bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Sensitivity of the Devonian Climate to Continental Configuration, Vegetation Cover, Orbital Configuration, CO 2 Concentration, and Insolation
Authors: Brugger Julia , Hofmann Matthias , Petri Stefan , Feulner Georg 
Published: July 2019

AbstractDuring the Devonian (419 to 359 million years ago), life on Earth witnessed decisive evolutionary breakthroughs, most prominently the colonization of land by vascular plants and vertebrates. However, it was also a period of major marine extinctions coinciding with marked changes in climate. The cause of these changes remains unknown, and it is therefore instructive to explore systematically how the Devonian climate responds to changes in boundary conditions. Here we use coupled climate model simulations to investigate separately the influence of changes in continental configuration, vegetation cover, carbon dioxide (CO2) concentrations, the solar constant, and orbital parameters on the Devonian climate. The biogeophysical effect of changes in vegetation cover is small, and the cooling due to continental drift is offset by the increasing solar constant. Variations of orbital parameters affect the Devonian climate, with the warmest climate states at high obliquity and high eccentricity. The prevailing mode of decadal to centennial climate variability relates to temperature fluctuations in high northern latitudes which are mediated by coupled oscillations involving sea ice cover, ocean convection, and a regional overturning circulation. The temperature evolution during the Devonian is dominated by the strong decrease in atmospheric CO2. Albedo changes due to increasing vegetation cover cannot explain the temperature rise found in Late Devonian proxy data. Finally, simulated temperatures are significantly lower than estimates based on oxygen isotope ratios, suggesting a lower δ18O ratio of Devonian seawater.
A Global Perspective on Local Meteoric Water Lines: Meta‐analytic Insight Into Fundamental Controls and Practical Constraints
Authors: Putman Annie L. , Fiorella Richard P. , Bowen Gabriel J. , Cai Zhongyin 
Published: July 2019

AbstractLocal meteoric water lines (LMWLs) represent the site‐specific long‐term covariation of hydrogen and oxygen stable isotope ratios. LMWLs have practical utility as a hydrologic framework and as benchmarks for evaluating hydroclimatic processes in isotope‐enabled climate models. In this manuscript, we characterize the global distribution of LMWLs and compare them to LMWLs from model data. To evaluate the sensitivity of the covariance of stable isotope ratios to data set length, we paired time series rarifaction with Bayesian ellipse estimation. We then applied a threshold of 48 months and estimated LMWLs at 398 sites in 25 Köppen climate classes using orthogonal distance regression. Slopes ranged from 4.8 to 10.9, with an average of 7.64 ± 0.64. Intercepts ranged from −24‰ to 27‰, with an average of 6.85 ± 6.2‰. We identified three processes: (1) subcloud evaporation of rain, (2) atmospheric remoistening by rainfall evaporation, and (3) conditions of snow formation as important controls on slopes and intercepts in arid, humid, and seasonally snowy regions, respectively. We compared observational LMWLs with those from a suite of isotope‐enabled climate models. At arid and snowy sites, model data produced higher slopes and intercepts than observational data. At humid sites, model data exhibited dampened variability in slopes and intercepts relative to observational data. These results indicate potential for improvement in the precipitation and/or isotope parameterizations of raindrop evaporation, advection of reevaporated water, evapotranspiration fractionation, and supersaturation in mixed‐phase clouds. This meta‐analysis demonstrates LMWLs utility for identifying specific hydroclimatic and isotopic processes in observations and models.
ADAMTS Sol narae cleaves extracellular Wingless to generate a novel active form that regulates cell proliferation in Drosophila
Authors: Won Jong-Hoon , Kim Go-Woon , Kim Ja-Young , Cho Dong-Gyu , Kwon Buki , Bae Young-Kyung , Cho Kyung-Ok 
Published: July 2019

