bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-preservation strategy for approaching global warming targets in the post-Paris Agreement era
Authors: Wei Yi-Ming , Han Rong , Wang Ce , Yu Biying , Liang Qiao-Mei , Yuan Xiao-Chen , Chang Junjie , Zhao Qingyu , Liao Hua , Tang Baojun , Yan Jinyue , Cheng Lijing , Yang Zili 
Published: April 2020

AbstractA strategy that informs on countries’ potential losses due to lack of climate action may facilitate global climate governance. Here, we quantify a distribution of mitigation effort whereby each country is economically better off than under current climate pledges. This effort-sharing optimizing approach applied to a 1.5 °C and 2 °C global warming threshold suggests self-preservation emissions trajectories to inform NDCs enhancement and long-term strategies. Results show that following the current emissions reduction efforts, the whole world would experience a washout of benefit, amounting to almost 126.68–616.12 trillion dollars until 2100 compared to 1.5 °C or well below 2 °C commensurate action. If countries are even unable to implement their current NDCs, the whole world would lose more benefit, almost 149.78–791.98 trillion dollars until 2100. On the contrary, all countries will be able to have a significant positive cumulative net income before 2100 if they follow the self-preservation strategy.
Drought alters the biogeochemistry of boreal stream networks
Authors: Gómez-Gener Lluís , Lupon Anna , Laudon Hjalmar , Sponseller Ryan A. 
Published: April 2020

AbstractDrought is a global phenomenon, with widespread implications for freshwater ecosystems. While droughts receive much attention at lower latitudes, their effects on northern river networks remain unstudied. We combine a reach-scale manipulation experiment, observations during the extreme 2018 drought, and historical monitoring data to examine the impact of drought in northern boreal streams. Increased water residence time during drought promoted reductions in aerobic metabolism and increased concentrations of reduced solutes in both stream and hyporheic water. Likewise, data during the 2018 drought revealed widespread hypoxic conditions and shifts towards anaerobic metabolism, especially in headwaters. Finally, long-term data confirmed that past summer droughts have led to similar metabolic alterations. Our results highlight the potential for drought to promote biogeochemical shifts that trigger poor water quality conditions in boreal streams. Given projected increases in hydrological extremes at northern latitudes, the consequences of drought for the health of running waters warrant attention.
SciBet as a portable and fast single cell type identifier
Authors: Li Chenwei , Liu Baolin , Kang Boxi , Liu Zedao , Liu Yedan , Chen Changya , Ren Xianwen , Zhang Zemin 
Published: April 2020

AbstractFast, robust and technology-independent computational methods are needed for supervised cell type annotation of single-cell RNA sequencing data. We present SciBet, a supervised cell type identifier that accurately predicts cell identity for newly sequenced cells with order-of-magnitude speed advantage. We enable web client deployment of SciBet for rapid local computation without uploading local data to the server. Facing the exponential growth in the size of single cell RNA datasets, this user-friendly and cross-platform tool can be widely useful for single cell type identification.
Obesity-induced overexpression of miR-802 impairs insulin transcription and secretion
Authors: Zhang Fangfang , Ma Dongshen , Zhao Wanli , Wang Danwei , Liu Tingsheng , Liu Yuhong , Yang Yue , Liu Yue , Mu Jinming , Li Bingbing , Zhang Yanfeng , Pan Yi , Guo Changying , Du Hong , Li Ling , Fu Xianghui , Cao Zhengyu , Jin Liang 
Published: April 2020

AbstractB cell dysfunction due to obesity can be associated with alterations in the levels of micro-RNAs (miRNAs). However, the role of miRNAs in these processes remains elusive. Here, we show that miR-802 is increased in the pancreatic islets of obese mouse models and demonstrate that inducible transgenic overexpression of miR-802 in mice causes impaired insulin transcription and secretion. We identify Foxo1 as a transcription factor of miR-802 promoting its transcription, and NeuroD1 and Fzd5 as targets of miR-802-dependent silencing. Repression of NeuroD1 in β cell and primary islets impairs insulin transcription and reduction of Fzd5 in β cell, which, in turn, impairs Ca2+ signaling, thereby repressing calcium influx and decreasing insulin secretion. We functionally create a novel network between obesity and β cell dysfunction via miR-802 regulation. Elucidation of the impact of obesity on microRNA expression can broaden our understanding of pathophysiological development of diabetes.
Elevated protein synthesis in microglia causes autism-like synaptic and behavioral aberrations
Authors: Xu Zhi-Xiang , Kim Gyu Hyun , Tan Ji-Wei , Riso Anna E. , Sun Ye , Xu Ethan Y. , Liao Guey-Ying , Xu Haifei , Lee Sang-Hoon , Do Na-Young , Lee Chan Hee , Clipperton-Allen Amy E. , Kwon Soonwook , Page Damon T. , Lee Kea Joo , Xu Baoji 
Published: April 2020

