bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterisation of tree vibrations based on the model of orthogonal oscillations
Authors: Kovacic Ivana , Radomirovic Dragi , Zukovic Miodrag , Pavel Benka , Nikolic Milutin
Published: May 2018

This study presents quantitative and qualitative insights into the analysis of data obtained by tracking the motion of reflective markers arranged along the trunk of a pole-like potted tree, which was recorded by a state-of-the-art infrared motion-tracking system. The experimental results showed in-plane damped trajectories of the markers with lateral displacements, i.e. out-of-plane vibrations of the tree under consideration. To explain such response and to determine the corresponding oscillatory characteristics, a completely new and original utilisation of the recorded in-plane damped trajectories is presented. The quantitative insight gained is based on the mechanical model that consists of two orthogonal springs and dampers placed in the plane where the motion takes place, and it is then directed towards the determination of the characteristics of the related orthogonal oscillations: two natural frequencies, the position of the principal axes to which they correspond, and two damping ratios. The qualitative insight gained involves analysing the shape and narrowness of the trajectory to assess how close-valued two natural frequencies are, and how small the overall damping is. The quantitative and qualitative methodologies presented herein are seen as beneficial for arboriculture, forestry and botany, but given the fact that orthogonal oscillations appears in many natural and engineering systems, they are also expected to be useful for specialists in other fields of science and engineering as well.
Synthetic Rhamnolipid Bolaforms trigger an innate immune response in Arabidopsis thaliana
Authors: Luzuriaga-Loaiza W. Patricio , Schellenberger Romain , De Gaetano Yannick , Obounou Akong Firmin , Villaume Sandra , Crouzet Jérôme , Haudrechy Arnaud , Baillieul Fabienne , Clément Christophe , Lins Laurence , Allais Florent , Ongena Marc , Bouquillon Sandrine , Deleu Magali , Dorey Stephan
Published: May 2018

Stimulation of plant innate immunity by natural and synthetic elicitors is a promising alternative to conventional pesticides for a more sustainable agriculture. Sugar-based bolaamphiphiles are known for their biocompatibility, biodegradability and low toxicity. In this work, we show that Synthetic Rhamnolipid Bolaforms (SRBs) that have been synthesized by green chemistry trigger Arabidopsis innate immunity. Using structure-function analysis, we demonstrate that SRBs, depending on the acyl chain length, differentially activate early and late immunity-related plant defense responses and provide local increase in resistance to plant pathogenic bacteria. Our biophysical data suggest that SRBs can interact with plant biomimetic plasma membrane and open the possibility of a lipid driven process for plant-triggered immunity by SRBs.
Impairment of photoreceptor ribbon synapses in a novel Pomt1 conditional knockout mouse model of dystroglycanopathy
Authors: Rubio-Fernández Marcos , Uribe Mary Luz , Vicente-Tejedor Javier , Germain Francisco , Susín-Lara Cristina , Quereda Cristina , Montoliu Lluis , de la Villa Pedro , Martín-Nieto José , Cruces Jesús
Published: May 2018

Hypoglycosylation of α-dystroglycan (α-DG) resulting from deficiency of protein O-mannosyltransferase 1 (POMT1) may cause severe neuromuscular dystrophies with brain and eye anomalies, named dystroglycanopathies. The retinal involvement of these disorders motivated us to generate a conditional knockout (cKO) mouse experiencing a Pomt1 intragenic deletion (exons 3–4) during the development of photoreceptors, mediated by the Cre recombinase expressed from the cone-rod homeobox (Crx) gene promoter. In this mouse, retinal α-DG was unglycosylated and incapable of binding laminin. Retinal POMT1 deficiency caused significant impairments in both electroretinographic recordings and optokinetic reflex in Pomt1 cKO mice, and immunohistochemical analyses revealed the absence of β-DG and of the α-DG-interacting protein, pikachurin, in the outer plexiform layer (OPL). At the ultrastructural level, noticeable alterations were observed in the ribbon synapses established between photoreceptors and bipolar cells. Therefore, O-mannosylation of α-DG in the retina carried out by POMT1 is crucial for the establishment of proper synapses at the OPL and transmission of visual information from cones and rods to their postsynaptic neurons.
A gender specific improved survival related to stromal miR-143 and miR-145 expression in non-small cell lung cancer
Authors: Skjefstad Kaja , Johannessen Charles , Grindstad Thea , Kilvaer Thomas , Paulsen Erna-Elise , Pedersen Mona , Donnem Tom , Andersen Sigve , Bremnes Roy , Richardsen Elin , Al-Saad Samer , Busund Lill-Tove
Published: May 2018

