bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostics of a WN2‐Type Major Sudden Stratospheric Warming Event in February 2018 Using a New Three‐Dimensional Wave Activity Flux
Authors: Harada Yayoi , Sato Kaoru , Kinoshita Takenari , Yasui Ryosuke , Hirooka Toshihiko , Naoe Hiroaki 
Published: May 2019

AbstractObservational features of atmospheric fields during a zonal wave number 2‐type major sudden stratospheric warming (MSSW) event in February 2018 (MSSW18) are analyzed using the Japanese 55‐year Reanalysis, satellite measurements by a microwave limb sounder, and a new three‐dimensional wave activity flux. MSSW18 is characterized by a clear polar vortex split, continuance of easterlies with evident double peaks, clear planetary wave propagation in the easterly region of the upper stratosphere and extraordinary upward propagation of wave number 2 planetary waves from the upper troposphere. The upward propagation peak is comparable to that during an MSSW event in January 2009 (MSSW09), although MSSW18 shows relatively modest warming, unclear disappearance of the stratopause and weak stratopause elevation compared to those during MSSW09. Further analyses reveal that wave packets propagates upward simultaneously in both the Eastern and Western Hemispheres. Those observed in the Eastern Hemisphere converge strongly at the western edge of the Aleutian High, and most of them do not propagate further into the upper stratosphere. The wave packets observed in the Western Hemisphere propagate locally into the upper stratosphere over North America despite the fact that easterlies were predominant there in the mature stage of MSSW18. Furthermore, the results of our study reveal that the regions and levels of wave packet attenuation correspond well to the areas that smaller‐scale waves have weak eastward phase tilt or are in the quasi‐barotropic condition during MSSW18, whereas during MSSW09 the westward phase tilts of smaller‐scale waves were clearly visible in the upper stratosphere.
Assessing Hydrograph Similarity and Rare Runoff Dynamics by Cross Recurrence Plots
Authors: Wendi Dadiyorto , Merz Bruno , Marwan Norbert 
Published: May 2019

AbstractThis paper introduces a novel measure to assess similarity between event hydrographs. It is based on cross recurrence plots (CRP) and recurrence quantification analysis (RQA), which have recently gained attention in a range of disciplines when dealing with complex systems. The method attempts to quantify the event runoff dynamics and is based on the time delay embedded phase space representation of discharge hydrographs. A phase space trajectory is reconstructed from the event hydrograph, and pairs of hydrographs are compared to each other based on the distance of their phase space trajectories. Time delay embedding allows considering the multidimensional relationships between different points in time within the event. Hence, the temporal succession of discharge values is taken into account, such as the impact of the initial conditions on the runoff event. We provide an introduction to cross recurrence plots and discuss their parameterization. An application example based on flood time series demonstrates how the method can be used to measure the similarity or dissimilarity of events, and how it can be used to detect events with rare runoff dynamics. It is argued that this methods provides a more comprehensive approach to quantify hydrograph similarity compared to conventional hydrological signatures.
A Century of Nonlinearity in the Geosciences
Authors: Ghil Michael 
Published: May 2019

AbstractThis paper provides a thumbnail sketch of the evolution of nonlinear ideas in the mathematics and physics of the geosciences, broadly construed, over the last hundred or so years. It emphasizes the mathematical concepts and methods and outlines simple examples of how they were, are, and maybe will be applied to the solid Earth—that is, the crust, mantle, and core—and its fluid envelopes—that is, the atmosphere and oceans.
Strong Dependence of Atmospheric Feedbacks on Mixed‐Phase Microphysics and Aerosol‐Cloud Interactions in HadGEM3
Authors: Bodas‐Salcedo A. , Mulcahy J. P. , Andrews T. , Williams K. D. , Ringer M. A. , Field P. R. , Elsaesser G. S. 
Published: May 2019