AbstractMutations that inactivate negative translation regulators cause autism spectrum disorders (ASD), which predominantly affect males and exhibit social interaction and communication deficits and repetitive behaviors. However, the cells that cause ASD through elevated protein synthesis resulting from these mutations remain unknown. Here we employ conditional overexpression of translation initiation factor eIF4E to increase protein synthesis in specific brain cells. We show that exaggerated translation in microglia, but not neurons or astrocytes, leads to autism-like behaviors in male mice. Although microglial eIF4E overexpression elevates translation in both sexes, it only increases microglial density and size in males, accompanied by microglial shift from homeostatic to a functional state with enhanced phagocytic capacity but reduced motility and synapse engulfment. Consequently, cortical neurons in the mice have higher synapse density, neuroligins, and excitation-to-inhibition ratio compared to control mice. We propose that functional perturbation of male microglia is an important cause for sex-biased ASD.
Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines
Authors: Cano-Gamez Eddie , Soskic Blagoje , Roumeliotis Theodoros I. , So Ernest , Smyth Deborah J. , Baldrighi Marta , Willé David , Nakic Nikolina , Esparza-Gordillo Jorge , Larminie Christopher G. C. , Bronson Paola G. , Tough David F. , Rowan Wendy C. , Choudhary Jyoti S. , Trynka Gosia 
Published: April 2020

AbstractNaïve CD4+T cells coordinate the immune response by acquiring an effector phenotype in response to cytokines. However, the cytokine responses in memory T cells remain largely understudied. Here we use quantitative proteomics, bulk RNA-seq, and single-cell RNA-seq of over 40,000 human naïve and memory CD4+T cells to show that responses to cytokines differ substantially between these cell types. Memory T cells are unable to differentiate into the Th2 phenotype, and acquire a Th17-like phenotype in response to iTreg polarization. Single-cell analyses show that T cells constitute a transcriptional continuum that progresses from naïve to central and effector memory T cells, forming an effectorness gradient accompanied by an increase in the expression of chemokines and cytokines. Finally, we show that T cell activation and cytokine responses are influenced by the effectorness gradient. Our results illustrate the heterogeneity of T cell responses, furthering our understanding of inflammation.
Single-atom-layer traps in a solid electrolyte for lithium batteries
Authors: Zhu Feng , Islam Md Shafiqul , Zhou Lin , Gu Zhenqi , Liu Ting , Wang Xinchao , Luo Jun , Nan Ce-Wen , Mo Yifei , Ma Cheng 
Published: April 2020

AbstractIn order to fully understand the lithium-ion transport mechanism in solid electrolytes for batteries, not only the periodic lattice but also the non-periodic features that disrupt the ideal periodicity must be comprehensively studied. At present only a limited number of non-periodic features such as point defects and grain boundaries are considered in mechanistic studies. Here, we discover an additional type of non-periodic feature that significantly influences ionic transport; this feature is termed a “single-atom-layer trap” (SALT). In a prototype solid electrolyte Li0.33La0.56TiO3, the single-atom-layer defects that form closed loops, i.e., SALTs, are found ubiquitous by atomic-resolution electron microscopy. According to ab initio calculations, these defect loops prevent large volumes of materials from participating in ionic transport, and thus severely degrade the total conductivity. This discovery points out the urgency of thoroughly investigating different types of non-periodic features, and motivates similar studies for other solid electrolytes.
Limiting oxidative DNA damage reduces microbe-induced colitis-associated colorectal cancer
Authors: Irrazabal Thergiory , Thakur Bhupesh K. , Kang Mingsong , Malaise Yann , Streutker Catherine , Wong Erin O. Y. , Copeland Julia , Gryfe Robert , Guttman David S. , Navarre William W. , Martin Alberto 
Published: April 2020

