bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Relative Importance of Different Flood‐Generating Mechanisms Across Europe
Authors: Berghuijs Wouter R. , Harrigan Shaun , Molnar Peter , Slater Louise J. , Kirchner James W. 
Published: May 2019

AbstractInferring the mechanisms causing river flooding is key to understanding past, present, and future flood risk. However, a quantitative spatially distributed overview of the mechanisms that drive flooding across Europe is currently unavailable. In addition, studies that classify catchments according to their flood‐driving mechanisms often identify a single mechanism per location, although multiple mechanisms typically contribute to flood risk. We introduce a new method that uses seasonality statistics to estimate the relative importance of extreme precipitation, soil moisture excess, and snowmelt as flood drivers. Applying this method to a European data set of maximum annual flow dates in several thousand catchments reveals that from 1960 to 2010 relatively few annual floods were caused by annual rainfall peaks. Instead, most European floods were caused by snowmelt and by the concurrence of heavy precipitation with high antecedent soil moisture. For most catchments, the relative importance of these mechanisms has not substantially changed during the past five decades. Exposing the regional mechanisms underlying Europe's most costly natural hazard is a key first step in identifying the processes that require most attention in future flood research.
Simulating C‐Band SAR Footprint‐Scale Backscatter Over Agricultural Area With a Physical Land Surface Model
Authors: Sun Leqiang , Dabboor Mohammed , Belair Stephane , Carrera Marco L. , Merzouki Amine 
Published: May 2019

AbstractRemotely sensed soil moisture products are ideal candidates for initializing soil moisture profiles of land surface models via data assimilation. This paper investigates the possibility of using a calibrated Integral Equation Model coupled with a hyperresolution land surface model, called Soil, Vegetation, and Snow (SVS) to simulate backscatter and compares the results with C‐band RADARSAT‐2 Synthetic Aperture Radar (SAR) backscatter signals in postharvest season when the field is considered bare soil or sparsely vegetated. Modifications to SVS evaporation scheme are shown to improve the comparison against SAR measurements. An improved effective soil roughness calculation scheme was also proposed to focus on the inversion of the root mean square height (Hrms) only. Soil dielectric constant compensation was suggested to reduce the inversion error and expand the dynamic range of Integral Equation Model. The combination of SVS soil moisture and effective roughness is found superior to the absence of either of them. This method is promising considering that it does not require any in situ measurements, and yet it still outperforms the original IEM model, which uses in situ measured soil moisture and soil roughness at point scale.
Suppression of a broad spectrum of liver autoimmune pathologies by single peptide-MHC-based nanomedicines
Authors: Umeshappa Channakeshava Sokke , Singha Santiswarup , Blanco Jesus , Shao Kun , Nanjundappa Roopa Hebbandi , Yamanouchi Jun , Parés Albert , Serra Pau , Yang Yang , Santamaria Pere 
Published: May 2019

AbstractPeptide-major histocompatibility complex class II (pMHCII)-based nanomedicines displaying tissue-specific autoantigenic epitopes can blunt specific autoimmune conditions by re-programming cognate antigen-experienced CD4+ T-cells into disease-suppressing T-regulatory type 1 (TR1) cells. Here, we show that single pMHCII-based nanomedicines displaying epitopes from mitochondrial, endoplasmic reticulum or cytoplasmic antigens associated with primary biliary cholangitis (PBC) or autoimmune hepatitis (AIH) can broadly blunt PBC, AIH and Primary Sclerosing Cholangitis in various murine models in an organ- rather than disease-specific manner, without suppressing general or local immunity against infection or metastatic tumors. Therapeutic activity is associated with cognate TR1 cell formation and expansion, TR1 cell recruitment to the liver and draining lymph nodes, local B-regulatory cell formation and profound suppression of the pro-inflammatory capacity of liver and liver-proximal myeloid dendritic cells and Kupffer cells. Thus, autoreactivity against liver-enriched autoantigens in liver autoimmunity is not disease-specific and can be harnessed to treat various liver autoimmune diseases broadly.
The mechanism of DNA unwinding by the eukaryotic replicative helicase
Authors: Burnham Daniel R. , Kose Hazal B. , Hoyle Rebecca B. , Yardimci Hasan 
Published: May 2019

