bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Interesting Objects in Large Spectral Surveys Using Highly Parallelized Machine Learning
Authors: Škoda Petr , Palička Andrej , Koza Jakub , Shakurova Ksenia
Published: May 2017

The current archives of LAMOST multi-object spectrograph contain millions of fully reduced spectra, from which the automatic pipelines have produced catalogues of many parameters of individual objects, including their approximate spectral classification. This is, however, mostly based on the global shape of the whole spectrum and on integral properties of spectra in given bandpasses, namely presence and equivalent width of prominent spectral lines, while for identification of some interesting object types (e.g. Be stars or quasars) the detailed shape of only a few lines is crucial. Here the machine learning is bringing a new methodology capable of improving the reliability of classification of such objects even in boundary cases.

We present results of Spark-based semi-supervised machine learning of LAMOST spectra attempting to automatically identify the single and double-peak emission of Hα line typical for Be and B[e] stars. The labelled sample was obtained from archive of 2m Perek telescope at Ondřejov observatory. A simple physical model of spectrograph resolution was used in domain adaptation to LAMOST training domain. The resulting list of candidates contains dozens of Be stars (some are likely yet unknown), but also a bunch of interesting objects resembling spectra of quasars and even blazars, as well as many instrumental artefacts. The verification of a nature of interesting candidates benefited considerably from cross-matching and visualisation in the Virtual Observatory environment.
Detection of quasars in the time domain
Authors: Graham Matthew J. , Djorgovski S. G. , Stern Daniel J. , Drake Andrew , Mahabal Ashish
Published: May 2017

The time domain is the emerging forefront of astronomical research with new facilities and instruments providing unprecedented amounts of data on the temporal behavior of astrophysical populations. Dealing with the size and complexity of this requires new techniques and methodologies. Quasars are an ideal work set for developing and applying these: they vary in a detectable but not easily quantifiable manner whose physical origins are poorly understood. In this paper, we will review how quasars are identified by their variability and how these techniques can be improved, what physical insights into their variability can be gained from studying extreme examples of variability, and what approaches can be taken to increase the number of quasars known. These will demonstrate how astroinformatics is essential to discovering and understanding this important population.
Deep data: discovery and visualization Application to hyperspectral ALMA imagery
Authors: Merényi Erzsébet , Taylor Joshua , Isella Andrea
Published: May 2017

Leading-edge telescopes such as the Atacama Large Millimeter and sub-millimeter Array (ALMA), and near-future ones, are capable of imaging the same sky area at hundreds-to-thousands of frequencies with both high spectral and spatial resolution. This provides unprecedented opportunities for discovery about the spatial, kinematical and compositional structure of sources such as molecular clouds or protoplanetary disks, and more. However, in addition to enormous volume, the data also exhibit unprecedented complexity, mandating new approaches for extracting and summarizing relevant information. Traditional techniques such as examining images at selected frequencies become intractable while tools that integrate data across frequencies or pixels (like moment maps) can no longer fully exploit and visualize the rich information. We present a neural map-based machine learning approach that can handle all spectral channels simultaneously, utilizing the full depth of these data for discovery and visualization of spectrally homogeneous spatial regions (spectral clusters) that characterize distinct kinematic behaviors. We demonstrate the effectiveness on an ALMA image cube of the protoplanetary disk HD142527. The tools we collectively name “NeuroScope” are efficient for “Big Data” due to intelligent data summarization that results in significant sparsity and noise reduction. We also demonstrate a new approach to automate our clustering for fast distillation of large data cubes.
Supercomputer simulations of structure formation in the Universe
Authors: Ishiyama Tomoaki
Published: May 2017

We describe the implementation and performance results of our massively parallel MPI†/OpenMP‡ hybrid TreePM code for large-scale cosmological N-body simulations. For domain decomposition, a recursive multi-section algorithm is used and the size of domains are automatically set so that the total calculation time is the same for all processes. We developed a highly-tuned gravity kernel for short-range forces, and a novel communication algorithm for long-range forces. For two trillion particles benchmark simulation, the average performance on the fullsystem of K computer (82,944 nodes, the total number of core is 663,552) is 5.8 Pflops, which corresponds to 55% of the peak speed.
Deep learning for studies of galaxy morphology
Authors: Tuccillo D. , Huertas-Company M. , Decencière E. , Velasco-Forero S.
Published: May 2017

Establishing accurate morphological measurements of galaxies in a reasonable amount of time for future big-data surveys such as EUCLID, the Large Synoptic Survey Telescope or the Wide Field Infrared Survey Telescope is a challenge. Because of its high level of abstraction with little human intervention, deep learning appears to be a promising approach. Deep learning is a rapidly growing discipline that models high-level patterns in data as complex multilayered networks. In this work we test the ability of deep convolutional networks to provide parametric properties of Hubble Space Telescope like galaxies (half-light radii, Sérsic indices, total flux etc..). We simulate a set of galaxies including point spread function and realistic noise from the CANDELS survey and try to recover the main galaxy parameters using deep-learning. We compare the results with the ones obtained with the commonly used profile fitting based software GALFIT. This way showing that with our method we obtain results at least equally good as the ones obtained with GALFIT but, once trained, with a factor 5 hundred time faster.
Cooperative photometric redshift estimation
Authors: Cavuoti S. , Tortora C. , Brescia M. , Longo G. , Radovich M. , Napolitano N. R. , Amaro V. , Vellucci C.
Published: May 2017

