bluuebunny/crossref_metadata_2025_split huggingface dataset:
Partial cross mapping eliminates indirect causal influences
Authors: Leng Siyang , Ma Huanfei , Kurths Jürgen , Lai Ying-Cheng , Lin Wei , Aihara Kazuyuki , Chen Luonan 
Published: May 2020

AbstractCausality detection likely misidentifies indirect causations as direct ones, due to the effect of causation transitivity. Although several methods in traditional frameworks have been proposed to avoid such misinterpretations, there still is a lack of feasible methods for identifying direct causations from indirect ones in the challenging situation where the variables of the underlying dynamical system are non-separable and weakly or moderately interacting. Here, we solve this problem by developing a data-based, model-independent method of partial cross mapping based on an articulated integration of three tools from nonlinear dynamics and statistics: phase-space reconstruction, mutual cross mapping, and partial correlation. We demonstrate our method by using data from different representative models and real-world systems. As direct causations are keys to the fundamental underpinnings of a variety of complex dynamics, we anticipate our method to be indispensable in unlocking and deciphering the inner mechanisms of real systems in diverse disciplines from data.
Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings
Authors: Almudi Isabel , Vizueta Joel , Wyatt Christopher D. R. , de Mendoza Alex , Marlétaz Ferdinand , Firbas Panos N. , Feuda Roberto , Masiero Giulio , Medina Patricia , Alcaina-Caro Ana , Cruz Fernando , Gómez-Garrido Jessica , Gut Marta , Alioto Tyler S. , Vargas-Chavez Carlos , Davie Kristofer , Misof Bernhard , González Josefa , Aerts Stein , Lister Ryan , Paps Jordi , Rozas Julio , Sánchez-Gracia Alejandro , Irimia Manuel , Maeso Ignacio , Casares Fernando 
Published: May 2020

AbstractThe evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture of the genomic changes that underlay this diversification. Mayflies, as one of the sister groups of all other winged insects, are key to understanding this radiation. Here, we describe the genome of the mayflyCloeon dipterumand its gene expression throughout its aquatic and aerial life cycle and specific organs. We discover an expansion of odorant-binding-protein genes, some expressed specifically in breathing gills of aquatic nymphs, suggesting a novel sensory role for this organ. In contrast, flying adults use an enlarged opsin set in a sexually dimorphic manner, with some expressed only in males. Finally, we identify a set of wing-associated genes deeply conserved in the pterygote insects and find transcriptomic similarities between gills and wings, suggesting a common genetic program. Globally, this comprehensive genomic and transcriptomic study uncovers the genetic basis of key evolutionary adaptations in mayflies and winged insects.
Participatory practices at work change attitudes and behavior toward societal authority and justice
Authors: Wu Sherry Jueyu , Paluck Elizabeth Levy 
Published: May 2020

AbstractGeneralized attitudes toward authority and justice are often conceptualized as individual differences that are resistant to enduring change. However, across two field experiments with Chinese factory workers and American university staff, small adjustments to people’s experience of participation in the workplace shifted these attitudes one month later. Both experiments randomly assigned work groups to a 20-minute participatory meeting once per week for six weeks, in which the supervisor stepped aside and workers discussed problems, ideas, and goals regarding their work (vs. a status quo meeting). Across 97 work groups and 1,924 workers, participatory meetings led workers to be less authoritarian and more critical about societal authority and justice, and to be more willing to participate in political, social, and familial decision-making. These findings provide rare experimental evidence of the theoretical predictions regarding participatory democracy: that local participatory experiences can influence broader democratic attitudes and empowerment.
Cryo-EM structures provide insight into how E. coli F1Fo ATP synthase accommodates symmetry mismatch
Authors: Sobti Meghna , Walshe James L. , Wu Di , Ishmukhametov Robert , Zeng Yi C. , Robinson Carol V. , Berry Richard M. , Stewart Alastair G. 
Published: May 2020

AbstractF1Fo ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the Fo motor generates rotation of the central stalk, inducing conformational changes in the F1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1–3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of Fo associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F1 and Fo motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the Fo motor.
Tuning the interfacial spin-orbit coupling with ferroelectricity
Authors: Fang Mei , Wang Yanmei , Wang Hui , Hou Yusheng , Vetter Eric , Kou Yunfang , Yang Wenting , Yin Lifeng , Xiao Zhu , Li Zhou , Jiang Lu , Lee Ho Nyung , Zhang Shufeng , Wu Ruqian , Xu Xiaoshan , Sun Dali , Shen Jian 
Published: May 2020

