bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atmospheric Modeling of 137Cs Plumes From the Fukushima Daiichi Nuclear Power Plant—Evaluation of the Model Intercomparison Data of the Science Council of Japan
Authors: Kitayama K. , Morino Y. , Takigawa M. , Nakajima T. , Hayami H. , Nagai H. , Terada H. , Saito K. , Shimbori T. , Kajino M. , Sekiyama T. T. , Didier D. , Mathieu A. , Quélo D. , Ohara T. , Tsuruta H. , Oura Y. , Ebihara M. , Moriguchi Y. , Shibata T. 
Published: July 2018

AbstractSince the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident in March 2011, atmospheric simulation models have improved our understanding of the atmospheric behavior of radionuclides. Model intercomparisons provide valuable and useful information for evaluating the validity and variability of individual model results. In this study, we compared results of seven atmospheric transport models used to simulate 137Cs released from the FDNPP to the atmosphere. All model results used in this analysis had been submitted for a model intercomparison project of the Science Council of Japan (2014, http://www.scj.go.jp/en/report/index.html). Here we assessed model performance by comparing model results with observed hourly atmospheric concentrations of 137Cs, with a particular focus on nine plumes over the Tohoku and Kanto regions. The intercomparison results showed that model performance in reproducing 137Cs concentrations was highly variable among different models and plumes. In general, models better reproduced plumes that passed over many observation stations. The performance among the models was consistent with the simulated wind fields and the source terms used. We also assessed model performance in relation to accumulated 137Cs deposition. Simulated areas of high 137Cs deposition were consistent with the simulated 137Cs plume pathways, though the models that best simulated atmospheric 137Cs concentrations were different from those that best simulated deposition. The ensemble mean of all models consistently reproduced atmospheric 137Cs concentrations and deposition well, suggesting that use of a multimodel ensemble results in more effective and consistent model performance.
Microfluidic-based flexible reflective multicolor display
Authors: Kobayashi Kazuhiro , Onoe Hiroaki 
Published: July 2018

AbstractThis paper describes a microfluidic-based flexible reflective display constructed using dyed water droplets and air gaps as pixel elements. Our display is composed of a flexible polydimethylsiloxane sheet with a connected pixel-patterned microchannel. Several types of dyed water droplets and air gaps are sequentially introduced to the microchannel through a suction process to display a multicolor image. The displayed image is stable and can be retained without an energy supply. To ensure that images are displayed correctly, the geometric parameters of the dot pixel design and minimum differential pressure necessary to drive the water droplets are evaluated. As a demonstration, we successfully display three-color dot-matrix reflective images and bitmap characters in the microchannel. Our proposed method can be applied to energy-less and color-changeable displays for use in future daily-life accessories, such as bags, shoes, and clothes, and can change the surface color and pattern of these accessories.
Network-based approach to prediction and population-based validation of in silico drug repurposing
Authors: Cheng Feixiong , Desai Rishi J. , Handy Diane E. , Wang Ruisheng , Schneeweiss Sebastian , Barabási Albert-László , Loscalzo Joseph 
Published: July 2018

AbstractHere we identify hundreds of new drug-disease associations for over 900 FDA-approved drugs by quantifying the network proximity of disease genes and drug targets in the human (protein–protein) interactome. We select four network-predicted associations to test their causal relationship using large healthcare databases with over 220 million patients and state-of-the-art pharmacoepidemiologic analyses. Using propensity score matching, two of four network-based predictions are validated in patient-level data: carbamazepine is associated with an increased risk of coronary artery disease (CAD) [hazard ratio (HR) 1.56, 95% confidence interval (CI) 1.12–2.18], and hydroxychloroquine is associated with a decreased risk of CAD (HR 0.76, 95% CI 0.59–0.97). In vitro experiments show that hydroxychloroquine attenuates pro-inflammatory cytokine-mediated activation in human aortic endothelial cells, supporting mechanistically its potential beneficial effect in CAD. In summary, we demonstrate that a unique integration of protein-protein interaction network proximity and large-scale patient-level longitudinal data complemented by mechanistic in vitro studies can facilitate drug repurposing.
Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR
Authors: Wang Jiaxu , Yuan Zenglin , Cui Yaqi , Xie Rong , Yang Guang , Kassab Muzaffer A. , Wang Mengxi , Ma Yinliang , Wu Chen , Yu Xiaochun , Liu Xiuhua 
Published: July 2018