In the modern galaxy surveys photometric redshifts play a central role in a broad range of studies, from gravitational lensing and dark matter distribution to galaxy evolution. Using a dataset of ~ 25,000 galaxies from the second data release of the Kilo Degree Survey (KiDS) we obtain photometric redshifts with five different methods: (i) Random forest, (ii) Multi Layer Perceptron with Quasi Newton Algorithm, (iii) Multi Layer Perceptron with an optimization network based on the Levenberg-Marquardt learning rule, (iv) the Bayesian Photometric Redshift model (or BPZ) and (v) a classical SED template fitting procedure (Le Phare). We show how SED fitting techniques could provide useful information on the galaxy spectral type which can be used to improve the capability of machine learning methods constraining systematic errors and reduce the occurrence of catastrophic outliers. We use such classification to train specialized regression estimators, by demonstrating that such hybrid approach, involving SED fitting and machine learning in a single collaborative framework, is capable to improve the overall prediction accuracy of photometric redshifts.
The Euclid Data Processing Challenges
Authors: Dubath Pierre , Apostolakos Nikolaos , Bonchi Andrea , Belikov Andrey , Brescia Massimo , Cavuoti Stefano , Capak Peter , Coupon Jean , Dabin Christophe , Degaudenzi Hubert , Desai Shantanu , Dubath Florian , Fontana Adriano , Fotopoulou Sotiria , Frailis Marco , Galametz Audrey , Hoar John , Holliman Mark , Hoyle Ben , Hudelot Patrick , Ilbert Olivier , Kuemmel Martin , Melchior Martin , Mellier Yannick , Mohr Joe , Morisset Nicolas , Paltani Stéphane , Pello Roser , Pilo Stefano , Polenta Gianluca , Poncet Maurice , Saglia Roberto , Salvato Mara , Sauvage Marc , Schefer Marc , Serrano Santiago , Soldati Marco , Tramacere Andrea , Williams Rees , Zacchei Andrea
Published: May 2017

Euclid is a Europe-led cosmology space mission dedicated to a visible and near infrared survey of the entire extra-galactic sky. Its purpose is to deepen our knowledge of the dark content of our Universe. After an overview of the Euclid mission and science, this contribution describes how the community is getting organized to face the data analysis challenges, both in software development and in operational data processing matters. It ends with a more specific account of some of the main contributions of the Swiss Science Data Center (SDC-CH).
Hierarchical Matching and Regression with Application to Photometric Redshift Estimation
Authors: Murtagh Fionn
Published: May 2017

This work emphasizes that heterogeneity, diversity, discontinuity, and discreteness in data is to be exploited in classification and regression problems. A global a priori model may not be desirable. For data analytics in cosmology, this is motivated by the variety of cosmological objects such as elliptical, spiral, active, and merging galaxies at a wide range of redshifts. Our aim is matching and similarity-based analytics that takes account of discrete relationships in the data. The information structure of the data is represented by a hierarchy or tree where the branch structure, rather than just the proximity, is important. The representation is related to p-adic number theory. The clustering or binning of the data values, related to the precision of the measurements, has a central role in this methodology. If used for regression, our approach is a method of cluster-wise regression, generalizing nearest neighbour regression. Both to exemplify this analytics approach, and to demonstrate computational benefits, we address the well-known photometric redshift or ‘photo-z’ problem, seeking to match Sloan Digital Sky Survey (SDSS) spectroscopic and photometric redshifts.
METAPHOR: Probability density estimation for machine learning based photometric redshifts
Authors: Amaro V. , Cavuoti S. , Brescia M. , Vellucci C. , Tortora C. , Longo G.
Published: May 2017

We present METAPHOR (Machine-learning Estimation Tool for Accurate PHOtometric Redshifts), a method able to provide a reliable PDF for photometric galaxy redshifts estimated through empirical techniques. METAPHOR is a modular workflow, mainly based on the MLPQNA neural network as internal engine to derive photometric galaxy redshifts, but giving the possibility to easily replace MLPQNA with any other method to predict photo-z’s and their PDF. We present here the results about a validation test of the workflow on the galaxies from SDSS-DR9, showing also the universality of the method by replacing MLPQNA with KNN and Random Forest models. The validation test include also a comparison with the PDF’s derived from a traditional SED template fitting method (Le Phare).
Morphogenesis of liquid crystal topological defects during the nematic-smectic A phase transition
Authors: Gim Min-Jun , Beller Daniel A. , Yoon Dong Ki
Published: May 2017

The liquid crystalline phases of matter each possess distinct types of defects that have drawn great interest in areas such as topology, self-assembly and material micropatterning. However, relatively little is known about how defects in one liquid crystalline phase arise from defects or deformations in another phase upon crossing a phase transition. Here, we directly examine defects in the in situ thermal phase transition from nematic to smectic A in hybrid-aligned liquid crystal droplets on water substrates, using experimental, theoretical and numerical analyses. The hybrid-aligned nematic droplet spontaneously generates boojum defects. During cooling, toric focal conic domains arise through a sequence of morphological transformations involving nematic stripes and locally aligned focal conic domains. This simple experiment reveals a surprisingly complex pathway by which very different types of defects may be related across the nematic–smectic A phase transition, and presents new possibilities for controlled deformation and patterning of liquid crystals.
Leukocyte integrin Mac-1 regulates thrombosis via interaction with platelet GPIbα
Authors: Wang Yunmei , Gao Huiyun , Shi Can , Erhardt Paul W. , Pavlovsky Alexander , A. Soloviev Dmitry , Bledzka Kamila , Ustinov Valentin , Zhu Liang , Qin Jun , Munday Adam D. , Lopez Jose , Plow Edward , Simon Daniel I.
Published: May 2017