Micro RNAs (miRNA) are small non-coding RNAs that post-transcriptionally regulate gene expression. Dysregulation of miRNA cluster 143/145 has been reported in several malignancies, but their role in non-small cell lung cancer (NSCLC) remains elusive. This study investigates the prognostic impact of miR-143 and miR-145 in primary tumors and metastatic lymph nodes in NSCLC tissue. Tissue from 553 primary tumors and 143 matched metastatic lymph nodes were collected and tissue microarrays were constructed. In situ hybridization was used to evaluate miR-143 and miR-145 expression in tumor epithelial cells and stromal cells in the primary tumors and lymph nodes. In vivo data was supplemented with functional studies of cell lines in vitro to evaluate the role of miR-143 and miR-145 in NSCLC tumorigenesis. In our cohort, stromal miR-143 (S-miR-143) and miR-145 (S-miR-145) expression in primary tumor tissue were independent prognosticators of improved disease-specific survival (DSS) in female (S-miR-143, HR: 0.53, p = 0.019) and male patients (S-miR-145, HR: 0.58, p = 0.021), respectively. Interesting correlations between the miR cluster 143/145 and previously investigated steroid hormone receptors from the same cohort were identified, substantiating their gender dependent significance.
The impact of using BARCIST 1.0 criteria on quantification of BAT volume and activity in three independent cohorts of adults
Authors: Martinez-Tellez Borja , Nahon Kimberly J. , Sanchez-Delgado Guillermo , Abreu-Vieira Gustavo , Llamas-Elvira Jose M. , van Velden Floris H. P. , Pereira Arias-Bouda Lenka M. , Rensen Patrick C. N. , Boon Mariëtte R. , Ruiz Jonatan R.
Published: May 2018

Human brown adipose tissue (BAT) is commonly assessed by cold-induced 18F-fluorodeoxyglucose (FDG) PET-CT using several quantification criteria. Uniform criteria for data analysis became available recently (BARCIST 1.0). We compared BAT volume and activity following BARCIST 1.0 criteria against the most commonly used criteria [Hounsfield Units (HU):-250, -50, standardized uptake value (SUV):2.0; HU: Not applied, SUV:2.0 and HU:-180, -10, SUV:1.5] in a prospective study using three independent cohorts of men including young lean adults, young overweight/obese adults and middle-aged overweight/obese adults. BAT volume was the most variable outcome between criteria. While BAT volume calculated using the HU: NA; SUV: 2.0 criteria was up to 207% higher than the BAT volume calculated based on BARCIST 1.0 criteria, it was up to 57% lower using the HU: -250, -50; SUV: 2.0 criteria compared to the BARCIST 1.0. Similarly, BAT activity (expressed as SUVmean) also differed between different thresholds mainly because SUVmean depends on BAT volume. SUVpeak was the most consistent BAT outcome across the four study criteria. Of note, we replicated these findings in three independent cohorts. In conclusion, BAT volume and activity as determined by 18F-FDG-PET/CT highly depend on the quantification criteria used. Future human BAT studies should conduct sensitivity analysis with different thresholds in order to understand whether results are driven by the selected HU and/or SUV thresholds. The design of the present study precludes providing any conclusive threshold, but before more definitive thresholds for HU and SUV are available, we support the use of BARCIST 1.0 criteria to facilitate interpretation of BAT characteristics between research groups.
Cell-free protein synthesis as a novel tool for directed glycoengineering of active erythropoietin
Authors: Zemella Anne , Thoring Lena , Hoffmeister Christian , Šamalíková Mária , Ehren Patricia , Wüstenhagen Doreen A. , Kubick Stefan
Published: May 2018

As one of the most complex post-translational modification, glycosylation is widely involved in cell adhesion, cell proliferation and immune response. Nevertheless glycoproteins with an identical polypeptide backbone mostly differ in their glycosylation patterns. Due to this heterogeneity, the mapping of different glycosylation patterns to their associated function is nearly impossible. In the last years, glycoengineering tools including cell line engineering, chemoenzymatic remodeling and site-specific glycosylation have attracted increasing interest. The therapeutic hormone erythropoietin (EPO) has been investigated in particular by various groups to establish a production process resulting in a defined glycosylation pattern. However commercially available recombinant human EPO shows batch-to-batch variations in its glycoforms. Therefore we present an alternative method for the synthesis of active glycosylated EPO with an engineered O-glycosylation site by combining eukaryotic cell-free protein synthesis and site-directed incorporation of non-canonical amino acids with subsequent chemoselective modifications.
Effective thresholds for reporting suspicions and improve early detection of avian influenza outbreaks in layer chickens
Authors: Gonzales Jose L. , Elbers Armin R. W.
Published: May 2018