AbstractAccurate DNA replication is tightly regulated in eukaryotes to ensure genome stability during cell division and is performed by the multi-protein replisome. At the core an AAA+ hetero-hexameric complex, Mcm2-7, together with GINS and Cdc45 form the active replicative helicase Cdc45/Mcm2-7/GINS (CMG). It is not clear how this replicative ring helicase translocates on, and unwinds, DNA. We measure real-time dynamics of purified recombinantDrosophila melanogasterCMG unwinding DNA with single-molecule magnetic tweezers. Our data demonstrates that CMG exhibits a biased random walk, not the expected unidirectional motion. Through building a kinetic model we find CMG may enter up to three paused states rather than unwinding, and should these be prevented, in vivo fork rates would be recovered in vitro. We propose a mechanism in which CMG couples ATP hydrolysis to unwinding by acting as a lazy Brownian ratchet, thus providing quantitative understanding of the central process in eukaryotic DNA replication.
Critical fluctuations and slowing down of chaos
Authors: Das Moupriya , Green Jason R. 
Published: May 2019

AbstractFluids cooled to the liquid–vapor critical point develop system-spanning fluctuations in density that transform their visual appearance. Despite a rich phenomenology, however, there is not currently an explanation of the mechanical instability in the molecular motion at this critical point. Here, we couple techniques from nonlinear dynamics and statistical physics to analyze the emergence of this singular state. Numerical simulations and analytical models show how the ordering mechanisms of critical dynamics are measurable through the hierarchy of spatiotemporal Lyapunov vectors. A subset of unstable vectors soften near the critical point, with a marked suppression in their characteristic exponents that reflects a weakened sensitivity to initial conditions. Finite-time fluctuations in these exponents exhibit sharply peaked dynamical timescales and power law signatures of the critical dynamics. Collectively, these results are symptomatic of a critical slowing down of chaos that sits at the root of our statistical understanding of the liquid–vapor critical point.
Extremely stretchable and self-healing conductor based on thermoplastic elastomer for all-three-dimensional printed triboelectric nanogenerator
Authors: Parida Kaushik , Thangavel Gurunathan , Cai Guofa , Zhou Xinran , Park Sangbaek , Xiong Jiaqing , Lee Pooi See 
Published: May 2019

AbstractAdvances in next-generation soft electronic devices rely on the development of highly deformable, healable, and printable energy generators to power these electronics. Development of deformable or wearable energy generators that can simultaneously attain extreme stretchability with superior healability remains a daunting challenge. We address this issue by developing a highly conductive, extremely stretchable, and healable composite based on thermoplastic elastomer with liquid metal and silver flakes as the stretchable conductor for triboelectric nanogenerators. The elastomer is used both as the matrix for the conductor and as the triboelectric layer. The nanogenerator showed a stretchability of 2500% and it recovered its energy-harvesting performance after extreme mechanical damage, due to the supramolecular hydrogen bonding of the thermoplastic elastomer. The composite of the thermoplastic elastomer, liquid metal particles, and silver flakes exhibited an initial conductivity of 6250 S cm−1 and recovered 96.0% of its conductivity after healing.
Dissociating task acquisition from expression during learning reveals latent knowledge
Authors: Kuchibhotla Kishore V. , Hindmarsh Sten Tom , Papadoyannis Eleni S. , Elnozahy Sarah , Fogelson Kelly A. , Kumar Rupesh , Boubenec Yves , Holland Peter C. , Ostojic Srdjan , Froemke Robert C. 
Published: May 2019