AbstractsWnt/ Wingless (Wg) is essential for embryonic development and adult homeostasis in all metazoans, but the mechanisms by which secreted Wnt/Wg is processed remain largely unknown. A Drosophila Sol narae (Sona) is a member of ADisintegrin And Metalloprotease with ThromboSpondin motif (ADAMTS) family, and positively regulates Wg signaling by promoting Wg secretion. Here we report that Sona and Wg are secreted by both conventional Golgi and exosomal transports, and Sona cleaves extracellular Wg at the two specific sites, leading to the generation of N-terminal domain (NTD) and C-terminal domain (CTD) fragments. The cleaved forms of extracellular Wg were detected in the extracellular region of fly wing discs, and its level was substantially reduced in sona mutants. Transient overexpression of Wg-CTD increased wing size while prolonged overexpression caused lethality and developmental defects. In contrast, Wg-NTD did not induce any phenotype. Moreover, the wing defects and lethality induced by sona RNAi were considerably rescued by Wg-CTD, indicating that a main function of extracellular Sona is the generation of Wg-CTD. Wg-CTD stabilized cytoplasmic Armadillo (Arm) and had genetic interactions with components of canonical Wg signaling. Wg-CTD also induced Wg downstream targets such as Distal-less (Dll) and Vestigial (Vg). Most importantly, Cyclin D (Cyc D) was induced by Wg-CTD but not by full-length Wg. Because Sona also induces Cyc D in a cell non-autonomous manner, Wg-CTD generated by Sona in the extracellular region activates a subset of Wg signaling whose major function is the regulation of cell proliferation.
Homocysteine enhances neural stem cell autophagy in in vivo and in vitro model of ischemic stroke
Authors: Wang Mengying , Liang Xiaoshan , Cheng Man , Yang Liu , Liu Huan , Wang Xuan , Sai Na , Zhang Xumei 
Published: July 2019

AbstractThe elevated level of the amino acid metabolite homocysteine (Hcy) is known as a risk factor for ischemic stroke. The molecular mechanisms responsible for neurotoxicity of Hcy remain largely unknown in ischemic brains. The previous studies have shown that Hcy decreases the proliferation and viability of neural stem cells (NSCs) in vivo and in vitro. Autophagy is required for the maintenance of NSCs homeostasis. In the current study, we hypothesized that the toxic effect of Hcy on NSCs may involve the changes in autophagy level following cerebral ischemia/reperfusion injury. The results showed that Hcy reduced cell viability, increased LDH release, and induced nonapoptotic cell death in primary NSCs exposed to oxygen–glucose deprivation)/reoxygenation (OGD/R). Treatment with autophagy inhibitor 3-methyladenine (3MA) partly reversed the decrease in the viability and prevented LDH release triggered by Hcy combined with OGD/R. Increased punctate LC3 dots co-localizing with Nestin-stained NSCs were also observed in the subventricular zone of Hcy-treated MCAO animals, which were partially blocked by 3MA. In vitro studies further revealed that Hcy induced the formation of autophagosomes, markedly increased the expression of the autophagic markers and decreased p-ERK, p-PI3K, p-AKT, and p-mTOR levels. In addition, MHY1485, an activator of mTOR, reduced Hcy-induced increase in LC3 and Beclin 1 protein levels, meanwhile ERK and PI3K activators (TPA, curcumin for ERK and IGF-1 for PI3K, respectively) enhanced Hcy-triggered mTOR inhibition in OGD/R NSCs. Our findings suggest that Hcy may cause excessive autophagy by downregulation of both PI3K-AKT- and ERK- dependent mTOR signaling, thereby facilitates the toxicity of Hcy on NSCs in ischemic brains.
Efficient and thermally stable organic solar cells based on small molecule donor and polymer acceptor
Authors: Zhang Zijian , Miao Junhui , Ding Zicheng , Kan Bin , Lin Baojun , Wan Xiangjian , Ma Wei , Chen Yongsheng , Long Xiaojing , Dou Chuandong , Zhang Jidong , Liu Jun , Wang Lixiang 
Published: July 2019

AbstractEfficient organic solar cells (OSCs) often use combination of polymer donor and small molecule acceptor. Herein we demonstrate efficient and thermally stable OSCs with combination of small molecule donor and polymer acceptor, which is expected to expand the research field of OSCs. Typical small molecule donors show strong intermolecular interactions and high crystallinity, and consequently do not match polymer acceptors because of large-size phase separation. We develop a small molecule donor with suppressed π-π stacking between molecular backbones by introducing large steric hindrance. As the result, the OSC exhibits small-size phase separation in the active layer and shows a power conversion efficiency of 8.0%. Moreover, this OSC exhibits much improved thermal stability, i.e. maintaining 89% of its initial efficiency after thermal annealing the active layer at 180 °C for 7 days. These results indicate a different kind of efficient and stable OSCs.
Involvement of G-quadruplex regions in mammalian replication origin activity
Authors: Prorok Paulina , Artufel Marie , Aze Antoine , Coulombe Philippe , Peiffer Isabelle , Lacroix Laurent , Guédin Aurore , Mergny Jean-Louis , Damaschke Julia , Schepers Aloys , Cayrou Christelle , Teulade-Fichou Marie-Paule , Ballester Benoit , Méchali Marcel 
Published: July 2019