Abstract53BP1 performs essential functions in DNA double-strand break (DSB) repair and it was recently reported that Tudor interacting repair regulator (TIRR) negatively regulates 53BP1 during DSB repair. Here, we present the crystal structure of the 53BP1 tandem Tudor domain (TTD) in complex with TIRR. Our results show that three loops from TIRR interact with 53BP1 TTD and mask the methylated lysine-binding pocket in TTD. Thus, TIRR competes with histone H4K20 methylation for 53BP1 binding. We map key interaction residues in 53BP1 TTD and TIRR, whose mutation abolishes complex formation. Moreover, TIRR suppresses the relocation of 53BP1 to DNA lesions and 53BP1-dependent DNA damage repair. Finally, despite the high-sequence homology between TIRR and NUDT16, NUDT16 does not directly interact with 53BP1 due to the absence of key residues required for binding. Taken together, our study provides insights into the molecular mechanism underlying TIRR-mediated suppression of 53BP1-dependent DNA damage repair.
An account of solvent accessibility in protein-RNA recognition
Authors: Mukherjee Sunandan , Bahadur Ranjit Prasad 
Published: July 2018

AbstractProtein–RNA recognition often induces conformational changes in binding partners. Consequently, the solvent accessible surface area (SASA) buried in contact estimated from the co-crystal structures may differ from that calculated using their unbound forms. To evaluate the change in accessibility upon binding, we compare SASA of 126 protein-RNA complexes between bound and unbound forms. We observe, in majority of cases the interface of both the binding partners gain accessibility upon binding, which is often associated with either large domain movements or secondary structural transitions in RNA-binding proteins (RBPs), and binding-induced conformational changes in RNAs. At the non-interface region, majority of RNAs lose accessibility upon binding, however, no such preference is observed for RBPs. Side chains of RBPs have major contribution in change in accessibility. In case of flexible binding, we find a moderate correlation between the binding free energy and change in accessibility at the interface. Finally, we introduce a parameter, the ratio of gain to loss of accessibility upon binding, which can be used to identify the native solution among the flexible docking models. Our findings provide fundamental insights into the relationship between flexibility and solvent accessibility, and advance our understanding on binding induced folding in protein-RNA recognition.
Novel Interplay Between Smad1 and Smad3 Phosphorylation via AGE Regulates the Progression of Diabetic Nephropathy
Authors: Ono Hiroyuki , Abe Hideharu , Sakurai Akiko , Ochi Arisa , Tominaga Tatsuya , Tamaki Masanori , Kishi Seiji , Murakami Taichi , Nagai Kojiro , Kohashi Masayuki , Doi Toshio 
Published: July 2018

AbstractDiabetic nephropathy (DN) is the major cause of end-stage renal failure and is associated with increased morbidity and mortality compared with other causes of renal diseases. We previously found that Smad1 plays a critical role in the development of DN both in vitro and in vivo. However, functional interaction between Smad1 and Smad3 signaling in DN is unclear. Here, we addressed the molecular interplay between Smad1 and Smad3 signaling under a diabetic condition by using Smad3-knockout diabetic mice. Extracellular matrix (ECM) protein overexpression and Smad1 activation were observed in the glomeruli of db/db mice but were suppressed in the glomeruli of Smad3+/−; db/db mice. Smad3 activation enhanced the phosphorylation of Smad1 C-terminal domain but decreased the phosphorylation of linker domain, thus regulating Smad1 activation in advanced glycation end product-treated mesangial cells (MCs). However, forced phosphorylation of the Smad1 linker domain did not affect Smad3 activation in MCs. Phosphorylation of the Smad1 linker domain increased in Smad3+/−; db/db mice and probucol-treated db/db mice, which was consistent with the attenuation of ECM overproduction. These results indicate that Smad3 expression and activation or probucol treatment alters Smad1 phosphorylation, thus suggesting new molecular mechanisms underlying DN development and progression.
Switchable plasmonic routers controlled by external magnetic fields by using magneto-plasmonic waveguides
Authors: Ho Kum-Song , Im Song-Jin , Pae Ji-Song , Ri Chol-Song , Han Yong-Ha , Herrmann Joachim 
Published: July 2018

