bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geodetic Measurements of Slow‐Slip Events Southeast of Parkfield, CA
Authors: Delbridge Brent G. , Carmichael Joshua D. , Nadeau Robert M. , Shelly David R. , Bürgmann Roland 
Published: March 2020

AbstractTremor and low‐frequency earthquakes are presumed to be indicative of surrounding slow, aseismic slip that is often below geodetic detection thresholds. This study uses data from borehole seismometers and long‐baseline laser strainmeters to observe both the seismic and geodetic signatures of episodic tremor and slip on the Parkfield region of the San Andreas Fault near Cholame, CA. The observed occurrence rates of both the tremors and co‐located families of low‐frequency earthquakes are not steady but instead exhibit quasiperiodic bursts of increased activity. We show that these periods of elevated seismic activity correlate with statistically significant stacked strain signals consisting of 44 slow‐slip events. Modeled individual slow‐slip events and their total summed moment, which are constrained by seismic signals and stacked strain, respectively, indicate that the individual moment magnitudes of these events range from
4.6–5.2. We find that the measured geodetic signal likely precedes the seismic signal by several hours, consistent with the aseismic slip preceding and driving the observed seismic tremor activity. We confirm that strike‐slip faults, in addition to subduction zones, are capable of producing episodic tremor and slip.
Thaw Transitions and Redox Conditions Drive Methane Oxidation in a Permafrost Peatland
Authors: Perryman Clarice R. , McCalley Carmody K. , Malhotra Avni , Fahnestock M. Florencia , Kashi Natalie N. , Bryce Julia G. , Giesler Reiner , Varner Ruth K. 
Published: March 2020

AbstractPermafrost peatlands are a significant source of methane (CH4) emissions to the atmosphere and could emit more CH4 with continued permafrost thaw. Aerobic methane‐oxidizing bacteria may attenuate a substantial fraction of CH4 emissions in thawing permafrost peatlands; however, the impact of permafrost thaw on CH4 oxidation is uncertain. We measured potential CH4 oxidation rates (hereafter, CH4 oxidation) and their predictors using laboratory incubations and in situ porewater redox chemistry across a permafrost thaw gradient of eight thaw stages at Stordalen Mire, a permafrost peatland complex in northernmost Sweden. Methane oxidation rates increased across a gradient of permafrost thaw and differed in transitional thaw stages relative to end‐member stages. Oxidation was consistently higher in submerged fens than in bogs or palsas across a range of CH4 concentrations. We also observed that CH4 oxidation increased with decreasing in situ redox potential and was highest in sites with lower redox potential (Eh < 10 mV) and high water table. Our results suggest that redox potential can be used as an important predictor of CH4 oxidation, especially in thawed permafrost peatlands. Our results also highlight the importance of considering transitional thaw stages when characterizing landscape‐scale CH4 dynamics, because these transitional areas have different rates and controls of CH4 oxidation relative to intact or completely thawed permafrost areas. As permafrost thaw increases the total area of semiwet and wet thaw stages in permafrost peatlands, CH4 oxidation represents an important control on CH4 emissions to the atmosphere.
Revisiting the Middle Eocene Climatic Optimum “Carbon Cycle Conundrum” With New Estimates of Atmospheric pCO2 From Boron Isotopes
Authors: Henehan Michael J. , Edgar Kirsty M. , Foster Gavin L. , Penman Donald E. , Hull Pincelli M. , Greenop Rosanna , Anagnostou Eleni , Pearson Paul N. 
Published: March 2020

AbstractThe Middle Eocene Climatic Optimum (MECO) was a gradual warming event and carbon cycle perturbation that occurred between 40.5 and 40.1 Ma. A number of characteristics, including greater‐than‐expected deep‐sea carbonate dissolution, a lack of globally coherent negative δ13C excursion in marine carbonates, a duration longer than the characteristic timescale of carbon cycle recovery, and the absence of a clear trigger mechanism, challenge our current understanding of the Earth system and its regulatory feedbacks. This makes the MECO one of the most enigmatic events in the Cenozoic, dubbed a middle Eocene “carbon cycle conundrum.” Here we use boron isotopes in planktic foraminifera to better constrain pCO2 changes over the event. Over the MECO itself, we find that pCO2 rose by only 0.55–0.75 doublings, thus requiring a much more modest carbon injection than previously indicated by the alkenone δ13C‐pCO2 proxy. In addition, this rise in pCO2 was focused around the peak of the 400 kyr warming trend. Before this, considerable global carbonate δ18O change was asynchronous with any coherent ocean pH (and hence pCO2) excursion. This finding suggests that middle Eocene climate (and perhaps a nascent cryosphere) was highly sensitive to small changes in radiative forcing.
Fundamental Hydraulics of Cross Sections in Natural Rivers: Preliminary Analysis of a Large Data Set of Acoustic Doppler Flow Measurements
Authors: Bjerklie David M. , Fulton John W. , Dingman S. Lawrence , Canova Michael G. , Minear Justin T. , Moramarco Tommaso 
Published: March 2020