AbstractGenome-wide studies of DNA replication origins revealed that origins preferentially associate with an Origin G-rich Repeated Element (OGRE), potentially forming G-quadruplexes (G4). Here, we functionally address their requirements for DNA replication initiation in a series of independent approaches. Deletion of the OGRE/G4 sequence strongly decreased the corresponding origin activity. Conversely, the insertion of an OGRE/G4 element created a new replication origin. This element also promoted replication of episomal EBV vectors lacking the viral origin, but not if the OGRE/G4 sequence was deleted. A potent G4 ligand, PhenDC3, stabilized G4s but did not alter the global origin activity. However, a set of new, G4-associated origins was created, whereas suppressed origins were largely G4-free. In vitro Xenopus laevis replication systems showed that OGRE/G4 sequences are involved in the activation of DNA replication, but not in the pre-replication complex formation. Altogether, these results converge to the functional importance of OGRE/G4 elements in DNA replication initiation.
Temperature and insulin signaling regulate body size in Hydra by the Wnt and TGF-beta pathways
Authors: Mortzfeld Benedikt M. , Taubenheim Jan , Klimovich Alexander V. , Fraune Sebastian , Rosenstiel Philip , Bosch Thomas C. G. 
Published: July 2019

AbstractHow multicellular organisms assess and control their size is a fundamental question in biology, yet the molecular and genetic mechanisms that control organ or organism size remain largely unsolved. The freshwater polypHydrademonstrates a high capacity to adapt its body size to different temperatures. Here we identify the molecular mechanisms controlling this phenotypic plasticity and show that temperature-induced cell number changes are controlled by Wnt- and TGF-β signaling. Further we show that insulin-like peptide receptor (INSR) and forkhead box protein O (FoxO) are important genetic drivers of size determination controlling the same developmental regulators. Thus, environmental and genetic factors directly affect developmental mechanisms in which cell number is the strongest determinant of body size. These findings identify the basic mechanisms as to how size is regulated on an organismic level and how phenotypic plasticity is integrated into conserved developmental pathways in an evolutionary informative model organism.
Spectroscopic disentanglement of the quantum states of highly excited Cu2
Authors: Beck M. , Bornhauser P. , Visser Bradley , Knopp G. , Bokhoven J. A. van , Radi P. P. 
Published: July 2019

AbstractTransition metals, characterised by their partially filled d orbitals, provide the basis for many of the most relevant processes in chemistry, biology, and physics. Embedded as single atoms or in small clusters, they give rise to exceptional optical, chemical, and magnetic properties. So far, it has proven impossible to disentangle the complex network of excited quantum states, which greatly hinders prediction and control of material properties. Here, we apply two-colour resonant four-wave mixing to quantitatively resolve the quantum states of the neutral copper dimer. This allows us to unwind the individual spectral lines by isotopic composition and rotational quantum number and reveals a rich network of bright and perturbing dark states. While this work presents a road map for the experimental study of the bonding between and with transition metal atoms, it also provides experimental reference data for prospective quantum chemical approaches on handling systems with a high density of states.
Observation of two types of charge-density-wave orders in superconducting La2-xSrxCuO4
Authors: Wen J.-J. , Huang H. , Lee S.-J. , Jang H. , Knight J. , Lee Y. S. , Fujita M. , Suzuki K. M. , Asano S. , Kivelson S. A. , Kao C.-C. , Lee J.-S. 
Published: July 2019

AbstractThe discovery of charge- and spin-density-wave (CDW/SDW) orders in superconducting cuprates has altered our perspective on the nature of high-temperature superconductivity (SC). However, it has proven difficult to fully elucidate the relationship between the density wave orders and SC. Here, using resonant soft X-ray scattering, we study the archetypal cuprate La2-xSrxCuO4 (LSCO) over a broad doping range. We reveal the existence of two types of CDW orders in LSCO, namely CDW stripe order and CDW short-range order (SRO). While the CDW-SRO is suppressed by SC, it is partially transformed into the CDW stripe order with developing SDW stripe order near the superconducting Tc. These findings indicate that the stripe orders and SC are inhomogeneously distributed in the superconducting CuO2 planes of LSCO. This further suggests a new perspective on the putative pair-density-wave order that coexists with SC, SDW, and CDW orders.
Combinatorial design of molecular seeds for chirality-controlled synthesis of single-walled carbon nanotubes
Authors: Tomada Joerg , Dienel Thomas , Hampel Frank , Fasel Roman , Amsharov Konstantin 
Published: July 2019