AbstractWe analytically and numerically investigate magneto-plasmons in metal films surrounded by a ferromagnetic dielectric. In such waveguide using a metal film with a thickness exceeding the Skin depth, an external magnetic field in the transverse direction can induce a significant spatial asymmetry of mode distribution. Superposition of the odd and the even asymmetric modes over a distance leads to a concentration of the energy on one interface which is switched to the other interface by the magnetic field reversal. The requested magnitude of magnetization is exponentially reduced with the increase of the metal film thickness. Based on this phenomenon, we propose a waveguide-integrated magnetically controlled switchable plasmonic routers with 99-%-high contrast within the optical bandwidth of tens of THz. This configuration can also operate as a magneto-plasmonic modulator.
Wnt4 is significantly upregulated during the early phases of cisplatin-induced acute kidney injury
Authors: He Yi-Xin , Diao Tian-Tian , Song Shu-Min , Wang Cen-Cen , Wang Yu , Zhou Chun-Lan , Bai Yi-Bing , Yu Shan-Shen , Mi Xuan , Yang Xin-Yu , Wei Qiu-Ju , Li Bing 
Published: July 2018

AbstractWnt4 is a secreted growth factor associated with renal tubulogenesis. Our previous studies identified that renal and urinary Wnt4 are upregulated following ischemia-reperfusion injury in mice, but the roles of Wnt4 in other forms of acute kidney injury (AKI) remain unclear. Here, we investigated the changes in Wnt4 expression using a cisplatin-induced AKI model. We found that renal and urinary Wnt4 expression increased as early as 12 hours, peaked at day 4 following cisplatin-induced AKI and was closely correlated with histopathological alterations. By contrast, the serum creatinine level was significantly elevated until day 3, indicating that Wnt4 is more sensitive to early tubular injury than serum creatinine. In addition, renal Wnt4 was co-stained with aquaporin-1 and thiazide-sensitive NaCl cotransporter, suggesting that Wnt4 can detect both proximal and distal tubular injuries. These data were further confirmed in a clinical study. Increased urinary Wnt4 expression was detected earlier than serum creatinine and eGFR in patients with contrast-induced AKI after vascular intervention. This study is the first to demonstrate that increased expression of renal and urinary Wnt4 can be detected earlier than serum creatinine after drug-induced AKI. In particular, urinary Wnt4 can potentially serve as a noninvasive biomarker for monitoring patients with tubular injury.
Enhancing the systems productivity and water use efficiency through coordinated soil water sharing and compensation in strip-intercropping
Authors: Chen Guodong , Kong Xuefu , Gan Yantai , Zhang Renzhi , Feng Fuxue , Yu Aizhong , Zhao Cai , Wan Sumei , Chai Qiang 
Published: July 2018

AbstractIn arid areas, water shortage is threating agricultural sustainability, and strip-intercropping may serve as a strategy to alleviate the challenge. Here we show that strip-intercropping enhances the spatial distributions of soil water across the 0–110 cm rooting zones, improves the coordination of soil water sharing during the co-growth period, and provides compensatory effect for available soil water. In a three-year (2009–2011) experiment, shorter-season pea (Pisum sativum L.) was sown in alternate strips with longer-season maize (Zea mays L.) without or with an artificially-inserted root barrier (a solid plastic sheet) between the strips. The intercropped pea used soil water mostly in the top 20-cm layers, whereas maize plants were able to absorb water from deeper-layers of the neighboring pea strips. After pea harvest, the intercropped maize obtained compensatory soil water from the pea strips. The pea-maize intercropping without the root barrier increased grain yield by 25% and enhanced water use efficiency by 24% compared with the intercropping with the root barrier. The improvement in crop yield and water use efficiency was partly attributable to the coordinated soil water sharing between the inter-strips and the compensatory effect from the early-maturing pea to the late-maturing maize.
Microemulsion formulation of a new biopesticide to control the diamondback moth (Lepidoptera: Plutellidae)
Authors: Shao Hainan , Xi Na , Zhang Yalin 
Published: July 2018