Inflammation and thrombosis occur together in many diseases. The leukocyte integrin Mac-1 (also known as integrin αMβ2, or CD11b/CD18) is crucial for leukocyte recruitment to the endothelium, and Mac-1 engagement of platelet GPIbα is required for injury responses in diverse disease models. However, the role of Mac-1 in thrombosis is undefined. Here we report that mice with Mac-1 deficiency (Mac-1−/−) or mutation of the Mac-1-binding site for GPIbα have delayed thrombosis after carotid artery and cremaster microvascular injury without affecting parameters of haemostasis. Adoptive wild-type leukocyte transfer rescues the thrombosis defect in Mac-1−/− mice, and Mac-1-dependent regulation of the transcription factor Foxp1 contributes to thrombosis as evidenced by delayed thrombosis in mice with monocyte-/macrophage-specific overexpression of Foxp1. Antibody and small-molecule targeting of Mac-1:GPIbα inhibits thrombosis. Our data identify a new pathway of thrombosis involving leukocyte Mac-1 and platelet GPIbα, and suggest that targeting this interaction has anti-thrombotic therapeutic potential with reduced bleeding risk.
Electric field imaging of single atoms
Authors: Shibata Naoya , Seki Takehito , Sánchez-Santolino Gabriel , Findlay Scott D. , Kohno Yuji , Matsumoto Takao , Ishikawa Ryo , Ikuhara Yuichi
Published: May 2017

In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures.
Modelling the role of groundwater hydro-refugia in East African hominin evolution and dispersal
Authors: Cuthbert M. O. , Gleeson T. , Reynolds S. C. , Bennett M. R. , Newton A. C. , McCormack C. J. , Ashley G. M.
Published: May 2017

Water is a fundamental resource, yet its spatiotemporal availability in East Africa is poorly understood. This is the area where most hominin first occurrences are located, and consequently the potential role of water in hominin evolution and dispersal remains unresolved. Here, we show that hundreds of springs currently distributed across East Africa could function as persistent groundwater hydro-refugia through orbital-scale climate cycles. Groundwater buffers climate variability according to spatially variable groundwater response times determined by geology and topography. Using an agent-based model, grounded on the present day landscape, we show that groundwater availability would have been critical to supporting isolated networks of hydro-refugia during dry periods when potable surface water was scarce. This may have facilitated unexpected variations in isolation and dispersal of hominin populations in the past. Our results therefore provide a new environmental framework in which to understand how patterns of taxonomic diversity in hominins may have developed.
Next-generation mammalian genetics toward organism-level systems biology
Authors: Susaki Etsuo A. , Ukai Hideki , Ueda Hiroki R.
Published: May 2017

Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.
Curing the Toxicity of Multi-Walled Carbon Nanotubes through Native Small-molecule Drugs
Authors: Qi Wei , Tian Longlong , An Wenzhen , Wu Qiang , Liu Jianli , Jiang Can , Yang Jun , Tang Bing , Zhang Yafeng , Xie Kangjun , Wang Xinling , Li Zhan , Wu Wangsuo
Published: May 2017

With the development and application of nanotechnology, large amounts of nanoparticles will be potentially released to the environment and possibly cause many severe health problems. Although the toxicity of nanoparticles has been investigated, prevention and treatment of damages caused by nanoparticles have been rarely studied. Therefore, isotope tracing and improved CT imaging techniques were used to investigate the biodistribution influence between oMWCNTs(oxidized multi-walled carbon nanotubes) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/or simvastatin (TD) in vivo. What’s more, biochemical indices in plasma and tissue histology were measured to further study therapeutic effects on the damages of oMWCNTs in mice. Isotope tracing and improved CT imaging results showed that low dosages of DOPC and TD didn’t affect the distribution of oMWCNTs in mice; conversely, the distribution and metabolism of DOPC and TD were influenced by oMWCNTs. Moreover, DOPC and/or TD improved the biocompatibility of oMWCNTs in erythrocyte suspension in vitro. Biochemical index and histopathological results indicated that DOPC and TD didn’t prevent injuries caused by oMWCNTs effectively. But TD showed a good therapeutic effect for damages. This study is the first to investigate prevention and treatment effects of drugs on damages caused by oMWCNTs and provides new insights and breakthroughs for management of nanoparticles on health hazards.
Expression and functional analysis of the lysine decarboxylase and copper amine oxidase genes from the endophytic fungus Colletotrichum gloeosporioides ES026
Authors: Zhang Xiangmei , Wang Zhangqian , Jan Saad , Yang Qian , Wang Mo
Published: May 2017