AbstractWe analyze the atmospheric processes that explain the large changes in radiative feedbacks between the two latest climate configurations of the Hadley Centre Global Environmental model. We use a large set of atmosphere‐only climate change simulations (amip and amip‐p4K) to separate the contributions to the differences in feedback parameter from all the atmospheric model developments between the two latest model configurations. We show that the differences are mostly driven by changes in the shortwave cloud radiative feedback in the midlatitudes, mainly over the Southern Ocean. Two new schemes explain most of the differences: the introduction of a new aerosol scheme and the development of a new mixed‐phase cloud scheme. Both schemes reduce the strength of the preexisting shortwave negative cloud feedback in the midlatitudes. The new aerosol scheme dampens a strong aerosol‐cloud interaction, and it also suppresses a negative clear‐sky shortwave feedback. The mixed‐phase scheme increases the amount of cloud liquid water path (LWP) in the present day and reduces the increase in LWP with warming. Both changes contribute to reducing the negative radiative feedback of the increase of LWP in the warmer climate. The mixed‐phase scheme also enhances a strong, preexisting, positive cloud fraction feedback. We assess the realism of the changes by comparing present‐day simulations against observations and discuss avenues that could help constrain the relevant processes.
Low-cost and versatile integration of microwire electrodes and optical waveguides into silicone elastomeric devices using modified xurographic methods
Authors: Liu Juncong , Mahony James B , Selvaganapathy Ponnambalam Ravi 
Published: May 2019

AbstractMicroelectrodes are used in microfluidic devices for a variety of purposes such as heating, applying electric fields, and electrochemical sensing. However, they are still manufactured by expensive deposition techniques such as sputtering or evaporation and patterned using photolithography methods. More recently, alternate methods including nanoparticle sintering and use of liquid metal flowing through microchannels have been used to fabricate microelectrodes. These methods are limited in the material choices or require post processing to be integrated into microchannels. Here we developed a low-cost and versatile method to integrate high-quality metal microwires into polydimethylsiloxane (PDMS) using xurography. The microwire integration process includes cutting slit pattern on PDMS substrate and subsequent writing metal microwires into the slit pattern using a specialized tip. Then the microwire-integrated PDMS was sealed/bonded using uncured PDMS prepolymer. This method enables integration of metal microwires of diameter as small as 15 μm into PDMS devices. Integration of multiple microwires with minimum spacing of 150 μm has also been demonstrated. The versatility of this method is demonstrated by the fabrication of metal microwire suspended in the middle of the microchannel, which is difficult to achieve using conventional electrode fabrication methods. This low-cost method avoids expensive clean room fabrication yet producing high-quality electrodes and can be used in a variety of microfluidic and MEMS applications.
Nanoimprint lithography steppers for volume fabrication of leading-edge semiconductor integrated circuits
Authors: Sreenivasan S.V. 
Published: May 2019

AbstractThis article discusses the transition of a form of nanoimprint lithography technology, known as Jet and Flash Imprint Lithography (J-FIL), from research to a commercial fabrication infrastructure for leading-edge semiconductor integrated circuits (ICs). Leading-edge semiconductor lithography has some of the most aggressive technology requirements, and has been a key driver in the 50-year history of semiconductor scaling. Introducing a new, disruptive capability into this arena is therefore a case study in a “high-risk-high-reward” opportunity. This article first discusses relevant literature in nanopatterning including advanced lithography options that have been explored by the IC fabrication industry, novel research ideas being explored, and literature in nanoimprint lithography. The article then focuses on the J-FIL process, and the interdisciplinary nature of risk, involving nanoscale precision systems, mechanics, materials, material delivery systems, contamination control, and process engineering. Next, the article discusses the strategic decisions that were made in the early phases of the project including: (i) choosing a step and repeat process approach; (ii) identifying the first target IC market for J-FIL; (iii) defining the product scope and the appropriate collaborations to share the risk-reward landscape; and (iv) properly leveraging existing infrastructure, including minimizing disruption to the widely accepted practices in photolithography. Finally, the paper discusses the commercial J-FIL stepper system and associated infrastructure, and the resulting advances in the key lithographic process metrics such as critical dimension control, overlay, throughput, process defects, and electrical yield over the past 5 years. This article concludes with the current state of the art in J-FIL technology for IC fabrication, including description of the high volume manufacturing stepper tools created for advanced memory manufacturing.
Polyclonal serum free light chain elevation is associated with increased risk of monoclonal gammopathies
Authors: Kumar Shaji , Larson Dirk R. , Dispenzieri Angela , Therneau Terry M. , Murray David L. , Leif Bergsagel P. , Kyle Robert A. , Vincent Rajkumar S. 
Published: May 2019