AbstractPerformance on cognitive tasks during learning is used to measure knowledge, yet it remains controversial since such testing is susceptible to contextual factors. To what extent does performance during learning depend on the testing context, rather than underlying knowledge? We trained mice, rats and ferrets on a range of tasks to examine how testing context impacts the acquisition of knowledge versus its expression. We interleaved reinforced trials with probe trials in which we omitted reinforcement. Across tasks, each animal species performed remarkably better in probe trials during learning and inter-animal variability was strikingly reduced. Reinforcement feedback is thus critical for learning-related behavioral improvements but, paradoxically masks the expression of underlying knowledge. We capture these results with a network model in which learning occurs during reinforced trials while context modulates only the read-out parameters. Probing learning by omitting reinforcement thus uncovers latent knowledge and identifies context- not “smartness”- as the major source of individual variability.
Simple non-fused electron acceptors for efficient and stable organic solar cells
Authors: Yu Zhi-Peng , Liu Zhi-Xi , Chen Fang-Xiao , Qin Ran , Lau Tsz-Ki , Yin Jing-Lin , Kong Xueqian , Lu Xinhui , Shi Minmin , Li Chang-Zhi , Chen Hongzheng 
Published: May 2019

AbstractThe flexibility in structural design of organic semiconductors endows organic solar cells (OSCs) not only great function-tunabilities, but also high potential toward practical application. In this work, simple non-fused-ring electron acceptors are developed through two-step synthesis from single aromatic units for constructing efficient OSCs. With the assistance of non-covalent interactions, these rotatable non-fused acceptors (in solution) allow transiting into planar and stackable conformation in condensed solid, promoting acceptors not only feasible solution-processability, but also excellent film characteristics. As results, decent power conversion efficiencies of 10.27% and 13.97% can be achieved in single and tandem OSCs consisting of simple solution-cast blends, in which the fully unfused acceptors exhibit exceptionally low synthetic complexity index. In addition, the unfused acceptor and its based OSCs exhibit promising stabilities under continuous illumination. Overall, this work reveals valuable insights on the structural design of simple and effective electron acceptors with great practical perspectives.
Fumigation and contact activities of 18 plant essential oils on Villosiclava virens, the pathogenic fungus of rice false smut
Authors: Zheng Jingge , Liu Tingting , Guo Zhixin , Zhang Lan , Mao Liangang , Zhang Yanning , Jiang Hongyun 
Published: May 2019

AbstractRice false smut (RFS), caused by Villosiclava virens, is an emerging devastating disease of rice panicles worldwide and produces yield loss and mycotoxin residues in rice. In this study, 18 plant essential oils (PEOs) were selected to evaluate antifungal activity via fumigation and contact methods against the mycelial growth and conidial germination of V. virens. The primary compositions of PEOs with stronger fungistatic activity were analyzed using gas chromatography (GC)-mass spectrometry (MS), and the changes in the mycelial morphology were observed using scanning electron microscopy (SEM). Antifungal tests showed that cinnamon bark oil and cinnamon oil had stronger fumigation and contact effects on V. virens than the other oils tested. The primary active composition in both cinnamon bark oil and cinnamon oil was trans-cinnamaldehyde, which exhibited contact activities with EC50 values of 2.13 and 35.9 μg/mL against mycelial growth and conidial germination, respectively. The hyphae surface morphological alterations caused by cinnamon bark oil, cinnamon oil and trans-cinnamaldehyde included shriveling, vacuolation and exfoliation. In conclusion, cinnamon bark oil and cinnamon oil have the potential to prevent and control RFS, and trans-cinnamaldehyde is a promising natural lead compound for new fungicide discoveries to control RFS contamination and mycotoxin residues in rice.
Dynamics of archaeal community in soil with application of composted tannery sludge
Authors: Miranda Ana Roberta Lima , Mendes Lucas William , Lemos Leandro Nascimento , Antunes Jadson Emanuel Lopes , Amorim Marineide Rodrigues , Melo Vania Maria Maciel , de Melo Wanderley Jose , Van den Brink Paul J. , Araujo Ademir Sergio Ferreira 
Published: May 2019