AbstractDetection and manipulation of spin current lie in the core of spintronics. Here we report an active control of a net spin Hall angle, θSHE(net), in Pt at an interface with a ferroelectric material PZT (PbZr0.2Ti0.8O3), using its ferroelectric polarization. The spin Hall angle in the ultra-thin Pt layer is measured using the inverse spin Hall effect with a pulsed tunneling current from a ferromagnetic La0.67Sr0.33MnO3 electrode. The effect of the ferroelectric polarization on θSHE(net) is enhanced when the thickness of the Pt layer is reduced. When the Pt layer is thinner than 6 nm, switching the ferroelectric polarization even changes the sign of θSHE(net). This is attributed to the reversed polarity of the spin Hall angle in the 1st-layer Pt at the PZT/Pt interface when the ferroelectric polarization is inverted, as supported by the first-principles calculations. These findings suggest a route for designing future energy efficient spin-orbitronic devices using ferroelectric control.
Establishing charge-transfer excitons in 2D perovskite heterostructures
Authors: Zhang Jia , Zhu Xixiang , Wang Miaosheng , Hu Bin 
Published: May 2020

AbstractCharge-transfer excitons (CTEs) immensely enrich property-tuning capabilities of semiconducting materials. However, such concept has been remaining as unexplored topic within halide perovskite structures. Here, we report that CTEs can be effectively formed in heterostructured 2D perovskites prepared by mixing PEA2PbI4:PEA2SnI4, functioning as host and guest components. Remarkably, a broad emission can be demonstrated with quick formation of 3 ps but prolonged lifetime of ~0.5 μs. This broad PL presents the hypothesis of CTEs, verified by the exclusion of lattice distortion and doping effects through demonstrating double-layered PEA2PbI4/PEA2SnI4 heterostructure when shearing-away PEA2SnI4 film onto the surface of PEA2PbI4 film by using hand-finger pressing method. The below-bandgap photocurrent indicates that CTEs are vital states formed at PEA2PbI4:PEA2SnI4 interfaces in 2D perovskite heterostructures. Electroluminescence shows that CTEs can be directly formed with electrically injected carriers in perovskite LEDs. Clearly, the CTEs presents a new mechanism to advance the multifunctionalities in 2D perovskites.
The Perlman syndrome DIS3L2 exoribonuclease safeguards endoplasmic reticulum-targeted mRNA translation and calcium ion homeostasis
Authors: Pirouz Mehdi , Wang Chih-Hao , Liu Qi , Ebrahimi Aref G. , Shamsi Farnaz , Tseng Yu-Hua , Gregory Richard I. 
Published: May 2020

AbstractDIS3L2-mediated decay (DMD) is a surveillance pathway for certain non-coding RNAs (ncRNAs) including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), and RMRP. While mutations in DIS3L2 are associated with Perlman syndrome, the biological significance of impaired DMD is obscure and pathological RNAs have not been identified. Here, by ribosome profiling (Ribo-seq) we find specific dysregulation of endoplasmic reticulum (ER)-targeted mRNA translation in DIS3L2-deficient cells. Mechanistically, DMD functions in the quality control of the 7SL ncRNA component of the signal recognition particle (SRP) required for ER-targeted translation. Upon DIS3L2 loss, sustained 3’-end uridylation of aberrant 7SL RNA impacts ER-targeted translation and causes ER calcium leakage. Consequently, elevated intracellular calcium in DIS3L2-deficient cells activates calcium signaling response genes and perturbs ESC differentiation. Thus, DMD is required to safeguard ER-targeted mRNA translation, intracellular calcium homeostasis, and stem cell differentiation.
Understanding the interface interaction between U3Si2 fuel and SiC cladding
Authors: Kocevski Vancho , Lopes Denise A. , Claisse Antoine J. , Besmann Theodore M. 
Published: May 2020