AbstractWe have assembled a comprehensive and publicly accessible U.S. Geological Survey (USGS) streamflow measurement data set, called HYDRoSWOT, from a USGS National Water Information System archive of acoustic Doppler current profiler river discharge measurements collected from a wide range of rivers throughout the United States. The data set provides a wealth of information on the range of hydraulic characteristics of river cross sections in the United States. Preliminary exploration of the data set, filtered for quality control, indicates that rivers tend toward consistent and predictable forms as discharge increases. The ratio of maximum‐to‐mean depth is highly predictable and is remarkably consistent across all river sizes and discharges. Distributions of hydraulic characteristics provide a large‐scale perspective on the general hydraulic characteristics of rivers. The data set affords the opportunity to analyze hydraulic relations for individual rivers as a function of stage, geomorphic setting, and energy environments and, combined with additional information contained in this data set, might yield predictive relations that could help constrain and parameterize river hydraulic models.
Assembly of platforms for signal transduction in the new era: dimerization, helical filament assembly, and beyond
Authors: Ha Hyun Ji , Chun Hye Lin , Park Hyun Ho 
Published: March 2020

AbstractSupramolecular organizing center (SMOC)-mediated signal transduction is an emerging concept in the field of signal transduction that is ushering in a new era. The formation of location-specific, higher-order SMOCs is particularly important for cell death and innate immune signaling processes. Several protein interaction domains, including the death domain (DD) superfamily and the CIDE domain, are representative mediators of SMOC assembly in cell death and innate immune signaling pathways. DD superfamily- and CIDE domain-containing proteins form SMOCs that activate various caspases and provide signaling scaffold platforms. These assemblies can lead to signal transduction and amplification during signaling events. In this review, we summarize recent findings on the molecular basis of DD superfamily- and CIDE domain-mediated SMOC formation.
Cdc37 suppression induces plasma cell immaturation and bortezomib resistance in multiple myeloma via Xbp1s
Authors: Zang Meirong , Guo Jiaojiao , Liu Lanting , Jin Fengyan , Feng Xiangling , An Gang , Qin Xiaoqi , Wu Yangbowen , Lei Qian , Meng Bin , Zhu Yinghong , Guan Yongjun , Deng Shuhui , Hao Mu , Xu Yan , Zou Dehui , Wu Minghua , Qiu Lugui , Zhou Wen 
Published: March 2020

AbstractMultiple myeloma (MM) is the second most prevalent hematologic malignancy. Although the use of bortezomib (BTZ) significantly improves MM therapy, intrinsic and acquired drug resistance to BTZ remains a major clinical problem. In this study, we find that Cdc37, a key co-chaperone of Hsp90, is downregulated in relapsed MM patients, especially after BTZ treatment, suggesting a link between Cdc37 and BTZ resistance. Suppression of Cdc37 or inhibition of Cdc37/Hsp90 association induces plasma cell dedifferentiation, quiescence of MM cells, and BTZ resistance in MM. Furthermore, we discover that Cdc37 expression correlates positively with Xbp1s, a critical transcription factor for plasma cell differentiation in MM samples. Depletion/inhibition of Cdc37 downregulates Xbp1s, while overexpression of Xbp1s in MM cell lines partially rescues plasma immaturation and BTZ resistance. It is suggested that Xbp1s may act as a key downstream effector of Cdc37. Experiments with a mouse model also demonstrate that Cdc37 inhibition promotes plasma cell immaturation, confers BTZ resistance, and increases MM progression in vivo. Together, we identify a critical factor and a new signaling mechanism that regulate plasma cell immaturation and BTZ resistance in MM cells. Our findings may constitute a novel strategy that overcomes BTZ resistance in MM therapy.
Patterns of change in treatment, response, and outcome in patients with follicular lymphoma over the last four decades: a single-center experience
Authors: Mozas Pablo , Nadeu Ferran , Rivas-Delgado Alfredo , Rivero Andrea , Garrote Marta , Balagué Olga , González-Farré Blanca , Veloza Luis , Baumann Tycho , Giné Eva , Delgado Julio , Villamor Neus , Campo Elías , Magnano Laura , López-Guillermo Armando 
Published: March 2020

