosity and increased cryosuction in the presence of pore ice, but not as well as the scheme that considered both effects, particularly in simulating soil temperature during freezing periods and estimating unfrozen water content near the mid‐depth of the active layer.
Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data
Authors: Yang Manqiu , Zhang Shufan , Jiang Rong , Chen Shaomu , Huang Moli 
Published: May 2023

AbstractIn cancer, extrachromosomal circular DNA (ecDNA), or megabase-pair amplified circular DNA, plays an essential role in intercellular heterogeneity and tumor cell revolution because of its non-Mendelian inheritance. We developed circlehunter (https://github.com/suda-huanglab/circlehunter), a tool for identifying ecDNA from ATAC-Seq data using the enhanced chromatin accessibility of ecDNA. Using simulated data, we showed that circlehunter has an F1 score of 0.93 at 30× local depth and read lengths as short as 35 bp. Based on 1312 ecDNAs predicted from 94 publicly available datasets of ATAC-Seq assays, we found 37 oncogenes contained in these ecDNAs with amplification characteristics. In small cell lung cancer cell lines, ecDNA containing MYC leads to amplification of MYC and cis-regulates the expression of NEUROD1, resulting in an expression pattern consistent with the NEUROD1 high expression subtype and sensitive to Aurora kinase inhibitors. This showcases that circlehunter could serve as a valuable pipeline for the investigation of tumorigenesis.
Epigenetic regulation in the tumor microenvironment: molecular mechanisms and therapeutic targets
Authors: Yang Jing , Xu Jin , Wang Wei , Zhang Bo , Yu Xianjun , Shi Si 
Published: May 2023

AbstractOver decades, researchers have focused on the epigenetic control of DNA-templated processes. Histone modification, DNA methylation, chromatin remodeling, RNA modification, and noncoding RNAs modulate many biological processes that are crucial to the development of cancers. Dysregulation of the epigenome drives aberrant transcriptional programs. A growing body of evidence suggests that the mechanisms of epigenetic modification are dysregulated in human cancers and might be excellent targets for tumor treatment. Epigenetics has also been shown to influence tumor immunogenicity and immune cells involved in antitumor responses. Thus, the development and application of epigenetic therapy and cancer immunotherapy and their combinations may have important implications for cancer treatment. Here, we present an up-to-date and thorough description of how epigenetic modifications in tumor cells influence immune cell responses in the tumor microenvironment (TME) and how epigenetics influence immune cells internally to modify the TME. Additionally, we highlight the therapeutic potential of targeting epigenetic regulators for cancer immunotherapy. Harnessing the complex interplay between epigenetics and cancer immunology to develop therapeutics that combine thereof is challenging but could yield significant benefits. The purpose of this review is to assist researchers in understanding how epigenetics impact immune responses in the TME, so that better cancer immunotherapies can be developed.
New insights into inflammatory osteoclast precursors as therapeutic targets for rheumatoid arthritis and periodontitis
Authors: Hascoët Emilie , Blanchard Frédéric , Blin-Wakkach Claudine , Guicheux Jérôme , Lesclous Philippe , Cloitre Alexandra 
Published: May 2023

AbstractRheumatoid arthritis (RA) and periodontitis are chronic inflammatory diseases leading to increased bone resorption. Preventing this inflammatory bone resorption is a major health challenge. Both diseases share immunopathogenic similarities and a common inflammatory environment. The autoimmune response or periodontal infection stimulates certain immune actors, leading in both cases to chronic inflammation that perpetuates bone resorption. Moreover, RA and periodontitis have a strong epidemiological association that could be explained by periodontal microbial dysbiosis. This dysbiosis is believed to be involved in the initiation of RA via three mechanisms. (i) The dissemination of periodontal pathogens triggers systemic inflammation. (ii) Periodontal pathogens can induce the generation of citrullinated neoepitopes, leading to the generation of anti-citrullinated peptide autoantibodies. (iii) Intracellular danger-associated molecular patterns accelerate local and systemic inflammation. Therefore, periodontal dysbiosis could promote or sustain bone resorption in distant inflamed joints. Interestingly, in inflammatory conditions, the existence of osteoclasts distinct from “classical osteoclasts” has recently been reported. They have proinflammatory origins and functions. Several populations of osteoclast precursors have been described in RA, such as classical monocytes, a dendritic cell subtype, and arthritis-associated osteoclastogenic macrophages. The aim of this review is to synthesize knowledge on osteoclasts and their precursors in inflammatory conditions, especially in RA and periodontitis. Special attention will be given to recent data related to RA that could be of potential value in periodontitis due to the immunopathogenic similarities between the two diseases. Improving our understanding of these pathogenic mechanisms should lead to the identification of new therapeutic targets involved in the pathological inflammatory bone resorption associated with these diseases.
Atlas of mRNA translation and decay for bacteria
Authors: Huch Susanne , Nersisyan Lilit , Ropat Maria , Barrett Donal , Wu Mengjun , Wang Jing , Valeriano Valerie D. , Vardazaryan Nelli , Huerta-Cepas Jaime , Wei Wu , Du Juan , Steinmetz Lars M. , Engstrand Lars , Pelechano Vicent 
Published: May 2023

AbstractRegulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5′ monophosphorylated mRNA decay intermediates (5′P), we show that cotranslational mRNA degradation is conserved among both Gram-positive and -negative bacteria. We demonstrate that, in species with 5′–3′ exonucleases, the exoribonuclease RNase J tracks the trailing ribosome to produce an in vivo single-nucleotide toeprint of the 5' position of the ribosome. In other species lacking 5′–3′ exonucleases, ribosome positioning alters endonucleolytic cleavage sites. Using our metadegradome (5′P degradome) sequencing approach, we characterize 5′P mRNA decay intermediates in 96 species including Bacillus subtilis, Escherichia coli, Synechocystis spp. and Prevotella copri and identify codon- and gene-level ribosome stalling responses to stress and drug treatment. We also apply 5′P sequencing to complex clinical and environmental microbiomes and demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations. Finally we produce a degradome atlas for 96 species to enable analysis of mechanisms of RNA degradation in bacteria. Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities.
Spatial dysregulation of T follicular helper cells impairs vaccine responses in aging
Authors: Silva-Cayetano Alyssa , Fra-Bido Sigrid , Robert Philippe A. , Innocentin Silvia , Burton Alice R. , Watson Emily M. , Lee Jia Le , Webb Louise M. C. , Foster William S. , McKenzie Ross C. J. , Bignon Alexandre , Vanderleyden Ine , Alterauge Dominik , Lemos Julia P. , Carr Edward J. , Hill Danika L. , Cinti Isabella , Balabanian Karl , Baumjohann Dirk , Espeli Marion , Meyer-Hermann Michael , Denton Alice E. , Linterman Michelle A. 
Published: May 2023

AbstractThe magnitude and quality of the germinal center (GC) response decline with age, resulting in poor vaccine-induced immunity in older individuals. A functional GC requires the co-ordination of multiple cell types across time and space, in particular across its two functionally distinct compartments: the light and dark zones. In aged mice, there is CXCR4-mediated mislocalization of T follicular helper (TFH) cells to the dark zone and a compressed network of follicular dendritic cells (FDCs) in the light zone. Here we show that TFH cell localization is critical for the quality of the antibody response and for the expansion of the FDC network upon immunization. The smaller GC and compressed FDC network in aged mice were corrected by provision of TFH cells that colocalize with FDCs using CXCR5. This demonstrates that the age-dependent defects in the GC response are reversible and shows that TFH cells support stromal cell responses to vaccines.
Phosphatidylserine-dependent structure of synaptogyrin remodels the synaptic vesicle membrane
Authors: Yu Taekyung , Flores-Solis David , Eastep Gunnar N. , Becker Stefan , Zweckstetter Markus 
Published: May 2023