AbstractTriuranium disilicide (U3Si2) fuel with silicon carbide (SiC) composite cladding is being considered as an advanced concept/accident tolerant fuel for light water reactors thus, understanding their chemical compatibility under operational and accident conditions is paramount. Here we provide a comprehensive view of the interaction between U3Si2 and SiC by utilizing density functional theory calculations supported by diffusion couple experiments. From the calculated reaction energies, we demonstrate that triuranium pentasilicide (U3Si5), uranium carbide (UC), U20Si16C3, and uranium silicide (USi) phases can form at the interface. A detailed study of U3Si2 and SiC defect formation energies of the equilibrated materials yielding the interfacial phases U20Si16C3, U3Si5 and UC reveal a thermodynamic driving force for generating defects in both fuel and cladding. The absence of either the U3Si2 or SiC phase, however, causes the defect formation energies in the other phase to be positive, removing the driving force for additional interfacial reactions. The diffusion couple experiments confirm the conclusion with demonstrated restricted formation of U3Si5, UC, and U20Si16C3/USi phases at the interface. The resulting lack of continuous interaction between the U3Si2 and SiC, reflects the diminishing driving force for defect formation, demonstrating the substantial stability of this fuel-cladding system.
Treatment of atherosclerosis by macrophage-biomimetic nanoparticles via targeted pharmacotherapy and sequestration of proinflammatory cytokines
Authors: Gao Cheng , Huang Qiaoxian , Liu Conghui , Kwong Cheryl H. T. , Yue Ludan , Wan Jian-Bo , Lee Simon M. Y. , Wang Ruibing 
Published: May 2020

AbstractVascular disease remains the leading cause of death and disability, the etiology of which often involves atherosclerosis. The current treatment of atherosclerosis by pharmacotherapy has limited therapeutic efficacy. Here we report a biomimetic drug delivery system derived from macrophage membrane coated ROS-responsive nanoparticles (NPs). The macrophage membrane not only avoids the clearance of NPs from the reticuloendothelial system, but also leads NPs to the inflammatory tissues, where the ROS-responsiveness of NPs enables specific payload release. Moreover, the macrophage membrane sequesters proinflammatory cytokines to suppress local inflammation. The synergistic effects of pharmacotherapy and inflammatory cytokines sequestration from such a biomimetic drug delivery system lead to improved therapeutic efficacy in atherosclerosis. Comparison to macrophage internalized with ROS-responsive NPs, as a live-cell based drug delivery system for treatment of atherosclerosis, suggests that cell membrane coated drug delivery approach is likely more suitable for dealing with an inflammatory disease than the live-cell approach.
The bromodomain containing protein BRD-9 orchestrates RAD51–RAD54 complex formation and regulates homologous recombination-mediated repair
Authors: Zhou Qin , Huang Jinzhou , Zhang Chao , Zhao Fei , Kim Wootae , Tu Xinyi , Zhang Yong , Nowsheen Somaira , Zhu Qian , Deng Min , Chen Yuping , Qin Bo , Luo Kuntian , Liu Baohua , Lou Zhenkun , Mutter Robert W. , Yuan Jian 
Published: May 2020

AbstractHomologous recombination (HR) is important for error-free DNA double strand break repair and maintenance of genomic stability. However, upregulated HR is also used by cancer cells to promote therapeutic resistance. Therefore, inducing HR deficiency (HRD) is a viable strategy to sensitize HR proficient cancers to DNA targeted therapies in order to overcome therapeutic resistance. A bromodomain containing protein, BRD9, was previously reported to regulate chromatin remodeling and transcription. Here, we discover that following DNA damage, the bromodomain of BRD9 binds acetylated K515 on RAD54 and facilitates RAD54’s interaction with RAD51, which is essential for HR. BRD9 is overexpressed in ovarian cancer and depleting BRD9 sensitizes cancer cells to olaparib and cisplatin. In addition, inhibitor of BRD9, I-BRD9, acts synergistically with olaparib in HR-proficient cancer cells. Overall, our results elucidate a role for BRD9 in HR and identify BRD9 as a potential therapeutic target to promote synthetic lethality and overcome chemoresistance.
International consensus on the diagnosis and management of dumping syndrome
Authors: Scarpellini Emidio , Arts Joris , Karamanolis George , Laurenius Anna , Siquini Walter , Suzuki Hidekazu , Ukleja Andrew , Van Beek Andre , Vanuytsel Tim , Bor Serhat , Ceppa Eugene , Di Lorenzo Carlo , Emous Marloes , Hammer Heinz , Hellström Per , Laville Martine , Lundell Lars , Masclee Ad , Ritz Patrick , Tack Jan 
Published: May 2020