AbstractMonoclonal gammopathies (MG) constitute a spectrum of disorders starting from a monoclonal gammopathy of undetermined significance (MGUS) to active disease requiring therapy such as multiple myeloma. MG are characterized by proliferation of clonal plasma cells (PC) secreting a monoclonal protein either as intact immunoglobulin or free kappa or lambda free light chains (FLC). We hypothesized that a polyclonal elevation of serum FLC may indicate an inflammatory state that precedes development of MG. We studied 15,630 individuals from Olmsted county, who did not have MGUS based on baseline screening studies. At a median follow-up of 18.1 years, 264 patients had developed a clonal PC disorder; 252 with MGUS, 1 with SMM, 8 with MM, and 3 with amyloidosis, translating to an annual incidence of development of a MG of 0.1%. We examined the baseline polyclonal ΣFLC (kappa + lambda FLC) from the initial screening and grouped them into deciles. The highest decile group had a 2.6-fold (95% CI; 1.8, 3.7) increase in the risk of developing a MG, P < 0.001. We demonstrate for the first time, the increased risk of developing MG in patients with elevated serum FLC, suggesting that an underlying inflammatory state may play an etiologic role.
Albumin tailoring fluorescence and photothermal conversion effect of near-infrared-II fluorophore with aggregation-induced emission characteristics
Authors: Gao Shuai , Wei Guoguang , Zhang Sihang , Zheng Binbin , Xu Jiaojiao , Chen Gaoxian , Li Mingwang , Song Shaoli , Fu Wei , Xiao Zeyu , Lu Wei 
Published: May 2019

AbstractFluorophores with donor-acceptor-donor groups with the emission spanning the second near-infrared window (NIR-II) have recently received great attention for biomedical application. Yet, the mechanism underlying the equilibrium between fluorescence (radiative decay) and photothermal effect (non-radiative decay) of these fluorophores remains elusive. Here, we demonstrate that a lipophilic NIR-II fluorophore, BPBBT, possesses both twisted intramolecular charge transfer (TICT) and aggregation-induced emission (AIE) characteristics. Human serum albumin (HSA) binds to BPBBT, which changes the planarity of the fluorophore and restricts its intramolecular rotation. The binding results in alteration to the equilibrium between AIE and TICT state of BPBBT, tailoring its fluorescence and photothermal efficiency. Under the guidance of intraoperative NIR-II fluorescence image, the prepared HSA-bound BPBBT nanoparticles delineate primary orthotopic mouse colon tumor and metastatic lesions with dimensions as small as 0.5 mm × 0.3 mm, and offer photothermal ablation therapy with optimized timing, dosing and area of the laser irradiation.
A Lieb-like lattice in a covalent-organic framework and its Stoner ferromagnetism
Authors: Jiang Wei , Huang Huaqing , Liu Feng 
Published: May 2019

AbstractLieb lattice has been extensively studied to realize ferromagnetism due to its exotic flat band. However, its material realization has remained elusive; so far only artificial Lieb lattices have been made experimentally. Here, based on first-principles and tight-binding calculations, we discover that a recently synthesized two-dimensional sp2 carbon-conjugated covalent-organic framework (sp2c-COF) represents a material realization of a Lieb-like lattice. The observed ferromagnetism upon doping arises from a Dirac (valence) band in a non-ideal Lieb lattice with strong electronic inhomogeneity (EI) rather than the topological flat band in an ideal Lieb lattice. The EI, as characterized with a large on-site energy difference and a strong dimerization interaction between the corner and edge-center ligands, quenches the kinetic energy of the usual dispersive Dirac band, subjecting to an instability against spin polarization. We predict an even higher spin density for monolayer sp2c-COF to accommodate a higher doping concentration with reduced interlayer interaction.
6mA-DNA-binding factor Jumu controls maternal-to-zygotic transition upstream of Zelda
Authors: He Shunmin , Zhang Guoqiang , Wang Jiajia , Gao Yajie , Sun Ruidi , Cao Zhijie , Chen Zhenping , Zheng Xiudeng , Yuan Jiao , Luo Yuewan , Wang Xiaona , Zhang Wenxin , Zhang Peng , Zhao Yi , He Chuan , Tao Yi , Sun Qinmiao , Chen Dahua 
Published: May 2019