AbstractSynaptic vesicles are small membrane-enclosed organelles that store neurotransmitters at presynaptic terminals. The uniform morphology of synaptic vesicles is important for brain function, because it enables the storage of well-defined amounts of neurotransmitters and thus reliable synaptic transmission. Here, we show that the synaptic vesicle membrane protein synaptogyrin cooperates with the lipid phosphatidylserine to remodel the synaptic vesicle membrane. Using NMR spectroscopy, we determine the high-resolution structure of synaptogyrin and identify specific binding sites for phosphatidylserine. We further show that phosphatidylserine binding changes the transmembrane structure of synaptogyrin and is critical for membrane bending and the formation of small vesicles. Cooperative binding of phosphatidylserine to both a cytoplasmic and intravesicular lysine-arginine cluster in synaptogyrin is required for the formation of small vesicles. Together with other synaptic vesicle proteins, synaptogyrin thus can sculpt the membrane of synaptic vesicles.
A blood and bronchoalveolar lavage protein signature of rapid FEV1 decline in smoking-associated COPD
Authors: DiLillo Katarina M. , Norman Katy C. , Freeman Christine M. , Christenson Stephanie A. , Alexis Neil E. , Anderson Wayne H. , Barjaktarevic Igor Z. , Barr R. Graham , Comellas Alejandro P. , Bleecker Eugene R. , Boucher Richard C. , Couper David J. , Criner Gerard J. , Doerschuk Claire M. , Wells J. Michael , Han MeiLan K. , Hoffman Eric A. , Hansel Nadia N. , Hastie Annette T. , Kaner Robert J. , Krishnan Jerry A. , Labaki Wassim W. , Martinez Fernando J. , Meyers Deborah A. , O’Neal Wanda K. , Ortega Victor E. , Paine Robert , Peters Stephen P. , Woodruff Prescott G. , Cooper Christopher B. , Bowler Russell P. , Curtis Jeffrey L. , Arnold Kelly B. ,   SPIROMICS investigators
Published: May 2023

AbstractAccelerated progression of chronic obstructive pulmonary disease (COPD) is associated with increased risks of hospitalization and death. Prognostic insights into mechanisms and markers of progression could facilitate development of disease-modifying therapies. Although individual biomarkers exhibit some predictive value, performance is modest and their univariate nature limits network-level insights. To overcome these limitations and gain insights into early pathways associated with rapid progression, we measured 1305 peripheral blood and 48 bronchoalveolar lavage proteins in individuals with COPD [n = 45, mean initial forced expiratory volume in one second (FEV1) 75.6 ± 17.4% predicted]. We applied a data-driven analysis pipeline, which enabled identification of protein signatures that predicted individuals at-risk for accelerated lung function decline (FEV1 decline ≥ 70 mL/year) ~ 6 years later, with high accuracy. Progression signatures suggested that early dysregulation in elements of the complement cascade is associated with accelerated decline. Our results propose potential biomarkers and early aberrant signaling mechanisms driving rapid progression in COPD.
Dedifferentiated fat cells administration ameliorates abnormal expressions of fatty acids metabolism-related protein expressions and intestinal tissue damage in experimental necrotizing enterocolitis
Authors: Mimatsu Haruka , Onoda Atsuto , Kazama Tomohiko , Nishijima Koji , Shimoyama Yoshie , Go Shoji , Ueda Kazuto , Takahashi Yoshiyuki , Matsumoto Taro , Hayakawa Masahiro , Sato Yoshiaki 
Published: May 2023

AbstractNeonatal necrotizing enterocolitis (NEC) is a serious disease of premature infants that necessitates intensive care and frequently results in life-threatening complications and high mortality. Dedifferentiated fat cells (DFATs) are mesenchymal stem cell-like cells derived from mature adipocytes. DFATs were intraperitoneally administrated to a rat NEC model, and the treatment effect and its mechanism were evaluated. The NEC model was created using rat pups hand fed with artificial milk, exposed to asphyxia and cold stress, and given oral lipopolysaccharides after cesarean section. The pups were sacrificed 96 h after birth for macroscopic histological examination and proteomics analysis. DFATs administration significantly improved the survival rate from 25.0 (vehicle group) to 60.6% (DFAT group) and revealed a significant reduction in macroscopical, histological, and apoptosis evaluation compared with the vehicle group. Additionally, the expression of C–C motif ligand 2 was significantly decreased, and that of interleukin-6 decreased in the DFAT group. DFAT administration ameliorated 93 proteins mainly related to proteins of fatty acid metabolism of the 436 proteins up-/down-regulated by NEC. DFATs improved mortality and restored damaged intestinal tissues in NEC, possibly by improving the abnormal expression of fatty acid-related proteins and reducing inflammation.