The objective of this study was to identify effective reporting thresholds for suspicions of both highly pathogenic (HPAI) and low pathogenic avian influenza (LPAI) outbreaks in layer farms. Daily mortality and egg-production data from 30 Dutch farms with no record of AI infection were analysed and thresholds set. Mortality rates above or egg-production below these thresholds for two consecutive days would trigger an alarm sign. The following thresholds were identified for mortality: (i) A mortality threshold of 0.08% or 0.13% for layers kept indoors or with free-range access respectively, (ii) a 2.9 times higher mortality than the average weekly mortality of the previous week, and iii) a moving-average threshold that could be implemented for each specific farm. For egg-production: (i) a weekly ratio lower than 0.94 in egg-production drop, and (ii) a moving-average threshold. The accuracy of these thresholds was assessed by quantifying their sensitivity, specificity and time to trigger disease detection using data from 15 infected and 31 non-infected farms. New thresholds were more sensitive and signalled infection two to six days earlier than the presently used thresholds. A high Specificity (97–100%) was obtained by combining mortality and egg production thresholds in a serial approach to trigger an alarm.
Biphasic regulation of tumorigenesis by PTK7 expression level in esophageal squamous cell carcinoma
Authors: Shin Won-Sik , Gim Jungsoo , Won Sungho , Lee Seung-Taek
Published: May 2018

Protein tyrosine kinase 7 (PTK7), also known as colon carcinoma kinase 4 (CCK-4), is a member of the catalytically defective receptor protein tyrosine kinase family and is upregulated in various cancers, where it is known to act as either an oncoprotein or a tumor suppressor. To understand the contrasting roles of PTK7 in tumorigenesis, we analyzed the tumorigenic characteristics of esophageal squamous cell carcinoma (ESCC) cells with low levels of endogenous PTK7 expression (TE-5 and TE-14 cells) and high levels of expression (TE-6 and TE-10 cells) after transfections with a PTK7 expression vector. PTK7 overexpression increased the proliferation of TE-5 and TE-14 cells but decreased the proliferation of TE-6 and TE-10 cells. In the ESCC cells, proliferation, migration, and invasion were initially increased and then decreased according to PTK7 expression levels, which were mirrored by initial increases and then decreases in the tyrosine phosphorylation of cellular proteins and phosphorylation of Src, Akt, and ERK. In ESCC patients included in The Cancer Genome Atlas database, those with higher PTK7 mRNA levels had a longer overall survival and lower relative risk than those with lower PTK7 mRNA levels. These results demonstrate that PTK7 biphasically regulates tumorigenesis in ESCC.
Modelling The Combined Effects Of Collagen and Cyclic Strain On Cellular Orientation In Collagenous Tissues
Authors: Ristori T. , Notermans T. M. W. , Foolen J. , Kurniawan N. A. , Bouten C. V. C. , Baaijens F. P. T. , Loerakker S.
Published: May 2018

Adherent cells are generally able to reorient in response to cyclic strain. In three-dimensional tissues, however, extracellular collagen can affect this cellular response. In this study, a computational model able to predict the combined effects of mechanical stimuli and collagen on cellular (re)orientation was developed. In particular, a recently proposed computational model (which only accounts for mechanical stimuli) was extended by considering two hypotheses on how collagen influences cellular (re)orientation: collagen contributes to cell alignment by providing topographical cues (contact guidance); or collagen causes a spatial obstruction for cellular reorientation (steric hindrance). In addition, we developed an evolution law to predict cell-induced collagen realignment. The hypotheses were tested by simulating bi- or uniaxially constrained cell-populated collagen gels with different collagen densities, subjected to immediate or delayed uniaxial cyclic strain with varying strain amplitudes. The simulation outcomes are in agreement with previous experimental reports. Taken together, our computational approach is a promising tool to understand and predict the remodeling of collagenous tissues, such as native or tissue-engineered arteries and heart valves.
Micro-computed tomography reconstructions of tibiae of stem cell transplanted osteogenesis imperfecta mice
Authors: Ranzoni Anna M. , Corcelli Michelangelo , Arnett Timothy R. , Guillot Pascale V.
Published: May 2018

Micro-computed tomography (micro-CT) is commonly used to assess bone quality and to evaluate the outcome of experimental therapies in animal models of bone diseases. Generating large datasets is however challenging and data are rarely made publicly available through shared repositories. Here we describe a dataset of micro-CT reconstructed scans of the proximal part of 21 tibiae from wild-type mice, osteogenesis imperfecta mice (homozygous oim/oim) and oim/oim mice transplanted with human amniotic fluid stem cells. The dataset contains, for each sample, 991 8-bit Bitmap reconstructed images and a 3D reconstruction of the bone in the PLY format, available at the online repository Figshare. In line with the increasing effort to make scientific datasets open-access, our data can be downloaded and used by other researchers to compare their observations with ours and to directly test scientific questions on osteogenesis imperfecta bones without the need to generate complete datasets.
Human grasping database for activities of daily living with depth, color and kinematic data streams
Authors: Saudabayev Artur , Rysbek Zhanibek , Khassenova Raykhan , Varol Huseyin Atakan
Published: May 2018