AbstractThe chirality-controlled synthesis of single-walled carbon nanotubes (SWCNTs) is a major challenge facing current nanomaterials science. The surface-assisted bottom-up fabrication from unimolecular CNT seeds (precursors), which unambiguously predefine the chirality of the tube during the growth, appears to be the most promising approach. This strategy opens a venue towards controlled synthesis of CNTs of virtually any possible chirality by applying properly designed precursor molecules. However, synthetic access to the required precursor molecules remains practically unexplored because of their complex structure. Here, we report a general strategy for the synthesis of molecular seeds for the controlled growth of SWCNTs possessing virtually any desired chirality by combinatorial multi-segmental assembly. The suggested combinatorial approach allows facile assembly of complex CNT precursors (with up to 100 carbon atoms immobilized at strictly predefined positions) just in one single step from complementary segments. The feasibility of the approach is demonstrated on the synthesis of the precursor molecules for 21 different SWCNT chiralities utilizing just three relatively simple building blocks.
The AAA + ATPase TorsinA polymerizes into hollow helical tubes with 8.5 subunits per turn
Authors: Demircioglu F. Esra , Zheng Weili , McQuown Alexander J. , Maier Nolan K. , Watson Nicki , Cheeseman Iain M. , Denic Vladimir , Egelman Edward H. , Schwartz Thomas U. 
Published: July 2019

AbstractTorsinA is an ER-resident AAA + ATPase, whose deletion of glutamate E303 results in the genetic neuromuscular disease primary dystonia. TorsinA is an unusual AAA + ATPase that needs an external activator. Also, it likely does not thread a peptide substrate through a narrow central channel, in contrast to its closest structural homologs. Here, we examined the oligomerization of TorsinA to get closer to a molecular understanding of its still enigmatic function. We observe TorsinA to form helical filaments, which we analyzed by cryo-electron microscopy using helical reconstruction. The 4.4 Å structure reveals long hollow tubes with a helical periodicity of 8.5 subunits per turn, and an inner channel of ~ 4 nm diameter. We further show that the protein is able to induce tubulation of membranes in vitro, an observation that may reflect an entirely new characteristic of AAA + ATPases. We discuss the implications of these observations for TorsinA function.
Ultra-thin solid electrolyte interphase evolution and wrinkling processes in molybdenum disulfide-based lithium-ion batteries
Authors: Wan Jing , Hao Yang , Shi Yang , Song Yue-Xian , Yan Hui-Juan , Zheng Jian , Wen Rui , Wan Li-Jun 
Published: July 2019

AbstractMolybdenum disulfide is considered one of the most promising anodes for lithium-ion batteries due to its high specific capacity; however, it suffers from an unstable solid electrolyte interphase. Understanding its structural evolution and reaction mechanism upon charging/discharging is crucial for further improvements in battery performance. Herein, the interfacial processes of solid electrolyte interphase film formation and lithiation/delithiation on ultra-flat monolayer molybdenum disulfide are monitored by in situ atomic force microscopy. The live formation of ultra-thin and dense films can be induced by the use of fluoroethylene carbonate as an additive to effectively protect the anode electrodes. The evolution of the fluoroethylene carbonate-derived solid electrolyte interphase film upon cycling is quantitatively analysed. Furthermore, the formation of wrinkle-structure networks upon lithiation process is distinguished in detailed steps, and accordingly, structure-reactivity correlations are proposed. These quantitative results provide an in-depth understanding of the interfacial mechanism in molybdenum disulfide-based lithium-ion batteries.
Methylation analysis of plasma DNA informs etiologies of Epstein-Barr virus-associated diseases
Authors: Lam W. K. Jacky , Jiang Peiyong , Chan K. C. Allen , Peng Wenlei , Shang Huimin , Heung Macy M. S. , Cheng Suk Hang , Zhang Haiqiang , Tse O. Y. Olivia , Raghupathy Radha , Ma Brigette B. Y. , Hui Edwin P. , Chan Anthony T. C. , Woo John K. S. , Chiu Rossa W. K. , Lo Y. M. Dennis 
Published: July 2019