Huperzine A (HupA) isolated from Huperzia serrata is an important compound used to treat Alzheimer’s disease (AD). Recently, HupA was reported in various endophytic fungi, with Colletotrichum gloeosporioides ES026 previously isolated from H. serrata shown to produce HupA. In this study, we performed next-generation sequencing and de novo RNA sequencing of C. gloeosporioides ES026 to elucidate the molecular functions, biological processes, and biochemical pathways of these unique sequences. Gene ontology and Kyoto Encyclopedia of Genes and Genomes assignments allowed annotation of lysine decarboxylase (LDC) and copper amine oxidase (CAO) for their conversion of L-lysine to 5-aminopentanal during HupA biosynthesis. Additionally, we constructed a stable, high-yielding HupA-expression system resulting from the overexpression of CgLDC and CgCAO from the HupA-producing endophytic fungus C. gloeosporioides ES026 in Escherichia coli. Quantitative reverse transcription polymerase chain reaction analysis confirmed CgLDC and CgCAO expression, and quantitative determination of HupA levels was assessed by liquid chromatography high-resolution mass spectrometry, which revealed that elevated expression of CgLDC and CgCAO produced higher yields of HupA than those derived from C. gloeosporioides ES026. These results revealed CgLDC and CgCAO involvement in HupA biosynthesis and their key role in regulating HupA content in C. gloeosporioides ES026.
Downregulation of UHRF1 increases tumor malignancy by activating the CXCR4/AKT-JNK/IL-6/Snail signaling axis in hepatocellular carcinoma cells
Authors: Kim Ji-Hyun , Shim Jae-Woong , Eum Da-Young , Kim Sung Dae , Choi Si Ho , Yang Kwangmo , Heo Kyu , Park Moon-Taek
Published: May 2017

UHRF1 (ubiquitin-like, with PHD and RING finger domains 1) plays a crucial role in DNA methylation, chromatin remodeling and gene expression and is aberrantly upregulated in various types of human cancers. However, the precise role of UHRF1 in cancer remains controversial. In this study, we observed that hypoxia-induced downregulation of UHRF1 contributes to the induction of the epithelial-mesenchymal transition (EMT) in hepatocellular carcinoma cells. By negatively modulating UHRF1 expression, we further showed that UHRF1 deficiency in itself is sufficient to increase the migratory and invasive properties of cells via inducing EMT, increasing the tumorigenic capacity of cells and leading to the expansion of cancer stem-like cells. Epigenetic changes caused by UHRF1 deficiency triggered the upregulation of CXCR4, thereby activating AKT and JNK to increase the expression and secretion of IL-6. In addition, IL-6 readily activated the JAK/STAT3/Snail signaling axis, which subsequently contributed to UHRF1 deficiency-induced EMT. Our results collectively demonstrate that UHRF1 deficiency may play a pivotal role in the malignant alteration of cancer cells.
Gold nanozyme-based paper chip for colorimetric detection of mercury ions
Authors: Han Kwi Nam , Choi Jong-Soon , Kwon Joseph
Published: May 2017

In this study, we developed a facile gold nanozyme-based paper chip (AuNZ-PAD) for Hg2+ detection. This device has the advantages of being simple, rapid, cost effective, sensitive, selective, high throughput, and applicable to onsite detection. The colorimetric mercury assay on the AuNZ-PAD is established based on the enzyme-like catalytic activity of gold nanoparticles promoted by the formation of Au–Hg amalgam, which is correlated to the intensity of the colorimetric response resulting from the catalytic reaction of 3,3′,5,5′-tetramethylbenzidine (TMB) and H2O2. Highly sensitive and selective detection of Hg2+ ions is achieved in both distilled and tap water samples, indicating the feasibility and applicability of our device for the determination of mercury pollution in real samples. Moreover, AuNZ-PAD analysis using a smartphone camera eliminates the need for expensive analytical equipment, thereby increasing the practicality of field monitoring of trace Hg2+ compared with other sensing methods.
Disruption of Small GTPase Rab7 Exacerbates the Severity of Acute Pancreatitis in Experimental Mouse Models
Authors: Takahashi Kenichi , Mashima Hirosato , Miura Kouichi , Maeda Daichi , Goto Akiteru , Goto Takashi , Sun-Wada Ge-Hong , Wada Yoh , Ohnishi Hirohide
Published: May 2017

Although aberrations of intracellular vesicle transport systems towards lysosomes including autophagy and endocytosis are involved in the onset and progression of acute pancreatitis, the molecular mechanisms underlying such aberrations remain unclear. The pathways of autophagy and endocytosis are closely related, and Rab7 plays crucial roles in both. In this study, we analyzed the function of Rab7 in acute pancreatitis using pancreas-specific Rab7 knockout (Rab7Δpan) mice. In Rab7Δpan pancreatic acinar cells, the maturation steps of both endosomes and autophagosomes were deteriorated, and the lysosomal functions were affected. In experimental models of acute pancreatitis, the histopathological severity, serum amylase concentration and intra-pancreatic trypsin activity were significantly higher in Rab7Δpan mice than in wild-type mice. Furthermore, the autophagy process was blocked in Rab7Δpan pancreas compared with wild-type mice. In addition, larger autophagic vacuoles that colocalize with early endosome antigen 1 (EEA1) but not with lysosomal-associated membrane protein (LAMP)-1 were much more frequently formed in Rab7Δpan pancreatic acinar cells. Accordingly, Rab7 deficiency exacerbates the severity of acute pancreatitis by impairing the autophagic and endocytic pathways toward lysosomes.
Application of Box-Behnken designs in parameters optimization of differential pulse anodic stripping voltammetry for lead(II) determination in two electrolytes
Authors: Yu Xiao-Lan , He Yong
Published: May 2017