This paper presents a grasping database collected from multiple human subjects for activities of daily living in unstructured environments. The main strength of this database is the use of three different sensing modalities: color images from a head-mounted action camera, distance data from a depth sensor on the dominant arm and upper body kinematic data acquired from an inertial motion capture suit. 3826 grasps were identified in the data collected during 9-hours of experiments. The grasps were grouped according to a hierarchical taxonomy into 35 different grasp types. The database contains information related to each grasp and associated sensor data acquired from the three sensor modalities. We also provide our data annotation software written in Matlab as an open-source tool. The size of the database is 172 GB. We believe this database can be used as a stepping stone to develop big data and machine learning techniques for grasping and manipulation with potential applications in rehabilitation robotics and intelligent automation.
Development of pyrene-stacked carbon nanotube-based hybrid: measurement of NO3−ions using fluorescence spectroscopy
Authors: Billing Beant Kaur , Mayank Mayank , Agnihotri Prabhat K. , Singh Narinder
Published: May 2018

CNT@pyrene hybrid for fluorescent recognition of nitrate ions.
Development of an ultra-sensitive assay for the determination of an aminoalkyl glucosaminide 4-phosphate, GSK1795091, in plasma to support a first time in human study
Authors: Licea-Perez Hermes , Junnotula Venkatraman , Bowen Chester L. , Fang Kasie , Qian Yanwen , Matheny Christopher
Published: May 2018

A chemical derivatization approach for the determination of an aminoalkyl glucosaminide 4-phosphate, GSK1795091 (or CRX-601).
Do we need a catalyst in the determination of dissolved organic carbon in environmental samples?
Authors: Grzybowski Waldemar , Tarasiewicz Paweł , Łukawska-Matuszewska Katarzyna , Szewczun Aleksandra
Published: May 2018

Removal of a platinum catalyst results in lower oxidation efficiency in samples of high organic content.
Development of glycosynthases with broad glycan specificity for the efficient glyco-remodeling of antibodies
Authors: Shivatare Sachin S. , Huang Lin-Ya , Zeng Yi-Fang , Liao Jung-Yu , You Tsai-Hong , Wang Shi-Yun , Cheng Ting , Chiu Chih-Wei , Chao Ping , Chen Li-Tzu , Tsai Tsung-I , Huang Chiu-Chen , Wu Chung-Yi , Lin Nan-Horng , Wong Chi-Huey
Published: May 2018

The first systematic investigation of the effect of IgG-Fc-glycans on their effector functions was achieved by the discovery of novel Endo-S2 mutants as broadly specific glycosynthases.
In situ XPS study of the surface chemistry of MAPI solar cells under operating conditions in vacuum
Authors: Das C. , Wussler M. , Hellmann T. , Mayer T. , Jaegermann W.
Published: May 2018

Organic–inorganic hybrid perovskite solar cells achieved a record efficiency of almost 23% in only a short time span of time.
Polyhedral perspectives on the capacity limit of cathode compounds for lithium-ion batteries: a case study for Li6CoO4
Authors: Chen Zhenlian , Zhang Zhifeng , Li Jun
Published: May 2018

Polyhedral connectivity plays important roles in redox mechanism and electric conductivity. Strategy of cathode design utilizing cumulative cationic and anionic redox is proposed for polyhedral structure of lithium oxide compounds for lithium ion batteries.
Acetylacetonato-based pincer-type nickel(ii) complexes: synthesis and catalysis in cross-couplings of aryl chlorides with aryl Grignard reagents
Authors: Asano Erika , Hatayama Yuki , Kurisu Nobutaka , Ohtani Atsufumi , Hashimoto Toru , Kurihara Youji , Ueda Kazuyoshi , Ishihara Shinji , Nagao Hirotaka , Yamaguchi Yoshitaka
Published: May 2018

The synthesis of acetylacetoneto-based pincer-type nickel(ii) complexes and their catalytic activity were investigated.
SiO2-protected shell mediated templating synthesis of Fe–N-doped carbon nanofibers and their enhanced oxygen reduction reaction performance
Authors: Hu Bi-Cheng , Wu Zhen-Yu , Chu Sheng-Qi , Zhu Hong-Wu , Liang Hai-Wei , Zhang Jing , Yu Shu-Hong
Published: May 2018