AbstractApplication of composted tannery sludge (CTS) could promote a shift in the structure of soil microbial communities. Although the effect of CTS on bacterial community has been studied, it is unclear how the composition and diversity of archaeal community respond to CTS amendment and which environmental factors drive the community over time. Here, we hypothesize that the Archaea structure and composition respond to CTS amendment over the time. CTS had been previously applied annually along 6 years and this assessment occurred for 180 days following the application in the 7th year by using different rates (0, 2.5, 5, 10 and 20 ton ha−1). We used amplicon 16S rRNA sequencing to assess the changes in the structure of the archaeal community. Thaumarchaeota and Euryarchaeota were the most abundant phyla found in soils with application of CTS, with Thaumarchaeota dominating the sequences in all samples with relative abundances of >98%. We observed a decreasing trend on the archaeal diversity over the time with increasing CTS application rate, together with an increase in the community similarity. The redundancy analyses (RDA) explained 43% of the total variation in operational taxonomic units and identified Na, pH, Cr and P as the main drivers of the archaeal community over time after application of highest CTS rates. CTS application changes the structure of Archaea community, with significant increase of Thaumarchaeota and Aenigmarchaeota groups, which can be further explored for its biotechnological use in contaminated soils.
First in-situ observation of a moving natural pyroclastic density current using Doppler radar
Authors: Scharff Lea , Hort Matthias , Varley Nick R. 
Published: May 2019

AbstractPyroclastic density currents are one of the most devastating volcanic hazards. Understanding their dynamics is a key to develop successful hazard mitigation strategies. The hazard associated with pyroclastic density currents is commonly investigated a posteriori from their deposits or a priori using analogue and numerical experiments. Despite the low probability of observing a natural moving pyroclastic density current, we present the first in-situ analysis of the internal particle velocities of pyroclastic density currents at Volcán de Colima using a Doppler radar. Our data show two Vulcanian explosions, immediately followed by column collapse and a first pyroclastic density current travelling down the south flank with an average speed of 30 m/s (>50 m/s maximum speed) to a distance of 3 km from the crater rim. The direction of the pyroclastic density current coincided with that of the radar beam enabling measurement of velocity spectra (histogram of particle velocities within the radar beam). The measurement geometry enables the simultaneous measurement of the dense undercurrent at the crater rim (with <20 m/s and an increasing echo power over 20 s) and the dilute cloud higher above the topography approaching the radar (with >20 m/s and approximately constant echo power). The presented data set may be used as a benchmark for future experimental and numerical models that simulate the dynamics of pyroclastic density currents. Using the measured velocities of the collapsing column as input for numerical models will permit the validation of the models for the prediction of the true run-out distance, and thus provide valuable information for hazard assessments.
MicroRNA-126 regulates Hypoxia-Inducible Factor-1α which inhibited migration, proliferation, and angiogenesis in replicative endothelial senescence
Authors: Alique Matilde , Bodega Guillermo , Giannarelli Chiara , Carracedo Julia , Ramírez Rafael 
Published: May 2019

AbstractWhereas a healthy endothelium maintains physiological vascular functions, endothelial damage contributes to the development of cardiovascular diseases. Endothelial senescence is the main determinant of endothelial dysfunction and thus of age-related cardiovascular disease. The objective of this study is to test the involvement of microRNA-126 and HIF-1α in a model of replicative endothelial senescence and the interrelationship between both molecules in this in vitro model. We demonstrated that senescent endothelial cells experience impaired tube formation and delayed wound healing. Senescent endothelial cells failed to express HIF-1α, and the microvesicles released by these cells failed to carry HIF-1α. Of note, HIF-1α protein levels were restored in HIF-1α stabilizer-treated senescent endothelial cells. Finally, we show that microRNA-126 was downregulated in senescent endothelial cells and microvesicles. With regard to the interplay between microRNA-126 and HIF-1α, transfection with a microRNA-126 inhibitor downregulated HIF-1α expression in early passage endothelial cells. Moreover, while HIF-1α inhibition reduced tube formation and wound healing closure, microRNA-126 levels remained unchanged. These data indicate that HIF-1α is a target of miRNA-126 in protective and reparative functions, and suggest that their therapeutic modulation could benefit age-related vascular disease.
Genome-wide association study of right-sided colonic diverticulosis in a Korean population
Authors: Choe Eun Kyung , Lee Jong-Eun , Chung Su Jin , Yang Sun Young , Kim Young Sun , Shin Eun-Soon , Choi Seung Ho , Bae Jung Ho 
Published: May 2019