Box-Behnken design was advantageous to parameters optimization of differential pulse anodic stripping voltammetry (DPASV) for the analysis of lead(II) with its high efficiency and accuracy. Five Box-Behnken designs were designed and conducted in the electrolyte of 0.1 mol/L acetate buffer and 0.1 mol/L HCl without the removal of oxygen. Significant parameters and interactions in each electrolyte were found (P-value < 0.05) and their quantitative effects on lead(II) determination were classified into two categories, linear and quadratic. Though significant parameters and interactions were not similar in different kinds of electrolytes, characteristic parameters of differential pulse voltammetry, which were pulse amplitude, pulse width and interval time, were found significant in both electrolytes. After optimization, peak currents and relative standard deviation at 20 μg/L along with detection limits in both electrolytes were superior than before. With the lower detection limit and R.S.D., 0.1 mol/L HCl was a better choice for electrolytes in this work. Meanwhile, with the combination of parameters optimization and background subtraction, the interference of dissolved oxygen for lead(II) determination was eliminated. It was important and necessary to apply Box-Behnken designs in parameters optimization of DPASV for lead(II) determination regardless of the electrolyte kinds.
Soil biochemical responses to nitrogen addition in a secondary evergreen broad-leaved forest ecosystem
Authors: Peng Yong , Chen Guangsheng , Chen Guantao , Li Shun , Peng Tianchi , Qiu Xirong , Luo Jie , Yang Shanshan , Hu Tingxing , Hu Hongling , Xu Zhenfeng , Liu Li , Tang Yi , Tu Lihua
Published: May 2017

In order to investigate the effects of N deposition on soil biochemistry in secondary forests, one N addition experiment was conducted in a secondary evergreen broad-leaved forest in the western edge of Sichuan Basin, with the highest level of background N deposition (about 95 kg N ha−1 yr−1) in China. Three N treatment levels (+0, +50, +150 kg N ha−1 yr−1) were monthly added to soil surface in this forest beginning in April 2013. Soil biochemistry and root biomass of the 0–10 cm soil horizon were measured from May 2014 to April 2015. Soil respiration was measured for two years (September 2013 to August 2015). It was showed that N additions were correlated to significantly lower soil pH, microbial biomass C (MBC) concentration, MBC/microbial biomass N (MBN) ratio, root biomass, and soil respiration rate, and significantly higher concentrations of ammonium (NH4+) and nitrate (NO3−). These results indicate that N additions had a significant effect on the size of soil microbial community. In addition, soil C storage may potentially increase due to the dropped soil C release under N addition.
CRISPR/Cas9-mediated p53 and Pten dual mutation accelerates hepatocarcinogenesis in adult hepatitis B virus transgenic mice
Authors: Liu Yongzhen , Qi Xuewei , Zeng Zhenzhen , Wang Lu , Wang Jie , Zhang Ting , Xu Qiang , Shen Congle , Zhou Guangde , Yang Shaomin , Chen Xiangmei , Lu Fengmin
Published: May 2017

The p53 mutation and altered Pten expression are two most common genetic events in Hepatitis B virus (HBV) infection related hepatocellular carcinoma (HCC). To confirm the causative role of p53 and Pten somatic mutation in HCC development, we established CRISPR/Cas9-mediated somatic gene disruption via hydrodynamic tail vein injection, allowing for in vivo targeting p53 and Pten simultaneously in adult HBV transgenic mice. Here we demonstrated that the utility of this approach resulted in macroscopic liver tumors as early as 4 months’ post injection and most tumors harbored both p53 and Pten loss-of-function alterations. Immunohistochemical (IHC) and histopathology analysis demonstrated that the tumors were positive for Glutamine synthetase (GS), a marker of HCC and accompanied with prominent lipid accumulation. The study here indicated that CRISPR/Cas9-mediated p53 and Pten somatic mutation accelerated hepatocarcinogenesis in adult HBV transgenic mice. This method also provides a fast and convenient system for generating mouse model of HCC with HBV infection characteristics.
See-through optical combiner for augmented reality head-mounted display: index-matched anisotropic crystal lens
Authors: Hong Jong-Young , Lee Chang-Kun , Lee Seungjae , Lee Byounghyo , Yoo Dongheon , Jang Changwon , Kim Jonghyun , Jeong Jinsoo , Lee Byoungho
Published: May 2017

A novel see-through optical device to combine the real world and the virtual image is proposed which is called an index-matched anisotropic crystal lens (IMACL). The convex lens made of anisotropic crystal is enveloped with the isotropic material having same refractive index with the extraordinary refractive index of the anisotropic crystal. This optical device functions as the transparent glass or lens according to the polarization state of the incident light. With the novel optical property, IMACL can be utilized in the see-through near eye display, or head-mounted display for augmented reality. The optical property of the proposed optical device is analyzed and aberration by the anisotropic property of the index-matched anisotropic crystal lens is described with the simulation. The concept of the head-mounted display using IMACL is introduced and various optical performances such as field of view, form factor and transmittance are analyzed. The prototype is implemented to verify the proposed system and experimental results show the mixture between the virtual image and real world scene.
Erythropoietin ameliorates diabetes-associated cognitive dysfunction in vitro and in vivo
Authors: Wang Meng , Yan Wenhui , Liu Yuan , Hu Hao , Sun Qiang , Chen Xinlin , Zang Weijin , Chen Lina
Published: May 2017