An effective SiO2-protecting pyrolysis method for the synthesis of highly active meso/microporous Fe–N-CNF catalysts is presented.
Granny Smith apple procyanidin extract upregulates tight junction protein expression and modulates oxidative stress and inflammation in lipopolysaccharide-induced Caco-2 cells
Authors: Wu H. , Luo T. , Li Y. M. , Gao Z. P. , Zhang K. Q. , Song J. Y. , Xiao J. S. , Cao Y. P.
Published: May 2018

Granny Smith apple procyanidin extracts upregulate tight junction protein expression, probably acting via the modulation of oxidative stress and inflammation in lipopolysaccharide-induced Caco-2 cells.
Synthesis and antiplasmodial activity of purine-based C-nucleoside analogues
Authors: Singh Kartikey , Joshi Prince , Mahar Rohit , Baranwal Pragati , Shukla Sanjeev K. , Tripathi Renu , Tripathi Rama Pati
Published: May 2018

A series of purine-based homologous C-nucleoside mimics have been synthesized and evaluated for their antiplasmodial activity.
Low-molecular-mass iron in healthy blood plasma is not predominately ferric citrate
Authors: Dziuba Nathaniel , Hardy Joanne , Lindahl Paul A.
Published: May 2018

The labile iron pool in blood consists of complexes with masses of 400–2500 Daltons that are not ferric citrate.
Correction: Computational approaches to cell–nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity
Authors: Ding Hong-ming , Ma Yu-qiang
Published: May 2018

Correction for ‘Computational approaches to cell–nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity’ by Hong-ming Ding et al., Nanoscale Horiz., 2018, 3, 6–27.
Selective two-photon absorption in carbon dots: a piece of the photoluminescence emission puzzle
Authors: Santos Carla I. M. , Mariz Inês F. A. , Pinto Sandra N. , Gonçalves Gil , Bdikin Igor , Marques Paula A. A. P. , Neves Maria Graça P. M. S. , Martinho José M. G. , Maçôas Ermelinda M. S.
Published: May 2018

Optical spectroscopy of carbon nanodots reveals excitation-mode-dependent emission. Linear and nonlinear excitation at the same total energy results in different emission spectra.
Magnetic field modulated SERS enhancement of CoPt hollow nanoparticles with sizes below 10 nm
Authors: Wang Yinong , Liu Qing , Sun Yinghui , Wang Rongming
Published: May 2018

CoPt hollow nanoparticles with mean size below 10 nm are synthesized by a simple solution method and their SERS properties with respect to magnetic field are studied.
Photoorganocatalysis, small organic molecules and light in the service of organic synthesis: the awakening of a sleeping giant
Authors: Sideri Ioanna K. , Voutyritsa Errika , Kokotos Christoforos G.
Published: May 2018

This review is focused on recent developments in the use of small organic molecules as photocatalysts.
Inhibition of lysozyme's polymerization activity using a polymer structural mimic
Authors: Morris D. L. , Leeper T. C. , Ziegler C. J.
Published: May 2018

Hen egg white lysozyme (HEWL) is a green catalyst capable of polymerizing the formation of 2-ethynylpyridine. 1,3-di(2-pyridyl)propane (DPP) is a mimic of the polymer repeating unit and a polymerization inhibitor. DPP's interaction with HEWL reveals structural insight into the mechanism of polymerization.
Increasing spin crossover cooperativity in 2D Hofmann-type materials with guest molecule removal
Authors: Zenere Katrina A. , Duyker Samuel G. , Trzop Elzbieta , Collet Eric , Chan Bun , Doheny Patrick W. , Kepert Cameron J. , Neville Suzanne M.
Published: May 2018

Ambient temperature spin crossover with wide hysteresis has been achieved in 2D Hofmann-type materials, where removal of guest molecules optimises ligand–ligand interactions, resulting in increased cooperativity.
A bottom-up synthesis of rare-earth-hydrotalcite monolayer nanosheets toward multimode imaging and synergetic therapy
Authors: Mei Xuan , Ma Jialing , Bai Xue , Zhang Xin , Zhang Shaomin , Liang Ruizheng , Wei Min , Evans David G. , Duan Xue
Published: May 2018

Gd3+ and Yb3+ co-doped LDH monolayer nanosheets are developed via a facile “bottom-up” method and exhibit excellent drug loading capacity for tri-mode imaging guided cancer therapy.
Large-bite diboranes for the μ(1,2) complexation of hydrazine and cyanide
Authors: Chen Chang-Hong , Gabbaï François P.
Published: May 2018