AbstractInflammatory bowel disease patients have a greatly increased risk of developing colitis-associated colon cancer (CAC); however, the basis for inflammation-induced genetic damage requisite for neoplasia is unclear. Using three models of CAC, we find that sustained inflammation triggers 8-oxoguanine DNA lesions. Strikingly, antioxidants or iNOS inhibitors reduce 8-oxoguanine and polyps in CAC models. Because the mismatch repair (MMR) system repairs 8-oxoguanine and is frequently defective in colorectal cancer (CRC), we test whether 8-oxoguanine mediates oncogenesis in a Lynch syndrome (MMR-deficient) model. We show that microbiota generates an accumulation of 8-oxoguanine lesions in MMR-deficient colons. Accordingly, we find that 8-oxoguanine is elevated in neoplastic tissue of Lynch syndrome patients compared to matched untransformed tissue or non-Lynch syndrome neoplastic tissue. While antioxidants reduce 8-oxoguanine, they do not reduce CRC in Lynch syndrome models. Hence, microbe-induced oxidative/nitrosative DNA damage play causative roles in inflammatory CRC models, but not in Lynch syndrome models.
Climate change rapidly warms and acidifies Australian estuaries
Authors: Scanes Elliot , Scanes Peter R. , Ross Pauline M. 
Published: April 2020

AbstractClimate change is impacting ecosystems worldwide. Estuaries are diverse and important aquatic ecosystems; and yet until now we have lacked information on the response of estuaries to climate change. Here we present data from a twelve-year monitoring program, involving 6200 observations of 166 estuaries along >1100 kilometres of the Australian coastline encompassing all estuary morphologies. Estuary temperatures increased by 2.16 °C on average over 12 years, at a rate of 0.2 °C year−1, with waters acidifying at a rate of 0.09 pH units and freshening at 0.086 PSU year−1. The response of estuaries to climate change is dependent on their morphology. Lagoons and rivers are warming and acidifying at the fastest rate because of shallow average depths and limited oceanic exchange. The changes measured are an order of magnitude faster than predicted by global ocean and atmospheric models, indicating that existing global models may not be useful to predict change in estuaries.
Invasive earthworms unlock arctic plant nitrogen limitation
Authors: Blume-Werry Gesche , Krab Eveline J. , Olofsson Johan , Sundqvist Maja K. , Väisänen Maria , Klaminder Jonatan 
Published: April 2020

AbstractArctic plant growth is predominantly nitrogen (N) limited. This limitation is generally attributed to slow soil microbial processes due to low temperatures. Here, we show that arctic plant-soil N cycling is also substantially constrained by the lack of larger detritivores (earthworms) able to mineralize and physically translocate litter and soil organic matter. These new functions provided by earthworms increased shrub and grass N concentration in our common garden experiment. Earthworm activity also increased either the height or number of floral shoots, while enhancing fine root production and vegetation greenness in heath and meadow communities to a level that exceeded the inherent differences between these two common arctic plant communities. Moreover, these worming effects on plant N and greening exceeded reported effects of warming, herbivory and nutrient addition, suggesting that human spreading of earthworms may lead to substantial changes in the structure and function of arctic ecosystems.
Alarmin-painted exosomes elicit persistent antitumor immunity in large established tumors in mice
Authors: Zuo Bingfeng , Qi Han , Lu Zhen , Chen Lu , Sun Bo , Yang Rong , Zhang Yang , Liu Zhili , Gao Xianjun , You Abin , Wu Li , Jing Renwei , Zhou Qibing , Yin HaiFang 
Published: April 2020

AbstractTreating large established tumors is challenging for dendritic cell (DC)-based immunotherapy. DC activation with tumor cell-derived exosomes (TEXs) carrying multiple tumor-associated antigen can enhance tumor recognition. Adding a potent adjuvant, high mobility group nucleosome-binding protein 1 (HMGN1), boosts DCs’ ability to activate T cells and improves vaccine efficiency. Here, we demonstrate that TEXs painted with the functional domain of HMGN1 (TEX-N1ND) via an exosomal anchor peptide potentiates DC immunogenicity. TEX-N1ND pulsed DCs (DCTEX-N1ND) elicit long-lasting antitumor immunity and tumor suppression in different syngeneic mouse models with large tumor burdens, most notably large, poorly immunogenic orthotopic hepatocellular carcinoma (HCC). DCTEX-N1NDshow increased homing to lymphoid tissues and contribute to augmented memory T cells. Importantly, N1ND-painted serum exosomes from cancer patients also promote DC activation. Our study demonstrates the potency of TEX-N1ND to strengthen DC immunogenicity and to suppress large established tumors, and thus provides an avenue to improve DC-based immunotherapy.
The Sox2 transcription factor binds RNA
Authors: Holmes Zachariah E. , Hamilton Desmond J. , Hwang Taeyoung , Parsonnet Nicholas V. , Rinn John L. , Wuttke Deborah S. , Batey Robert T. 
Published: April 2020