AbstractDumping syndrome is a common but underdiagnosed complication of gastric and oesophageal surgery. We initiated a Delphi consensus process with international multidisciplinary experts. We defined the scope, proposed statements and searched electronic databases to survey the literature. Eighteen experts participated in the literature summary and voting process evaluating 62 statements. We evaluated the quality of evidence using grading of recommendations assessment, development and evaluation (GRADE) criteria. Consensus (defined as >80% agreement) was reached for 33 of 62 statements, including the definition and symptom profile of dumping syndrome and its effect on quality of life. The panel agreed on the pathophysiological relevance of rapid passage of nutrients to the small bowel, on the role of decreased gastric volume capacity and release of glucagon-like peptide 1. Symptom recognition is crucial, and the modified oral glucose tolerance test, but not gastric emptying testing, is useful for diagnosis. An increase in haematocrit >3% or in pulse rate >10 bpm 30 min after the start of the glucose intake are diagnostic of early dumping syndrome, and a nadir hypoglycaemia level <50 mg/dl is diagnostic of late dumping syndrome. Dietary adjustment is the agreed first treatment step; acarbose is effective for late dumping syndrome symptoms and somatostatin analogues are preferred for patients who do not respond to diet adjustments and acarbose.
Discovery of a new sialic acid binding region that regulates Siglec-7
Authors: Yamakawa Nao , Yasuda Yu , Yoshimura Atsushi , Goshima Ami , Crocker Paul R. , Vergoten Gérard , Nishiura Yuji , Takahashi Takashi , Hanashima Shinya , Matsumoto Kana , Yamaguchi Yoshiki , Tanaka Hiroshi , Kitajima Ken , Sato Chihiro 
Published: May 2020

AbstractSiglec-7 is a human CD33-like siglec, and is localised predominantly on human natural killer (NK) cells and monocytes. Siglec-7 is considered to function as an immunoreceptor in a sialic acid-dependent manner. However, the underlying mechanisms linking sialic acid-binding and function remain unknown. Here, to gain new insights into the ligand-binding properties of Siglec-7, we carried out in silico analysis and site-directed mutagenesis, and found a new sialic acid-binding region (site 2 containing R67) in addition to the well-known primary ligand-binding region (site 1 containing R124). This was supported by equilibrium dialysis, STD-NMR experiments, and inhibition analysis of GD3-binding toward Siglec-7 using synthetic sialoglycoconjugates and a comprehensive set of ganglioside-based glycoconjugates. Our results suggest that the two ligand-binding sites are potentially controlled by each other due to the flexible conformation of the C-C′ loop of Siglec-7.
Origin of ω-phase formation in metastable β-type Ti-Mo alloys: cluster structure and stacking fault
Authors: Li Mingjia , Min Xiaohua 
Published: May 2020

AbstractThe ω-phase formation and its collapsed structures in metastable β-type Ti-Mo alloys were illustrated by first-principles calculations and experimental evidence of a partially collapsed ω-phase in the nano-scale Mo-depleted region under a rapid cooling via high-angle annular dark-field scanning transmission electron microscopy. The ease of ω-phase formation within -Mo-Ti-Mo- poor cluster structure was not only due to the low energy barrier in the collapse pathway, which was caused by the reduced lattice distortion, but also due to the softening of the shear modulus (G111) as a result of the small charge density difference. The most stable collapsed structure of the ω-phase strongly depended on the minimum stacking fault energy among different collapse degrees in accordance to the smallest charge density difference. Therefore, the concurrent compositional and structural instabilities of the ω-phase was attributed to the coupling effect of the cluster structure with stacking fault from the atomic and electronic basis.
Nyctinastic thallus movement in the liverwort Marchantia polymorpha is regulated by a circadian clock
Authors: Lagercrantz Ulf , Billhardt Anja , Rousku Sabine N. , Ljung Karin , Eklund D. Magnus 
Published: May 2020

AbstractThe circadian clock coordinates an organism’s growth, development and physiology with environmental factors. One illuminating example is the rhythmic growth of hypocotyls and cotyledons in Arabidopsis thaliana. Such daily oscillations in leaf position are often referred to as sleep movements or nyctinasty. Here, we report that plantlets of the liverwort Marchantia polymorpha show analogous rhythmic movements of thallus lobes, and that the circadian clock controls this rhythm, with auxin a likely output pathway affecting these movements. The mechanisms of this circadian clock are partly conserved as compared to angiosperms, with homologs to the core clock genes PRR, RVE and TOC1 forming a core transcriptional feedback loop also in M. polymorpha.
Non-invasive identification of swallows via deep learning in high resolution cervical auscultation recordings
Authors: Khalifa Yassin , Coyle James L. , Sejdić Ervin 
Published: May 2020