A diborane based on the 1,8-biphenylenediyl backbone displays a high affinity for hydrazine while also behaving as a cyanide sponge.
Annulation cascade of arylnitriles with alkynes to stable delocalized PAH carbocations via intramolecular rhodium migration
Authors: Yin Jiangliang , Zhou Fulin , Zhu Lei , Yang Mufan , Lan Yu , You Jingsong
Published: May 2018

An annulation cascade of arylnitriles with alkynes is disclosed to provide stable delocalized carbocations with the ability to specifically target lysosomes.
Room temperature catalytic carbon–hydrogen bond alumination of unactivated arenes: mechanism and selectivity
Authors: Hooper Thomas N. , Garçon Martí , White Andrew J. P. , Crimmin Mark R.
Published: May 2018

We report the first catalytic methods for the transformation of C–H bonds of unactivated arenes into C–Al bonds.
The seven sisters DANCe
Authors: Olivares J. , Sarro L. M. , Moraux E. , Berihuete A. , Bouy H. , Hernández-Jiménez S. , Bertin E. , Galli P. A. B. , Huelamo N. , Bouvier J. , Barrado D.
Published: May 2018

Context. The photometric and astrometric measurements of the Pleiades DANCe DR2 survey provide an excellent test case for the benchmarking of statistical tools aiming at the disentanglement and characterisation of nearby young open cluster (NYOC) stellar populations.

Aims. We aim to develop, test, and characterise of a new statistical tool (intelligent system) for the sifting and analysis of NYOC populations.

Methods. Using a Bayesian formalism, with this statistical tool we were able to obtain the posterior distributions of parameters governing the cluster model. It also used hierarchical bayesian models to establish weakly informative priors, and incorporates the treatment of missing values and non-homogeneous (heteroscedastic) observational uncertainties.

Results. From simulations, we estimated that this statistical tool renders kinematic (proper motion) and photometric (luminosity) distributions of the cluster population with a contamination rate of 5.8 ± 0.2%. The luminosity distributions and present day mass function agree with the ones found in a recent study, on the completeness interval of the survey. At the probability threshold of maximum accuracy, the classifier recovers ≈90% of the recently published candidate members and finds 10% of new ones.

Conclusions. A new statistical tool for the analysis of NYOC is introduced, tested, and characterised. Its comprehensive modelling of the data properties allows it to get rid of the biases present in previous works. In particular, those resulting from the use of only completely observed (non-missing) data and the assumption of homoskedastic uncertainties. Also, its Bayesian framework allows it to properly propagate observational uncertainties into membership probabilities and cluster velocity and luminosity distributions. Our results are in a general agreement with those from the literature, although we provide the most up-to-date and extended list of candidate members of the Pleiades cluster.
Modelling of integrated-light spectra from the optical to the near-infrared: the globular cluster G280 in M31
Authors: Larsen S. S. , Pugliese G. , Brodie J. P.
Published: May 2018

Context. In previous papers, we introduced our method for measuring chemical abundances from integrated-light spectra of globular clusters and applied it to a variety of extragalactic star clusters. Our work so far, however, has concentrated primarily on the optical range 4200 Å –6200 Å.

Aims. Here we extend our analysis technique to the infrared and test it on an H-band spectrum of the massive globular cluster G280 in M 31.

Methods. We simultaneously analyse an optical spectrum of G280, obtained with the HIRES spectrograph on the Keck I telescope, and an H-band spectrum obtained with NIRSPEC on Keck II. We discuss the sensitivity of our results to various modifications of the input assumptions, such as different line lists and isochrones and the possible presence of a metallicity spread in G280.

Results. When using the most recent version of the Kurucz line list, we measure iron abundances of [Fe/H] = −0.68±0.02 from the optical spectrum and [Fe/H] = −0.60±0.07 from the infrared spectrum. These values agree well with previous spectroscopic determinations of the metallicity of G280. While the small difference between the optical and infrared measurements is insignificant given the uncertainties, it is also consistent with a metallicity spread similar to that observed in massive GCs such as ω Cen and G1, and also hinted at by the colour-magnitude diagram of G280. The optical and infrared spectra both indicate an α-enhancement of about 0.3–0.4 dex relative to solar-scaled abundances, as typically also observed in Milky Way GCs.

Conclusions. From this analysis, it appears that our integrated-light analysis technique also performs well in the H-band. However, complications due to the presence of molecular bands and telluric contamination are more severe in the infrared, and accurate modelling of the coolest giants is more critical.
Extended percolation analysis of the cosmic web
Authors: Einasto J. , Suhhonenko I. , Liivamägi L. J. , Einasto M.
Published: May 2018

Aims. We develop an extended percolation method to allow the comparison of geometrical properties of the real cosmic web with the simulated dark matter (DM) web for an ensemble of over- and under-density systems.