Several studies indicate that erythropoietin (EPO) has remarkable neuroprotective effects in various central nervous system disorders, while little is known about the effects of EPO in diabetes-associated cognitive dysfunction. Therefore, the present study aimed to investigate whether EPO ameliorates diabetes-associated cognitive dysfunction in vivo and in vitro. We investigated the protective effects of EPO on high-glucose (HG)-induced PC12 cell death and oxidative stress. The effects of EPO (300 U/kg administered three times a week for 4 weeks) on diabetes-associated cognitive decline were investigated in diabetic rats. EPO significantly increased cell viability, increased the activity of superoxide dismutase, decreased the production of malondialdehyde and reactive oxygen species, and decreased the apoptosis rate. Additionally, LY294002, a phosphatidylinositol 3-kinase (PI3K) inhibitor, abolished the protective effects of EPO in HG-treated PC12 cells. In diabetic rats, EPO prevented deficits in spatial learning and memory in the Morris water maze test. The results of real-time PCR and Western blotting showed that EPO upregulated EPO receptor, PI3K, and phosphorylated Akt2 relative to unphosphorylated Akt2 (p-Akt2/Akt2) and downregulated glycogen synthase kinase-3β (GSK-3β). These studies demonstrate that EPO is an effective neuroprotective agent in the context of diabetes-associated cognitive dysfunction and show that this effect involves the PI3K/Akt/GSK-3β pathway.
Micro-drive and headgear for chronic implant and recovery of optoelectronic probes
Authors: Chung Jinho , Sharif Farnaz , Jung Dajung , Kim Soyoun , Royer Sebastien
Published: May 2017

Silicon probes are multisite electrodes used for the electrophysiological recording of large neuronal ensembles. Optoelectronic probes (OEPs) are recent upgrades that allow, in parallel, the delivery of local optical stimuli. The procedures to use these delicate electrodes for chronic experiments in mice are still underdeveloped and typically assume one-time uses. Here, we developed a micro-drive, a support for OEPs optical fibers, and a hat enclosure, which fabrications consist in fitting and fastening together plastic parts made with 3D printers. Excluding two parts, all components and electrodes are relatively simple to recover after the experiments, via the loosening of screws. To prevent the plugging of OEPs laser sources from altering the stability of recordings, the OEPs fibers can be transiently anchored to the hat via the tightening of screws. We test the stability of recordings in the mouse hippocampus under three different conditions: acute head-fixed, chronic head-fixed, and chronic freely moving. Drift in spike waveforms is significantly smaller in chronic compared to acute conditions, with the plugging/unplugging of head-stage and fiber connectors not affecting much the recording stability. Overall, these tools generate stable recordings of place cell in chronic conditions, and make the recovery and reuse of electrode packages relatively simple.
Probing the early stages of shock-induced chondritic meteorite formation at the mesoscale
Authors: Rutherford Michael E. , Chapman David J. , Derrick James G. , Patten Jack R. W. , Bland Philip A. , Rack Alexander , Collins Gareth S. , Eakins Daniel E.
Published: May 2017

Chondritic meteorites are fragments of asteroids, the building blocks of planets, that retain a record of primordial processes. Important in their early evolution was impact-driven lithification, where a porous mixture of millimetre-scale chondrule inclusions and sub-micrometre dust was compacted into rock. In this Article, the shock compression of analogue precursor chondrite material was probed using state of the art dynamic X-ray radiography. Spatially-resolved shock and particle velocities, and shock front thicknesses were extracted directly from the radiographs, representing a greatly enhanced scope of data than could be measured in surface-based studies. A statistical interpretation of the measured velocities showed that mean values were in good agreement with those predicted using continuum-level modelling and mixture theory. However, the distribution and evolution of wave velocities and wavefront thicknesses were observed to be intimately linked to the mesoscopic structure of the sample. This Article provides the first detailed experimental insight into the distribution of extreme states within a shocked powder mixture, and represents the first mesoscopic validation of leading theories concerning the variation in extreme pressure-temperature states during the formation of primordial planetary bodies.
In vivo endoscopic mass spectrometry using a moving string sampling probe
Authors: Chen Lee Chuin , Naito Tsubasa , Tsutsui Satoru , Yamada Yuki , Ninomiya Satoshi , Yoshimura Kentaro , Takeda Sen , Hiraoka Kenzo
Published: May 2017

A novel moving string sampling probe and sample transportation system for performing in situ and in vivo endoscopic MS.
Potential of electrospray ionization mass spectrometry (ESI-MS), using direct infusion, to quantify fatty acid methyl esters (FAMEs) in biodiesel
Authors: Leal Rodrigo V. P. , Sarmanho Gabriel F. , Leal Luiz H. , Garrido Bruno C. , Carvalho Lucas J. , Rego Eliane C. P. , Seidl Peter R.
Published: May 2017

Fatty acid methyl ester (FAME) intensities, by ESI-MS, used to their quantification in biodiesel.
Immunoaffinity nanogold coupled with direct analysis in real time (DART) mass spectrometry for analytical toxicology
Authors: Evans-Nguyen K. M. , Hargraves T. L. , Quinto A. N.
Published: May 2017