AbstractA long-standing question in the field of embryogenesis is how the zygotic genome is precisely activated by maternal factors, allowing normal early embryonic development. We have previously shown that N6-methyladenine (6mA) DNA modification is highly dynamic in early Drosophila embryos and forms an epigenetic mark. However, little is known about how 6mA-formed epigenetic information is decoded. Here we report that the Fox-family protein Jumu binds 6mA-marked DNA and acts as a maternal factor to regulate the maternal-to-zygotic transition. We find that zelda encoding the pioneer factor Zelda is marked by 6mA. Our genetic assays suggest that Jumu controls the proper zygotic genome activation (ZGA) in early embryos, at least in part, by regulating zelda expression. Thus, our findings not only support that the 6mA-formed epigenetic marks can be read by specific transcription factors, but also uncover a mechanism by which the Jumu regulates ZGA partially through Zelda in early embryos.
In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release
Authors: Ding Ke , Celma Cristina C. , Zhang Xing , Chang Thomas , Shen Wesley , Atanasov Ivo , Roy Polly , Zhou Z. Hong 
Published: May 2019

AbstractTranscribing and replicating a double-stranded genome require protein modules to unwind, transcribe/replicate nucleic acid substrates, and release products. Here we present in situ cryo-electron microscopy structures of rotavirus dsRNA-dependent RNA polymerase (RdRp) in two states pertaining to transcription. In addition to the previously discovered universal “hand-shaped” polymerase core domain shared by DNA polymerases and telomerases, our results show the function of N- and C-terminal domains of RdRp: the former opens the genome duplex to isolate the template strand; the latter splits the emerging template-transcript hybrid, guides genome reannealing to form a transcription bubble, and opens a capsid shell protein (CSP) to release the transcript. These two “helicase” domains also extensively interact with CSP, which has a switchable N-terminal helix that, like cellular transcriptional factors, either inhibits or promotes RdRp activity. The in situ structures of RdRp, CSP, and RNA in action inform mechanisms of not only transcription, but also replication.
Functional rare and low frequency variants in BLK and BANK1 contribute to human lupus
Authors: Jiang Simon H. , Athanasopoulos Vicki , Ellyard Julia I. , Chuah Aaron , Cappello Jean , Cook Amelia , Prabhu Savit B. , Cardenas Jacob , Gu Jinghua , Stanley Maurice , Roco Jonathan A. , Papa Ilenia , Yabas Mehmet , Walters Giles D. , Burgio Gaetan , McKeon Kathryn , Byers James M. , Burrin Charlotte , Enders Anselm , Miosge Lisa A. , Canete Pablo F. , Jelusic Marija , Tasic Velibor , Lungu Adrian C. , Alexander Stephen I. , Kitching Arthur R. , Fulcher David A. , Shen Nan , Arsov Todor , Gatenby Paul A. , Babon Jeff J. , Mallon Dominic F. , de Lucas Collantes Carmen , Stone Eric A. , Wu Philip , Field Matthew A. , Andrews Thomas D. , Cho Eun , Pascual Virginia , Cook Matthew C. , Vinuesa Carola G. 
Published: May 2019

AbstractSystemic lupus erythematosus (SLE) is the prototypic systemic autoimmune disease. It is thought that many common variant gene loci of weak effect act additively to predispose to common autoimmune diseases, while the contribution of rare variants remains unclear. Here we describe that rare coding variants in lupus-risk genes are present in most SLE patients and healthy controls. We demonstrate the functional consequences of rare and low frequency missense variants in the interacting proteins BLK and BANK1, which are present alone, or in combination, in a substantial proportion of lupus patients. The rare variants found in patients, but not those found exclusively in controls, impair suppression of IRF5 and type-I IFN in human B cell lines and increase pathogenic lymphocytes in lupus-prone mice. Thus, rare gene variants are common in SLE and likely contribute to genetic risk.
Nonlinearity of root trait relationships and the root economics spectrum
Authors: Kong Deliang , Wang Junjian , Wu Huifang , Valverde-Barrantes Oscar J. , Wang Ruili , Zeng Hui , Kardol Paul , Zhang Haiyan , Feng Yulong 
Published: May 2019