Methods. We scanned density fields of DM model and Sloan Digital Sky Survey (SDSS) observational samples and found connected over- and under-density regions in a large range of threshold densities. Lengths, filling factors, and numbers of largest clusters and voids as functions of the threshold density were used as percolation functions.

Results. We find that percolation functions of DM models of varying box sizes are very similar to each other. This stability suggests that properties of the cosmic web, as found in the present paper, can be applied to the cosmic web as a whole. Percolation functions depend strongly on the smoothing length. At smoothing length 1 h−1 Mpc the percolation threshold density for clusters is log PC = 0.718 ± 0.014, and for voids such density is log PV = −0.816 ± 0.015; this is very different from percolation thresholds for random samples, which are log P0 = 0.00 ± 0.02.

Conclusions. The extended percolation analysis is a versatile method to study various geometrical properties of the cosmic web in a wide range of parameters. Percolation functions of the SDSS sample are very different from percolation functions of DM model samples. The SDSS sample has only one large percolating void that fills almost the whole volume. The SDSS sample contains numerous small isolated clusters at low threshold densities, instead of one single percolating DM cluster. These differences are due to the tenuous DM web, which is present in model samples but absent in real observational samples.
An updated stellar census of the Quintuplet cluster
Authors: Clark J. S. , Lohr M. E. , Patrick L. R. , Najarro F. , Dong H. , Figer D. F.
Published: May 2018

Context. Found within the central molecular zone, the Quintuplet is one of the most massive young clusters in the Galaxy. As a consequence it offers the prospect of constraining stellar formation and evolution in extreme environments. However, current observations suggest that it comprises a remarkably diverse stellar population that is difficult to reconcile with an instantaneous formation event.

Aims. To better understand the nature of the cluster our aim is to improve observational constraints on the constituent stars.

Methods. In order to accomplish this goal we present Hubble Space Telescope/NICMOS+WFC3 photometry and Very Large Telescope/SINFONI+KMOS spectroscopy for ∼100 and 71 cluster members, respectively.

Results. Spectroscopy of the cluster members reveals the Quintuplet to be far more homogeneous than previously expected. All supergiants are classified as either O7–8 Ia or O9–B0 Ia, with only one object of earlier (O5 I–III) spectral type. These stars form a smooth morphological sequence with a cohort of seven early-B hypergiants and six luminous blue variables and WN9-11h stars, which comprise the richest population of such stars of any stellar aggregate known. In parallel, we identify a smaller population of late-O hypergiants and spectroscopically similar WN8–9ha stars. No further H-free Wolf–Rayet (WR) stars are identified, leaving an unexpectedly extreme ratio of 13:1 for WC/WN stars. A subset of the O9–B0 supergiants are unexpectedly faint, suggesting they are both less massive and older than the greater cluster population. Finally, no main sequence objects were identifiable.

Conclusions. Due to uncertainties over which extinction law to apply, it was not possible to quantitatively determine a cluster age via isochrone fitting. Nevertheless, we find an impressive coincidence between the properties of cluster members preceding the H-free WR phase and the evolutionary predictions for a single, non-rotating 60 M⊙ star; in turn this implies an age of ∼3.0–3.6 Myr for the Quintuplet. Neither the late O-hypergiants nor the low luminosity supergiants are predicted by such a path; we suggest that the former either result from rapid rotators or are the products of binary driven mass-stripping, while the latter may be interlopers. The H-free WRs must evolve from stars with an initial mass in excess of 60 M⊙ but it appears difficult to reconcile their observational properties with theoretical expectations. This is important since one would expect the most massive stars within the Quintuplet to be undergoing core-collapse/SNe at this time; since the WRs represent an evolutionary phase directly preceding this event,their physical properties are crucial to understanding both this process and the nature of the resultant relativistic remnant. As such, the Quintuplet provides unique observational constraints on the evolution and death of the most massive stars forming in the local, high metallicity Universe.
Climate, weather, space weather: model development in an operational context
Authors: Folini Doris
Published: May 2018