AbstractCertain transcription factors are proposed to form functional interactions with RNA to facilitate proper regulation of gene expression. Sox2, a transcription factor critical for maintenance of pluripotency and neurogenesis, has been found associated with several lncRNAs, although it is unknown whether these interactions are direct or via other proteins. Here we demonstrate that human Sox2 interacts directly with one of these lncRNAs with high affinity through its HMG DNA-binding domain in vitro. These interactions are primarily with double-stranded RNA in a non-sequence specific fashion, mediated by a similar but not identical interaction surface. We further determined that Sox2 directly binds RNA in mouse embryonic stem cells by UV-cross-linked immunoprecipitation of Sox2 and more than a thousand Sox2-RNA interactions in vivo were identified using fRIP-seq. Together, these data reveal that Sox2 employs a high-affinity/low-specificity paradigm for RNA binding in vitro and in vivo.
Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics
Authors: Sadek Jouliana , Wuo Michael G. , Rooklin David , Hauenstein Arthur , Hong Seong Ho , Gautam Archana , Wu Hao , Zhang Yingkai , Cesarman Ethel , Arora Paramjit S. 
Published: April 2020

AbstractProtein-protein interactions featuring intricate binding epitopes remain challenging targets for synthetic inhibitors. Interactions of NEMO, a scaffolding protein central to NF-κB signaling, exemplify this challenge. Various regulators are known to interact with different coiled coil regions of NEMO, but the topological complexity of this protein has limited inhibitor design. We undertook a comprehensive effort to block the interaction between vFLIP, a Kaposi’s sarcoma herpesviral oncoprotein, and NEMO using small molecule screening and rational design. Our efforts reveal that a tertiary protein structure mimic of NEMO is necessary for potent inhibition. The rationally designed mimic engages vFLIP directly causing complex disruption, protein degradation and suppression of NF-κB signaling in primary effusion lymphoma (PEL). NEMO mimic treatment induces cell death and delays tumor growth in a PEL xenograft model. Our studies with this inhibitor reveal the critical nexus of signaling complex stability in the regulation of NF-κB by a viral oncoprotein.
Sediment controls dynamic behavior of a Cordilleran Ice Stream at the Last Glacial Maximum
Authors: Cowan Ellen A. , Zellers Sarah D. , Müller Juliane , Walczak Maureen H. , Worthington Lindsay L. , Caissie Beth E. , Clary Wesley A. , Jaeger John M. , Gulick Sean P. S. , Pratt Jacob W. , Mix Alan C. , Fallon Stewart J. 
Published: April 2020

AbstractThe uncertain response of marine terminating outlet glaciers to climate change at time scales beyond short-term observation limits models of future sea level rise. At temperate tidewater margins, abundant subglacial meltwater forms morainal banks (marine shoals) or ice-contact deltas that reduce water depth, stabilizing grounding lines and slowing or reversing glacial retreat. Here we present a radiocarbon-dated record from Integrated Ocean Drilling Program (IODP) Site U1421 that tracks the terminus of the largest Alaskan Cordilleran Ice Sheet outlet glacier during Last Glacial Maximum climate transitions. Sedimentation rates, ice-rafted debris, and microfossil and biogeochemical proxies, show repeated abrupt collapses and slow advances typical of the tidewater glacier cycle observed in modern systems. When global sea level rise exceeded the local rate of bank building, the cycle of readvances stopped leading to irreversible retreat. These results support theory that suggests sediment dynamics can control tidewater terminus position on an open shelf under temperate conditions delaying climate-driven retreat.
Dynamic wrinkling pattern exhibiting tunable fluorescence for anticounterfeiting applications
Authors: Ma Tianjiao , Li Tiantian , Zhou Liangwei , Ma Xiaodong , Yin Jie , Jiang Xuesong 
Published: April 2020