AbstractThe root economics spectrum (RES), a common hypothesis postulating a tradeoff between resource acquisition and conservation traits, is being challenged by conflicting relationships between root diameter, tissue density (RTD) and root nitrogen concentration (RN). Here, we analyze a global trait dataset of absorptive roots for over 800 plant species. For woody species (but not for non-woody species), we find nonlinear relationships between root diameter and RTD and RN, which stem from the allometric relationship between stele and cortical tissues. These nonlinear relationships explain how sampling bias from different ends of the nonlinear curves can result in conflicting trait relationships. Further, the shape of the relationships varies depending on evolutionary context and mycorrhizal affiliation. Importantly, the observed nonlinear trait relationships do not support the RES predictions. Allometry-based nonlinearity of root trait relationships improves our understanding of the ecology, physiology and evolution of absorptive roots.
Geometric description of self-interaction potential in symmetric protein complexes
Authors: Empereur-Mot Charly , Garcia-Seisdedos Hector , Elad Nadav , Dey Sucharita , Levy Emmanuel D. 
Published: May 2019

AbstractProteins can self-associate with copies of themselves to form symmetric complexes called homomers. Homomers are widespread in all kingdoms of life and allow for unique geometric and functional properties, as reflected in viral capsids or allostery. Once a protein forms a homomer, however, its internal symmetry can compound the effect of point mutations and trigger uncontrolled self-assembly into high-order structures. We identified mutation hot spots for supramolecular assembly, which are predictable by geometry. Here, we present a dataset of descriptors that characterize these hot spot positions both geometrically and chemically, as well as computer scripts allowing the calculation and visualization of these properties for homomers of choice. Since the biological relevance of homomers is not readily available from their X-ray crystallographic structure, we also provide reliability estimates obtained by methods we recently developed. These data have implications in the study of disease-causing mutations, protein evolution and can be exploited in the design of biomaterials.
Dry season soil water potential maps of a 50 hectare tropical forest plot on Barro Colorado Island, Panama
Authors: Kupers Stefan J. , Wirth Christian , Engelbrecht Bettina M. J. , Rüger Nadja 
Published: May 2019

AbstractFine scale spatial variation in soil moisture influences plant performance, species distributions and diversity. However, detailed information on local soil moisture variation is scarce, particularly in species-rich tropical forests. We measured soil water potential and soil water content in the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, one of the best-studied tropical forests in the world. We present maps of soil water potential for several dry season stages during a regular year and during an El Niño drought. Additionally, we provide code that allows users to create maps for specific dates. The maps can be combined with other freely available datasets such as long-term vegetation censuses (ranging from seeds to adult trees), data on other resources (e.g. light and nutrients) and remote sensing data (e.g. LiDAR and imaging spectroscopy). Users can study questions in various disciplines such as population and community ecology, plant physiology and hydrology under current and future climate conditions.
Expansion of different subpopulations of CD26−/low T cells in allergic and non-allergic asthmatics
Authors: Nieto-Fontarigo Juan José , Salgado Francisco Javier , San-José María Esther , Cruz María Jesús , Valdés Luis , Pérez-Díaz Amparo , Arias Pilar , Nogueira Montserrat , González-Barcala Francisco Javier 
Published: May 2019

AbstractCD26 displays variable levels between effector (TH17 ≫ TH1 > TH2 > Treg) and naïve/memory (memory > naïve) CD4+ T lymphocytes. Besides, IL-6/IL−6R is associated with TH17-differentiation and asthma severity. Allergic/atopic asthma (AA) is dominated by TH2 responses, while TH17 immunity might either modulate the TH2-dependent inflammation in AA or be an important mechanism boosting non-allergic asthma (NAA). Therefore, in this work we have compared the expression of CD26 and CD126 (IL-6Rα) in lymphocytes from different groups of donors: allergic (AA) and non-allergic (NAA) asthma, rhinitis, and healthy subjects. For this purpose, flow cytometry, haematological/biochemical, and in vitro proliferation assays were performed. Our results show a strong CD26-CD126 correlation and an over-representation of CD26− subsets with a highly-differentiated effector phenotype in AA (CD4+CD26−/low T cells) and NAA (CD4−CD26− γδ-T cells). In addition, we found that circulating levels of CD26 (sCD26) were reduced in both AA and NAA, while loss of CD126 expression on different leukocytes correlated with higher disease severity. Finally, selective inhibition of CD26-mRNA translation led to enhanced T cell proliferation in vitro. These findings support that CD26 down-modulation could play a role in facilitating the expansion of highly-differentiated effector T cell subsets in asthma.