AbstractAlthough the introduction of immunotherapy has improved outcomes for follicular lymphoma (FL) patients, histological transformation (HT) and early relapse still confer a poor prognosis. We sought to describe the patterns of change in treatment, response, and outcome of FL patients at our institution over the last four decades. Seven hundred and twenty-seven patients (389 F/338 M; median age, 57 years) consecutively diagnosed with grade 1-3a FL between 1980 and 2017, categorized into four decades according to the time of diagnosis, constituted the study population. Clinical characteristics, treatment, response, absolute and relative survival, HT, second malignancies (SM), and causes of death were assessed. Median OS for the entire cohort was 17.6 years. From decade 1 to 4, there was an increase in the complete response rate (48 to 70%), progression-free survival (40 to 56% at 5 years), OS (77 to 86% at 5 years), and relative survival ratio (0.83 to 0.94 at 5 years), with no significant differences in the risk of HT or SM. Lymphoma remained the most common cause of death in all four decades. These findings illustrate the overall improvement in outcome for FL patients, but support the need for further research into risk stratification and management.
TRPC6-dependent Ca2+ signaling mediates airway inflammation in response to oxidative stress via ERK pathway
Authors: Chen Qingzi , Zhou Yubo , Zhou Lifen , Fu Zhaodi , Yang Chuntao , Zhao Lei , Li Shuni , Chen Yan , Wu Yousen , Ling Zhenwei , Wang Yufeng , Huang Jianrong , Li Jianhua 
Published: March 2020

AbstractOzone (O3) plays an extremely important role in airway inflammation by generating reactive oxygen species (ROS) including hydrogen peroxide, then promoting redox actions and causing oxidative stress. Evidences indicate that TRPC6 (canonical transient receptor potential channel 6) is a redox-regulated Ca2+ permeable nonselective cation channel, but its role in the setting of oxidative stress-related airway inflammation remains unknown. Here, we found that both TRPC6−/− mice and mice pretreated with SAR7334, a potent TRPC6 inhibitor, were protected from O3-induced airway inflammatory responses. In vitro, both knockdown of TRPC6 expression with shRNA and TRPC6 blockage markedly attenuated the release of cytokines IL-6 and IL-8 induced by O3 or H2O2 in 16HBE cells (human bronchial epithelial cell line). Treatment with O3 or H2O2 enhanced TRPC6 protein expression in vivo and vitro. We also observed that TRPC6-dependent increase of intracellular Ca2+ concentration ([Ca2+]i) was triggered by H2O2, which consisted of the release from intracellular calcium store and the influx of extracellular Ca2+ and could be further strengthened by 6-h O3 exposure in both 16HBE cells and HBEpiCs (primary human bronchial epithelial cells). Moreover, we confirmed that the activation of MAPK signals (ERK1/2, p38, JNK) was required for the inflammatory response induced by O3 or H2O2 while only the phosphorylation of ERK pathway was diminished in the TRPC6-knockdown situation. These results demonstrate that oxidative stress regulates TRPC6-mediated Ca2+ cascade, which leads to the activation of ERK pathway and inflammation and could become a potential target to treat oxidative stress-associated airway inflammatory diseases.
Aggravation of reactive nitrogen flow driven by human production and consumption in Guangzhou City China
Authors: Dong Yue , Xu Linyu , Yang Zhifeng , Zheng Hanzhong , Chen Lei 
Published: March 2020

AbstractHuman activities reshape the global nitrogen (N) cycle and affect environment and human health through reactive nitrogen (Nr) loss during production and consumption. In urbanized regions, the N cycle is greatly mediated by complex interactions between human and natural factors. However, the variations in sources, magnitude, spatiotemporal patterns and drivers of Nr flows remain unclear. Here we show by model simulations, anthropogenic perturbations not only intensify Nr input to sustain increasing demands for production and consumption in Guangzhou city, China, but also greatly change the Nr distribution pattern in the urban system, showing a substantial Nr enrichment in the atmosphere and a relatively low retention capacity of Nr in the terrestrial system. Our results highlight the strong anthropogenic effect of urban systems on the N cycle to suggest sustainable human activity changes to harmonize the relationship between Nr behaviors and human drivers.
Trajectory-based differential expression analysis for single-cell sequencing data
Authors: Van den Berge Koen , Roux de Bézieux Hector , Street Kelly , Saelens Wouter , Cannoodt Robrecht , Saeys Yvan , Dudoit Sandrine , Clement Lieven 
Published: March 2020