A rapid, definitive trace drug identification technique using nanogold surfaces with mass spectrometry was developed.
Electrolyte-assisted microemulsion breaking in vortex-agitated solidified floating organic drop microextraction for preconcentration and analysis of Sudan dyes in chili products
Authors: Sricharoen Phitchan , Limchoowong Nunticha , Sripakdee Thitiya , Nuengmatcha Prawit , Chanthai Saksit
Published: May 2017

For the extraction and determination of Sudan I–IV dyes in chili product samples, a simple and efficient liquid phase microextraction technique was developed.
Parallel and antiparallel cyclic d/l peptide nanotubes
Authors: Silk Mitchell R. , Newman Janet , Ratcliffe Julian C. , White Jacinta F. , Caradoc-Davies Tom , Price Jason R. , Perrier Sébastien , Thompson Philip E. , Chalmers David K.
Published: May 2017

Novel X-ray crystal structures of cyclic d/l peptide nanotubes in antiparallel and parallel configurations.
Gram-scale free radical polymerization of an azaborine vinyl monomer
Authors: van de Wouw Heidi L. , Lee Jae Young , Klausen Rebekka S.
Published: May 2017

The gram-scale polymerization of a novel azaborine vinyl monomer is reported.
Highly efficient complexation of sanguinarine alkaloid by carboxylatopillar[6]arene: pKashift, increased solubility and enhanced antibacterial activity
Authors: Ping Guchuan , Wang Yiliang , Shen Lingyun , Wang Yuting , Hu Xiaoshi , Chen Junyi , Hu Bingwen , Cui Lei , Meng Qingbin , Li Chunju
Published: May 2017

Efficient complexation of sanguinarine by carboxylatopillar[6]arene. The pKashift, increased solubility, and enhanced antibacterial activity are described.
Modulation of the catalytic activity of Pt nanoparticles through charge-transfer interactions with metal–organic frameworks
Authors: Yoshimaru Shotaro , Sadakiyo Masaaki , Staykov Aleksandar , Kato Kenichi , Yamauchi Miho
Published: May 2017

A charge transfer interaction between Pt nanoparticles and MOFs modulated the catalytic activity of Pt for a CO oxidation reaction.
Effects of third-order susceptibility in sum frequency generation spectra: a molecular dynamics study in liquid water
Authors: Joutsuka Tatsuya , Hirano Tomonori , Sprik Michiel , Morita Akihiro
Published: May 2017

χ(2) and χ(3) at charged interfaces in SFG spectroscopy are distinctively calculated using MD simulations.
Reliability of interacting quantum atoms (IQA) data computed from post-HF densities: impact of the approximation used
Authors: Cukrowski Ignacy , Polestshuk Pavel M.
Published: May 2017

The BBC1 approximation is recommended for IQA calculations; MP2/BBC1 and CCSD/BBC1 produced highly comparable FAMSEC-based interpretations of intramolecular interactions.
Hierarchically structured composites for ultrafast liquid sensing and smart leak-plugging
Authors: Wu Xiaodong , Han Yangyang , Zhang Xinxing , Lu Canhui
Published: May 2017

Hierarchically structured conductive polymer composites with an ultrafast response to solvent stimuli for real-time liquid sensing and smart leak-plugging.
Collision-induced dissociation of sodiated glucose and identification of anomeric configuration
Authors: Chen Jien-Lian , Nguan Hock Seng , Hsu Po-Jen , Tsai Shang-Ting , Liew Chia Yen , Kuo Jer-Lai , Hu Wei-Ping , Ni Chi-Kung
Published: May 2017

Difference in dehydration barrier heights results in different branching ratio, a simple and fast method for anomeric configuration identification.
Anchoring ceria nanoparticles on graphene oxide and their radical scavenge properties under gamma irradiation environment
Authors: Xia Wei , Zhao Jun , Wang Tao , Song Li , Gong Hao , Guo Hu , Gao Bing , Fan Xiaoli , He Jianping
Published: May 2017

The working mechanism of CG for their radical scavenge properties in the epoxy resin during radiation environment.
DNA intrastrand cross-links induced by the purine-type deoxyguanosine-8-yl radical: a DFT study
Authors: Wang Shoushan , Zhang Min , Liu Peng , Xie Shilei , Cheng Faliang , Wang Lishi
Published: May 2017

DNA intrastrand cross-link lesions induced by the purine-type deoxyguanosine-8-yl radical.
Positron annihilation characteristics, water uptake and proton conductivity of composite Nafion membranes
Authors: Yin Chongshan , Wang Lingtao , Li Jingjing , Zhou Yawei , Zhang Haining , Fang Pengfei , He Chunqing
Published: May 2017

The connection between microstructure evolution, in terms of o-Ps lifetime, and proton conductivity in Nafion membranes with different water uptakes.
Atomic-scale observation of pressure-dependent reduction dynamics of W18O49nanowires using environmental TEM
Authors: Zhang Zhengfei , Sheng Liping , Chen Lu , Zhang Ze , Wang Yong
Published: May 2017

The oxygen pressure dependent reduction of W18O49nanowires was observed byin situTEM through electron beam irradiation.
Syntheses of asymmetric zinc porphyrins bearing different pseudo-pyridine substituents and their photosensitization for visible-light-driven H2 production activity
Authors: Zheng Ya , Wang Jinming , Zhang Jing , Peng Tianyou , Li Renjie
Published: May 2017