AbstractThis study was designed to develop a microemulsion formulation of norcantharidin for the control of the diamondback moth (DBM), Plutella xylostella (Linnaeus), a notorious pest of brassica crops worldwide. The oil phase was screened and selected based on norcantharidin solubility while the surfactants were selected on the basis of their efficiency to form microemulsion. Optimized batches were selected using pseudo ternary phase diagrams. The microemulsion system were stabilized using mixtures composed of norcantharidin, surfactants (Tx13 and Tw80), and cosurfactant (ethanol). Its physicochemical characteristics were also demonstrated to have a higher cloud point than 72 °C as well as good thermodynamic and dilution stability. In additon, a subsequent insecticidal bioassay indicated that the acute LC50 for norcantharidin microemulsion to P. xylostella was estimated to be 12.477 mg/L (11.58–13.41, 95% CL). Our results provide an environment-friendly promising alternative to control P. xylostella and possibly contribute to ameliorating any pesticide resistance in P. xylostella.
Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana
Authors: Koester Julie A. , Berthiaume Chris T. , Hiranuma Naozumi , Parker Micaela S. , Iverson Vaughn , Morales Rhonda , Ruzzo Walter L. , Armbrust E. Virginia 
Published: July 2018

AbstractSexual reproduction roots the eukaryotic tree of life, although its loss occurs across diverse taxa. Asexual reproduction and clonal lineages persist in these taxa despite theoretical arguments suggesting that individual clones should be evolutionarily short-lived due to limited phenotypic diversity. Here, we present quantitative evidence that an obligate asexual lineage emerged from a sexual population of the marine diatom Thalassiosira pseudonana and rapidly expanded throughout the world’s oceans. Whole genome comparisons identified two lineages with characteristics expected of sexually reproducing strains in Hardy-Weinberg equilibrium. A third lineage displays genomic signatures for the functional loss of sexual reproduction followed by a recent global colonization by a single ancestral genotype. Extant members of this lineage are genetically differentiated and phenotypically plastic, potentially allowing for rapid adaptation when they are challenged by natural selection. Such mechanisms may be expected to generate new clones within marginal populations of additional unicellular species, facilitating the exploration and colonization of novel environments, aided by exponential growth and ease of dispersal.
Tunable double-Weyl Fermion semimetal state in the SrSi2 materials class
Authors: Singh Bahadur , Chang Guoqing , Chang Tay-Rong , Huang Shin-Ming , Su Chenliang , Lin Ming-Chieh , Lin Hsin , Bansil Arun 
Published: July 2018

AbstractWe discuss first-principles topological electronic structure of noncentrosymmetric SrSi2 materials class based on the hybrid exchange-correlation functional. Topological phase diagram of SrSi2 is mapped out as a function of the lattice constant with focus on the semimetal order. A tunable double-Weyl Fermion state in Sr1−xCaxSi2 and Sr1−xBaxSi2 alloys is identified. Ca doping in SrSi2 is shown to yield a double-Weyl semimetal with a large Fermi arc length, while Ba doping leads to a transition from the topological semimetal to a gapped insulator state. Our study indicates that SrSi2 materials family could provide an interesting platform for accessing the unique topological properties of Weyl semimetals.
Reference values for white blood-cell-based inflammatory markers in the Rotterdam Study: a population-based prospective cohort study
Authors: Fest Jesse , Ruiter Rikje , Ikram M. Arfan , Voortman Trudy , van Eijck Casper H. J. , Stricker Bruno H. 
Published: July 2018

AbstractNovel prognostic inflammatory markers of cancer survival and cardiovascular disease are; the neutrophil-to-lymphocyte ratio (NLR), the platelet-to-lymphocyte ratio (PLR) and the systemic immune-inflammation index (SII). As normal values for these markers are unknown, our objective was to obtain reference values in the general population. We obtained data from a population-based prospective cohort study of individuals aged 45 years and over between 2002 and 2014. Absolute blood counts were used to calculate the NLR, PLR and SII. All inflammatory indices followed a log-normal distribution. We calculated the mean and 95% reference intervals in an unselected population. Furthermore we studied whether the inflammatory markers differed between age categories and gender. In total 8,711 participants (57.1% female; mean age 65.9 years, standard deviation 10.5 years) were included. Mean values and corresponding 95% reference intervals for the NLR were: 1.76 (0.83–3.92), for PLR: 120 (61–239) and for SII: 459 (189–1168). The inflammatory markers increased with age. The PLR and SII were higher in females, whilst the NLR was higher in males. In conclusion, we provided reference values for new inflammatory markers. All increase with age and vary with gender. This provides context that allows for proper interpretation of their potential value in future clinical practice and research.
High speed error correction for continuous-variable quantum key distribution with multi-edge type LDPC code
Authors: Wang Xiangyu , Zhang Yichen , Yu Song , Guo Hong 
Published: July 2018