AbstractTrajectory inference has radically enhanced single-cell RNA-seq research by enabling the study of dynamic changes in gene expression. Downstream of trajectory inference, it is vital to discover genes that are (i) associated with the lineages in the trajectory, or (ii) differentially expressed between lineages, to illuminate the underlying biological processes. Current data analysis procedures, however, either fail to exploit the continuous resolution provided by trajectory inference, or fail to pinpoint the exact types of differential expression. We introduce tradeSeq, a powerful generalized additive model framework based on the negative binomial distribution that allows flexible inference of both within-lineage and between-lineage differential expression. By incorporating observation-level weights, the model additionally allows to account for zero inflation. We evaluate the method on simulated datasets and on real datasets from droplet-based and full-length protocols, and show that it yields biological insights through a clear interpretation of the data.
Electrochemical deposition as a universal route for fabricating single-atom catalysts
Authors: Zhang Zhirong , Feng Chen , Liu Chunxiao , Zuo Ming , Qin Lang , Yan Xupeng , Xing Yulin , Li Hongliang , Si Rui , Zhou Shiming , Zeng Jie 
Published: March 2020

AbstractSingle-atom catalysts (SACs) exhibit intriguing catalytic performance owing to their maximized atom utilizations and unique electronic structures. However, the reported strategies for synthesizing SACs generally have special requirements for either the anchored metals or the supports. Herein, we report a universal approach of electrochemical deposition that is applicable to a wide range of metals and supports for the fabrication of SACs. The depositions were conducted on both cathode and anode, where the different redox reactions endowed the SACs with distinct electronic states. The SACs from cathodic deposition exhibited high activities towards hydrogen evolution reaction, while those from anodic deposition were highly active towards oxygen evolution reaction. When cathodically- and anodically-deposited Ir single atoms on Co0.8Fe0.2Se2@Ni foam were integrated into a two-electrode cell for overall water splitting, a voltage of 1.39 V was required at 10 mA cm−2 in alkaline electrolyte.
Simultaneous enhanced efficiency and thermal stability in organic solar cells from a polymer acceptor additive
Authors: Yang Wenyan , Luo Zhenghui , Sun Rui , Guo Jie , Wang Tao , Wu Yao , Wang Wei , Guo Jing , Wu Qiang , Shi Mumin , Li Hongneng , Yang Chuluo , Min Jie 
Published: March 2020

AbstractThe thermal stability of organic solar cells is critical for practical applications of this emerging technology. Thus, effective approaches and strategies need to be found to alleviate their inherent thermal instability. Here, we show a polymer acceptor-doping general strategy and report a thermally stable bulk heterojunction photovoltaic system, which exhibits an improved power conversion efficiency of 15.10%. Supported by statistical analyses of device degradation data, and morphological characteristics and physical mechanisms study, this polymer-doping blend shows a longer lifetime, nearly keeping its efficiency (t = 800 h) under accelerated aging tests at 150 oC. Further analysis of the degradation behaviors indicates a bright future of this system in outer space applications. Notably, the use of polymer acceptor as a dual function additive in the other four photovoltaic systems was also confirmed, demonstrating the good generality of this polymer-doping strategy.
Anti-angiogenic effects of VEGF stimulation on endothelium deficient in phosphoinositide recycling
Authors: Stratman Amber N. , Farrelly Olivia M. , Mikelis Constantinos M. , Miller Mayumi F. , Wang Zhiyong , Pham Van N. , Davis Andrew E. , Burns Margaret C. , Pezoa Sofia A. , Castranova Daniel , Yano Joseph J. , Kilts Tina M. , Davis George E. , Gutkind J. Silvio , Weinstein Brant M. 
Published: March 2020