AbstractA dynamic surface pattern with a topography and fluorescence in response to environmental stimulus can enable information recording, hiding, and reading. Such patterns are therefore widely used in information security and anticounterfeiting. Here, we demonstrate a dynamic dual pattern using a supramolecular network comprising a copolymer containing pyridine (P4VP-nBA-S) and hydroxyl distyrylpyridine (DSP-OH) as the skin layer for bilayer wrinkling systems, in which both the wrinkle morphology and fluorescence color can be simultaneously regulated by visible light-triggered isomerization of DSP-OH, or acids. Acid-induced protonation of pyridines can dynamically regulate the cross-linking of the skin layer through hydrogen bonding, and the fluorescence of DSP-OH. On selective irradiation with 450 nm visible light or acid treatment, the resulting hierarchical patterned surface becomes smooth and wrinkled reversibly, and simultaneously its fluorescence changes dynamically from blue to orange-red. The smart surfaces with dynamic hierarchical wrinkles and fluorescence can find potential application in anticounterfeiting.
Glycolytic reprograming in Salmonella counters NOX2-mediated dissipation of ΔpH
Authors: Chakraborty Sangeeta , Liu Lin , Fitzsimmons Liam , Porwollik Steffen , Kim Ju-Sim , Desai Prerak , McClelland Michael , Vazquez-Torres Andres 
Published: April 2020

AbstractThe microbial adaptations to the respiratory burst remain poorly understood, and establishing how the NADPH oxidase (NOX2) kills microbes has proven elusive. Here we demonstrate that NOX2 collapses the ΔpH of intracellular Salmonella Typhimurium. The depolarization experienced by Salmonella undergoing oxidative stress impairs folding of periplasmic proteins. Depolarization in respiring Salmonella mediates intense bactericidal activity of reactive oxygen species (ROS). Salmonella adapts to the challenges oxidative stress imposes on membrane bioenergetics by shifting redox balance to glycolysis and fermentation, thereby diminishing electron flow through the membrane, meeting energetic requirements and anaplerotically generating tricarboxylic acid intermediates. By diverting electrons away from the respiratory chain, glycolysis also enables thiol/disulfide exchange-mediated folding of bacterial cell envelope proteins during periods of oxidative stress. Thus, primordial metabolic pathways, already present in bacteria before aerobic respiration evolved, offer a solution to the stress ROS exert on molecular targets at the bacterial cell envelope.
RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2
Authors: Alecki Célia , Chiwara Victoria , Sanz Lionel A. , Grau Daniel , Arias Pérez Osvaldo , Boulier Elodie L. , Armache Karim-Jean , Chédin Frédéric , Francis Nicole J. 
Published: April 2020

AbstractPolycomb Group (PcG) proteins form memory of transient transcriptional repression that is necessary for development. InDrosophila, DNA elements termed Polycomb Response Elements (PREs) recruit PcG proteins. How PcG activities are targeted to PREs to maintain repressed states only in appropriate developmental contexts has been difficult to elucidate. PcG complexes modify chromatin, but also interact with both RNA and DNA, and RNA is implicated in PcG targeting and function. Here we show that R-loops form at many PREs inDrosophilaembryos, and correlate with repressive states. In vitro, both PRC1 and PRC2 can recognize R-loops and open DNA bubbles. Unexpectedly, we find that PRC2 drives formation of RNA-DNA hybrids, the key component of R-loops, from RNA and dsDNA. Our results identify R-loop formation as a feature ofDrosophilaPREs that can be recognized by PcG complexes, and RNA-DNA strand exchange as a PRC2 activity that could contribute to R-loop formation.
Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses
Authors: Nass Karol , Gorel Alexander , Abdullah Malik M. , V. Martin Andrew , Kloos Marco , Marinelli Agostino , Aquila Andrew , Barends Thomas R. M. , Decker Franz-Josef , Bruce Doak R. , Foucar Lutz , Hartmann Elisabeth , Hilpert Mario , Hunter Mark S. , Jurek Zoltan , Koglin Jason E. , Kozlov Alexander , Lutman Alberto A. , Kovacs Gabriela Nass , Roome Christopher M. , Shoeman Robert L. , Santra Robin , Quiney Harry M. , Ziaja Beata , Boutet Sébastien , Schlichting Ilme 
Published: April 2020

AbstractX-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter’s correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.