AbstractHigh resolution cervical auscultation is a very promising noninvasive method for dysphagia screening and aspiration detection, as it does not involve the use of harmful ionizing radiation approaches. Automatic extraction of swallowing events in cervical auscultation is a key step for swallowing analysis to be clinically effective. Using time-varying spectral estimation of swallowing signals and deep feed forward neural networks, we propose an automatic segmentation algorithm for swallowing accelerometry and sounds that works directly on the raw swallowing signals in an online fashion. The algorithm was validated qualitatively and quantitatively using the swallowing data collected from 248 patients, yielding over 3000 swallows manually labeled by experienced speech language pathologists. With a detection accuracy that exceeded 95%, the algorithm has shown superior performance in comparison to the existing algorithms and demonstrated its generalizability when tested over 76 completely unseen swallows from a different population. The proposed method is not only of great importance to any subsequent swallowing signal analysis steps, but also provides an evidence that such signals can capture the physiological signature of the swallowing process.
RNA Sequencing Analyses Reveal the Potential Mechanism of Pulmonary Injury Induced by Gallium Arsenide Particles in Human Bronchial Epithelioid Cells
Authors: Ouyang Yabo , Liu Xiaodong , Li Haibing , Cui Shiwei , Yan Huifang , Pan Xingfu 
Published: May 2020

AbstractExtensive use of gallium arsenide (GaAs) has led to increased exposure to humans working in the semiconductor industry. This study employed physicochemical characterization of GaAs obtained from a workplace, cytotoxicity analysis of damage induced by GaAs in 16HBE cells, RNA-seq and related bioinformatic analysis, qRT-PCR verification and survival analysis to comprehensively understand the potential mechanism leading to lung toxicity induced by GaAs. We found that GaAs-induced abnormal gene expression was mainly related to the cellular response to chemical stimuli, the regulation of signalling, cell differentiation and the cell cycle, which are involved in transcriptional misregulation in cancer, the MAPK signalling pathway, the TGF-β signalling pathway and pulmonary disease-related pathways. Ten upregulated genes (FOS, JUN, HSP90AA1, CDKN1A, ESR1, MYC, RAC1, CTNNB1, MAPK8 and FOXO1) and 7 downregulated genes (TP53, AKT1, NFKB1, SMAD3, CDK1, E2F1 and PLK1) related to GaAs-induced pulmonary toxicity were identified. High expression of HSP90AA1, RAC1 and CDKN1A was significantly associated with a lower rate of overall survival in lung cancers. The results of this study indicate that GaAs-associated toxicities affected the misregulation of oncogenes and tumour suppressing genes, activation of the TGF-β/MAPK pathway, and regulation of cell differentiation and the cell cycle. These results help to elucidate the molecular mechanism underlying GaAs-induced pulmonary injury.
Wildfires lead to decreased carbon and increased nitrogen concentrations in upland arctic streams
Authors: Rodríguez-Cardona B. M. , Coble A. A. , Wymore A. S. , Kolosov R. , Podgorski D. C. , Zito P. , Spencer R. G. M. , Prokushkin A. S. , McDowell W. H. 
Published: May 2020

AbstractThe Central Siberian Plateau is undergoing rapid climate change that has resulted in increased frequency of forest fires and subsequent alteration of watershed carbon and nutrient dynamics. Across a watershed chronosequence (3 to >100 years since wildfire) we quantified the effects of fire on quantity and composition of dissolved organic matter (DOM), stream water nutrient concentrations, as well as in-stream nutrient uptake. Wildfires increased concentrations of nitrate for a decade, while decreasing concentrations of dissolved organic carbon and nitrogen (DOC and DON) and aliphatic DOM contribution for five decades. These post-wildfire changes in stream DOM result in lower uptake efficiency of in-stream nitrate in recently burned watersheds. Nitrate uptake (as uptake velocity) is strongly dependent on DOM composition (e.g. polyphenolics), ambient dissolved inorganic nitrogen (DIN), and DOC to DIN ratios. Our observations and experiments suggest that a decade-long pulse of inorganic nitrogen and a reduction of DOC export occur following wildfires in streams draining the Central Siberian Plateau. Increased fire frequency in the region is thus likely to both decrease DOM and increase nitrate delivery to the main stem Yenisei River, and ultimately the Arctic Ocean, in the coming decades.