AbstractAnti-angiogenic therapies have generated significant interest for their potential to combat tumor growth. However, tumor overproduction of pro-angiogenic ligands can overcome these therapies, hampering success of this approach. To circumvent this problem, we target the resynthesis of phosphoinositides consumed during intracellular transduction of pro-angiogenic signals in endothelial cells (EC), thus harnessing the tumor’s own production of excess stimulatory ligands to deplete adjacent ECs of the capacity to respond to these signals. Using zebrafish and human endothelial cells in vitro, we show ECs deficient in CDP-diacylglycerol synthase 2 are uniquely sensitive to increased vascular endothelial growth factor (VEGF) stimulation due to a reduced capacity to re-synthesize phosphoinositides, including phosphatidylinositol-(4,5)-bisphosphate (PIP2), resulting in VEGF-exacerbated defects in angiogenesis and angiogenic signaling. Using murine tumor allograft models, we show that systemic or EC specific suppression of phosphoinositide recycling results in reduced tumor growth and tumor angiogenesis. Our results suggest inhibition of phosphoinositide recycling provides a useful anti-angiogenic approach.
A signal cascade originated from epidermis defines apical-basal patterning of Arabidopsis shoot apical meristems
Authors: Han Han , Yan An , Li Lihong , Zhu Yingfang , Feng Bill , Liu Xing , Zhou Yun 
Published: March 2020

AbstractIn multicellular organisms, a long-standing question is how spatial patterns of distinct cell types are initiated and maintained during continuous cell division and proliferation. Along the vertical axis of plant shoot apical meristems (SAMs), stem cells are located at the top while cells specifying the stem cells are located more basally, forming a robust apical-basal pattern. We previously found that in Arabidopsis SAMs, the HAIRY MERISTEM (HAM) family transcription factors form a concentration gradient from the epidermis to the interior cell layers, and this gradient is essential for the stem cell specification and the apical-basal patterning of the SAMs. Here, we uncover that epidermis specific transcription factors, ARABIDOPSIS THALIANA MERISTEM LAYER 1 (ATML1) and its close homolog, define the concentration gradient of HAM in the SAM through activating a group of microRNAs. This study provides a molecular framework linking the epidermis-derived signal to the stem cell homeostasis in plants.
A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium
Authors: Hernandez-Valdes Jhonatan A. , van Gestel Jordi , Kuipers Oscar P. 
Published: March 2020

AbstractAuxotrophy, the inability to produce an organic compound essential for growth, is widespread among bacteria. Auxotrophic bacteria rely on transporters to acquire these compounds from their environment. Here, we study the expression of both low- and high-affinity transporters of the costly amino acid methionine in an auxotrophic lactic acid bacterium, Lactococcus lactis. We show that the high-affinity transporter (Met-transporter) is heterogeneously expressed at low methionine concentrations, resulting in two isogenic subpopulations that sequester methionine in different ways: one subpopulation primarily relies on the high-affinity transporter (high expression of the Met-transporter) and the other subpopulation primarily relies on the low-affinity transporter (low expression of the Met-transporter). The phenotypic heterogeneity is remarkably stable, inherited for tens of generations, and apparent at the colony level. This heterogeneity results from a T-box riboswitch in the promoter region of the met operon encoding the high-affinity Met-transporter. We hypothesize that T-box riboswitches, which are commonly found in the Lactobacillales, may play as-yet unexplored roles in the predominantly auxotrophic lifestyle of these bacteria.
Quantifying exchange forces of a spin spiral on the atomic scale
Authors: Hauptmann Nadine , Haldar Soumyajyoti , Hung Tzu-Chao , Jolie Wouter , Gutzeit Mara , Wegner Daniel , Heinze Stefan , Khajetoorians Alexander A. 
Published: March 2020

AbstractThe large interest in chiral magnetic structures for realization of nanoscale magnetic storage or logic devices has necessitated methods which can quantify magnetic interactions at the atomic scale. To overcome the limitations of the typically used current-based sensing of atomic-scale exchange interactions, a force-based detection scheme is highly advantageous. Here, we quantify the atomic-scale exchange force field between a ferromagnetic tip and a cycloidal spin spiral using our developed combination of current and exchange force detection. Compared to the surprisingly weak spin polarization, the exchange force field is more sensitive to atomic-scale variations in the magnetization. First-principles calculations reveal that the measured atomic-scale variations in the exchange force originate from different contributions of direct and indirect (Zener type) exchange mechanisms, depending on the chemical tip termination. Our work opens the perspective of quantifying different exchange mechanisms of chiral magnetic structures with atomic-scale precision using 3D magnetic exchange force field measurements.