Asymmetric zinc porphyrins bearing different pseudo-pyridine substituents were synthesized and used to sensitize Pt/g-C3N4 for photocatalytic H2 production.
Interfacial structure and structural forces in mixtures of ionic liquid with a polar solvent
Authors: Coles Samuel W. , Smith Alexander M. , Fedorov Maxim V. , Hausen Florian , Perkin Susan
Published: May 2017

Oscillatory and monotonic decay in mixtures of salt and solvent at interfaces with varying surface charge.
Organs-on-chips with integrated electrodes for trans-epithelial electrical resistance (TEER) measurements of human epithelial barrier function
Authors: Henry Olivier Y. F. , Villenave Remi , Cronce Michael J. , Leineweber William D. , Benz Maximilian A. , Ingber Donald E.
Published: May 2017

Trans-epithelial electrical resistance (TEER) monitoring of human lung airway epithelium during long term maturation and experimental manipulation in an organ-on-a-chip.
An encoded viral micropatch for multiplex cell-based assays through localized gene delivery
Authors: Han Sangkwon , Bae Hyung Jong , Kim Su Deok , Park Wook , Kwon Sunghoon
Published: May 2017

An encoded viral micropatch is presented for localized target gene expression for high-throughput, high-content cell-based assays.
Chemically modified biopolymer as an eco-friendly corrosion inhibitor for mild steel in a neutral chloride environment
Authors: K. Vimal Kumar , B. V. Appa Rao
Published: May 2017

The present work mainly focuses on the development of an eco-friendly corrosion inhibitor (phosphorylated chitin) which enables us to minimize the use of hazardous substances as corrosion inhibitors.
Magnetic and dielectric properties of a lanthanum-doped yttrium copper titanate ceramic
Authors: Sharma S. , Singh M. M. , Mandal K. D.
Published: May 2017

In this study, the microstructure and dielectric and magnetic properties of a lanthanum-doped yttrium copper titanate ceramic (YLCTO) are reported and have been discussed.
A study of Moroccan pupils' difficulties at second Baccalaureat year in solving chemistry problems relating to the reactivity of ethanoate ions and to copper–aluminium cells
Authors: Ouasri Ali
Published: May 2017

This paper investigates the difficulties that Moroccan pupils (18–19) of the second Baccalaureat year encountered in solving chemical equilibrium problems relating to ethanoate ions' reactivity with water and methanoic acid, and to copper–aluminum cells. The pupils were asked to provide answers to questions derived from two problems. The questions were classified into different tasks according to whether their answers required declarative and (or) procedural knowledge. The written responses evaluated and counted as the percentage of successful, failed and unprocessed tasks revealed that pupils completed with success tasks on the reactivity of ethanoate ions with water more easily than those of two other studied cases. The pupils encountered difficulties in appropriating procedural knowledge on equilibriums involved in ethanoate ions' reactivity with methanoic acid and in copper–aluminum cells. The impact of the tasks' organization on knowledge development seems to be not verified as it was shown in the hierarchy prevalence of problems from simple to complex ones.
Sizes and albedos of Mars-crossing asteroids from WISE/NEOWISE data
Authors: Alí-Lagoa V. , Delbo’ M.
Published: May 2017

Context.Mars-crossing asteroids (MCs) are a dynamically unstable group between the main belt and the near-Earth populations. Characterising the physical properties of a large sample of MCs can help to understand the original sources of many near-Earth asteroids, some of which may produce meteorites on Earth.

Aims.Our aim is to provide diameters and albedos of MCs with available WISE/NEOWISE data.

Methods.We used the near-Earth asteroid thermal model to find the best-fitting values of equivalent diameter and, whenever possible, the infrared beaming parameter. With the diameter and tabulated asteroid absolute magnitudes we also computed the visible geometric albedos.

Results.We determined the diameters and beaming parameters of 404 objects observed during the fully cryogenic phase of the WISE mission, most of which have not been published elsewhere. We also obtained 1572 diameters from data from the 3-Band and posterior non-cryogenic phases using a default value of beaming parameter. The average beaming parameter is 1.2 ± 0.2 for objects smaller than 10 km, which constitute most of our sample. This is higher than the typical value of 1.0 found for the whole main belt and is possibly related to the fact that WISE is able to observe many more small objects at shorter heliocentric distances, i.e. at higher phase angles. We argue that this is a better default value for modelling Mars-crossing asteroids from the WISE/NEOWISE catalogue and discuss the effects of this choice on the diameter and albedo distributions. We find a double-peaked distribution for the visible geometric albedos, which is expected since this population is compositionally diverse and includes objects in the major spectral complexes. However, the distribution of beaming parameters is homogeneous for both low- and high-albedo objects.
Radical Metal-Free Borylation of Aryl Iodides
Authors: Pinet Sandra , Pucheault Mathieu , Liautard Virginie , Debiais Mégane
Published: May 2017

A simple metal-free borylation of aryl iodides mediated by a fluoride sp2–sp3 diboron adduct is described. The reaction conditions are compatible with various functional groups. Electronic effects of substituents do not affect the borylation while steric hindrance does. The reaction proceeds via a radical mechanism in which pyridine serves to stabilize the boryl radicals, generated in situ.