AbstractDiverticulosis results from complex interactions related to aging, environmental factors and genetic predisposition. Despite epidemiologic evidence of genetic risk factors, there has been no attempt to identify genes that confer susceptibility to colonic diverticulosis. We performed the first genome-wide association study (GWAS) on susceptibility to diverticulosis in a Korean population. A GWAS was carried out in 7,948 healthy individuals: 893 patients and 1,075 controls comprised the test set, and 346 patients and 305 controls comprised the replication set. Diverticulosis was diagnosed by colonoscopy during comprehensive medical check-ups, and single-nucleotide polymorphisms (SNPs) related to diverticulosis were detected with the Affymetrix Axiom KORV1.1-96 Array. In all, 9 SNPs were identified in three SNP aggregates in the test set (P < 10−3, within 200 kb) after adjusting for sex. All the SNPs were replicated in the replication set (P < 0.05). Three SNPs were near the WNT4 gene, four near the RHOU gene, and two in the OAS1/3 genes. The top SNP associated with right-sided colonic diverticulosis was rs22538787, located near the WNT4 gene [combined set, P-value = 3.128 × 10−6, odds ratio = 1.415 (95% confidence interval: 1.223–1.637)]. These 9 novel SNP alleles associated with the WNT4, RHOU, and OAS1/3 genes are possibly involved in the underlying genetic susceptibility to right-sided diverticulosis. Our results provide basic knowledge about the development of diverticulosis in an Asian population.
DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks
Authors: Sureyya Rifaioglu Ahmet , Doğan Tunca , Jesus Martin Maria , Cetin-Atalay Rengul , Atalay Volkan 
Published: May 2019

AbstractAutomated protein function prediction is critical for the annotation of uncharacterized protein sequences, where accurate prediction methods are still required. Recently, deep learning based methods have outperformed conventional algorithms in computer vision and natural language processing due to the prevention of overfitting and efficient training. Here, we propose DEEPred, a hierarchical stack of multi-task feed-forward deep neural networks, as a solution to Gene Ontology (GO) based protein function prediction. DEEPred was optimized through rigorous hyper-parameter tests, and benchmarked using three types of protein descriptors, training datasets with varying sizes and GO terms form different levels. Furthermore, in order to explore how training with larger but potentially noisy data would change the performance, electronically made GO annotations were also included in the training process. The overall predictive performance of DEEPred was assessed using CAFA2 and CAFA3 challenge datasets, in comparison with the state-of-the-art protein function prediction methods. Finally, we evaluated selected novel annotations produced by DEEPred with a literature-based case study considering the ‘biofilm formation process’ in Pseudomonas aeruginosa. This study reports that deep learning algorithms have significant potential in protein function prediction; particularly when the source data is large. The neural network architecture of DEEPred can also be applied to the prediction of the other types of ontological associations. The source code and all datasets used in this study are available at: https://github.com/cansyl/DEEPred.
Tailoring optical properties and stimulated emission in nanostructured polythiophene
Authors: Portone Alberto , Ganzer Lucia , Branchi Federico , Ramos Rodrigo , Caldas Marília J. , Pisignano Dario , Molinari Elisa , Cerullo Giulio , Persano Luana , Prezzi Deborah , Virgili Tersilla 
Published: May 2019

AbstractPolythiophenes are the most widely utilized semiconducting polymers in organic electronics, but they are scarcely exploited in photonics due to their high photo-induced absorption caused by interchain polaron pairs, which prevents the establishment of a window of net optical gain. Here we study the photophysics of poly(3-hexylthiophene) configured with different degrees of supramolecular ordering, spin-coated thin films and templated nanowires, and find marked differences in their optical properties. Transient absorption measurements evidence a partially-polarized stimulated emission band in the nanowire samples, in contrast with the photo-induced absorption band observed in spin-coated thin films. In combination with theoretical modeling, our experimental results reveal the origin of the primary photoexcitations dominating the dynamics for different supramolecular ordering, with singlet excitons in the nanostructured samples superseding the presence of polaron pairs, which are present in the disordered films. Our approach demonstrates a viable strategy to direct optical properties through structural control, and the observation of optical gain opens the possibility to the use of polythiophene nanostructures as building blocks of organic optical amplifiers and active photonic devices.