AbstractError correction is a significant step in postprocessing of continuous-variable quantum key distribution system, which is used to make two distant legitimate parties share identical corrected keys. We propose an experiment demonstration of high speed error correction with multi-edge type low-density parity check (MET-LDPC) codes based on graphic processing unit (GPU). GPU supports to calculate the messages of MET-LDPC codes simultaneously and decode multiple codewords in parallel. We optimize the memory structure of parity check matrix and the belief propagation decoding algorithm to reduce computational complexity. Our results show that GPU-based decoding algorithm greatly improves the error correction speed. For the three typical code rate, i.e., 0.1, 0.05 and 0.02, when the block length is 106 and the iteration number are 100, 150 and 200, the average error correction speed can be respectively achieved to 30.39 Mbits/s (over three times faster than previous demonstrations), 21.23 Mbits/s and 16.41 Mbits/s with 64 codewords decoding in parallel, which supports high-speed real-time continuous-variable quantum key distribution system.
The tomato subtilase family includes several cell death-related proteinases with caspase specificity
Authors: Reichardt Sven , Repper Dagmar , Tuzhikov Alexander I. , Galiullina Raisa A. , Planas-Marquès Marc , Chichkova Nina V. , Vartapetian Andrey B. , Stintzi Annick , Schaller Andreas 
Published: July 2018

AbstractPhytaspases are Asp-specific subtilisin-like plant proteases that have been likened to animal caspases with respect to their regulatory function in programmed cell death (PCD). We identified twelve putative phytaspase genes in tomato that differed widely in expression level and tissue-specific expression patterns. Most phytaspase genes are tandemly arranged on tomato chromosomes one, four, and eight, and many belong to taxon-specific clades, e.g. the P69 clade in the nightshade family, suggesting that these genes evolved by gene duplication after speciation. Five tomato phytaspases (SlPhyts) were expressed in N. benthamiana and purified to homogeneity. Substrate specificity was analyzed in a proteomics assay and with a panel of fluorogenic peptide substrates. Similar to animal caspases, SlPhyts recognized an extended sequence motif including Asp at the cleavage site. Clear differences in cleavage site preference were observed implying different substrates in vivo and, consequently, different physiological functions. A caspase-like function in PCD was confirmed for five of the seven tested phytaspases. Cell death was triggered by ectopic expression of SlPhyts 2, 3, 4, 5, 6 in tomato leaves by agro-infiltration, as well as in stably transformed transgenic tomato plants. SlPhyts 3, 4, and 5 were found to contribute to cell death under oxidative stress conditions.
Acoustic Complexity of vocal fish communities: a field and controlled validation
Authors: Bolgan Marta , Amorim M. Clara P. , Fonseca Paulo J. , Di Iorio Lucia , Parmentier Eric 
Published: July 2018

AbstractThe Acoustic Complexity Index (ACI) is increasingly applied to the study of biodiversity in aquatic habitats. However, it remains unknown which types of acoustic information are highlighted by this index in underwater environments. This study explored the robustness of the ACI to fine variations in fish sound abundance (i.e. number of sounds) and sound diversity (i.e. number of sound types) in field recordings and controlled experiments. The ACI was found to be sensitive to variations in both sound abundance and sound diversity, making it difficult to discern between these variables. Furthermore, the ACI was strongly dependent on the settings used for its calculation (i.e. frequency and temporal resolution of the ACI algorithm, amplitude filter). Care should thus be taken when comparing ACI absolute values between studies, or between sites with site-specific characteristics (e.g. species diversity, fish vocal community composition). As the use of ecoacoustic indices presents a promising tool for the monitoring of vulnerable environments, methodological validations like those presented in this paper are of paramount importance in understanding which biologically important information can be gathered by applying acoustic indices to Passive Acoustic Monitoring data.