AbstractEpstein-Barr virus (EBV) is associated with a number of diseases, including malignancies. Currently, it is not known whether patients with different EBV-associated diseases have different methylation profiles of circulating EBV DNA. Through whole-genome methylation analysis of plasma samples from patients with nasopharyngeal carcinoma (NPC), EBV-associated lymphoma and infectious mononucleosis, we demonstrate that EBV DNA methylation profiles exhibit a disease-associated pattern. This observation implies a significant potential for the development of methylation analysis of plasma EBV DNA for NPC diagnostics. We further analyse the plasma EBV DNA methylome of NPC and non-NPC subjects from a prospective screening cohort. Plasma EBV DNA fragments demonstrate differential methylation patterns between NPC and non-NPC subjects. Combining such differential methylation patterns with the fractional concentration (count) and size of plasma EBV DNA, population screening of NPC is performed with an improved positive predictive value of 35.1%, compared to a count- and size-based only protocol.
Nanometer-precision non-local deformation reconstruction using nanodiamond sensing
Authors: Xia Kangwei , Liu Chu-Feng , Leong Weng-Hang , Kwok Man-Hin , Yang Zhi-Yuan , Feng Xi , Liu Ren-Bao , Li Quan 
Published: July 2019

AbstractSpatially resolved information about material deformation upon loading is critical to evaluating mechanical properties of materials, and to understanding mechano-response of live systems. Existing techniques may access local properties of materials at nanoscale, but not at locations away from the force-loading positions. Moreover, interpretation of the local measurement relies on correct modeling, the validation of which is not straightforward. Here we demonstrate an approach to evaluating non-local material deformation based on the integration of nanodiamond orientation sensing and atomic force microscopy nanoindentation. This approach features a 5 nm precision in the loading direction and a sub-hundred nanometer lateral resolution, high enough to disclose the surface/interface effects in the material deformation. The non-local deformation profile can validate the models needed for mechanical property determination. The non-local nanometer-precision sensing of deformation facilitates studying mechanical response of complex material systems ranging from impact transfer in nanocomposites to mechano-response of live systems.
Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells
Authors: Bossel Ben-Moshe Noa , Hen-Avivi Shelly , Levitin Natalia , Yehezkel Dror , Oosting Marije , Joosten Leo A. B. , Netea Mihai G. , Avraham Roi 
Published: July 2019

AbstractComplex interactions between different host immune cell types can determine the outcome of pathogen infections. Advances in single cell RNA-sequencing (scRNA-seq) allow probing of these immune interactions, such as cell-type compositions, which are then interpreted by deconvolution algorithms using bulk RNA-seq measurements. However, not all aspects of immune surveillance are represented by current algorithms. Here, using scRNA-seq of human peripheral blood cells infected withSalmonella, we develop a deconvolution algorithm for inferring cell-type specific infection responses from bulk measurements. We apply our dynamic deconvolution algorithm to a cohort of healthy individuals challenged ex vivo withSalmonella, and to three cohorts of tuberculosis patients during different stages of disease. We reveal cell-type specific immune responses associated not only with ex vivo infection phenotype but also with clinical disease stage. We propose that our approach provides a predictive power to identify risk for disease, and human infection outcomes.
Programmable responsive hydrogels inspired by classical conditioning algorithm
Authors: Zhang Hang , Zeng Hao , Priimagi Arri , Ikkala Olli 
Published: July 2019

AbstractLiving systems have inspired research on non-biological dynamic materials and systems chemistry to mimic specific complex biological functions. Upon pursuing ever more complex life-inspired non-biological systems, mimicking even the most elementary aspects of learning is a grand challenge. We demonstrate a programmable hydrogel-based model system, whose behaviour is inspired by associative learning, i.e., conditioning, which is among the simplest forms of learning. Algorithmically, associative learning minimally requires responsivity to two different stimuli and a memory element. Herein, nanoparticles form the memory element, where a photoacid-driven pH-change leads to their chain-like assembly with a modified spectral behaviour. On associating selected light irradiation with heating, the gel starts to melt upon the irradiation, originally a neutral stimulus. A logic diagram describes such an evolution of the material response. Coupled chemical reactions drive the system out-of-equilibrium, allowing forgetting and memory recovery. The findings encourage to search non-biological materials towards associative and dynamic properties.