Aspects of operational modeling for climate, weather, and space weather forecasts are contrasted, with a particular focus on the somewhat conflicting demands of “operational stability” versus “dynamic development” of the involved models. Some common key elements are identified, indicating potential for fruitful exchange across communities. Operational model development is compelling, driven by factors that broadly fall into four categories: model skill, basic physics, advances in computer architecture, and new aspects to be covered, from costumer needs over physics to observational data. Evaluation of model skill as part of the operational chain goes beyond an automated skill score. Permanent interaction between “pure research” and “operational forecast” people is beneficial to both sides. This includes joint model development projects, although ultimate responsibility for the operational code remains with the forecast provider. The pace of model development reflects operational lead times. The points are illustrated with selected examples, many of which reflect the author’s background and personal contacts, notably with the Swiss Weather Service and the Max Planck Institute for Meteorology, Hamburg, Germany. In view of current and future challenges, large collaborations covering a range of expertise are a must − within and across climate, weather, and space weather. To profit from and cope with the rapid progress of computer architectures, supercompute centers must form part of the team.
The Integration of Metabolomics and Next-Generation Sequencing Data to Elucidate the Pathways of Natural Product Metabolism in Medicinal Plants
Authors: Scossa Federico , Benina Maria , Alseekh Saleh , Zhang Youjun , Fernie Alisdair
Published: May 2018

Plants have always been used as medicines since ancient times to treat diseases. The knowledge around the active components of herbal preparations has remained nevertheless fragmentary: the biosynthetic pathways of many secondary metabolites of pharmacological importance have been clarified only in a few species, while the chemodiversity present in many medicinal plants has remained largely unexplored. Despite the advancements of synthetic biology for production of medicinal compounds in heterologous hosts, the native plant species are often the most reliable and economic source for their production. It thus becomes fundamental to investigate the metabolic composition of medicinal plants to characterize their natural metabolic diversity and to define the biosynthetic routes in planta of important compounds to develop strategies to further increase their content. We present here a number of case studies for selected classes of secondary metabolites and we review their health benefits and the historical developments in their structural elucidation and characterization of biosynthetic genes. We cover the cases of benzoisoquinoline and monoterpenoid indole alkaloids, cannabinoids, caffeine, ginsenosides, withanolides, artemisinin, and taxol; we show how the “early” biochemical or the more recent integrative approaches–based on omics-analyses–have helped to elucidate their metabolic pathways and cellular compartmentation. We also summarize how the knowledge generated about their biosynthesis has been used to develop metabolic engineering strategies in heterologous and native hosts. We conclude that following the advent of novel, high-throughput and cost-effective analytical technologies, the secondary metabolism of medicinal plants can now be examined under the lens of systems biology.
De Novo Transcriptome Assembly and Characterization of Lithospermum officinale to Discover Putative Genes Involved in Specialized Metabolites Biosynthesis
Authors: Rai Amit , Nakaya Taiki , Shimizu Yohei , Rai Megha , Nakamura Michimi , Suzuki Hideyuki , Saito Kazuki , Yamazaki Mami
Published: May 2018

Lithospermum officinale is a valuable source of bioactive metabolites with medicinal and industrial values. However, little is known about genes involved in the biosynthesis of these metabolites, primarily due to the lack of genome or transcriptome resources. This study presents the first effort to establish and characterize de novo transcriptome assembly resource for L. officinale and expression analysis for three of its tissues, namely leaf, stem, and root. Using over 4Gbps of RNA-sequencing datasets, we obtained de novo transcriptome assembly of L. officinale, consisting of 77,047 unigenes with assembly N50 value as 1524 bps. Based on transcriptome annotation and functional classification, 52,766 unigenes were assigned with putative genes functions, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. KEGG pathway and gene ontology enrichment analysis using highly expressed unigenes across three tissues and targeted metabolome analysis showed active secondary metabolic processes enriched specifically in the root of L. officinale. Using co-expression analysis, we also identified 20 and 48 unigenes representing different enzymes of lithospermic/chlorogenic acid and shikonin biosynthesis pathways, respectively. We further identified 15 candidate unigenes annotated as cytochrome P450 with the highest expression in the root of L. officinale as novel genes with a role in key biochemical reactions toward shikonin biosynthesis. Thus, through this study, we not only generated a high-quality genomic resource for L. officinale but also propose candidate genes to be involved in shikonin biosynthesis pathways for further functional characterization.
Chromium-Catalyzed Asymmetric Dearomatization–Addition Reactions of Halomethyloxazoles and Indoles
Authors: He Wei-Min , Zhang Guozhu , Wang Zheng , Ji Hongtao , Xiong Yang
Published: May 2018

The asymmetric dearomatization–addition reaction of halo­methyloxazoles and halomethylindoles with aldehydes is realized in the presence of a carbazole-based bisoxazoline CrCl2 complex to afford the corresponding enantioenriched, hydroxylated oxazoline and indoline products. The observed excellent chemo-, regio-, diastereo- and enantioselectivities are notable advantages of this protocol. The strategy established in this study is expected to find application in the synthesis of azaheterocycles with biological significance and useful functionalities.
Stereoselective Oxidation of Titanium(IV) Enolates with Oxygen
Authors: Romea Pedro , Urpí Fèlix , Gómez-Palomino Alejandro
Published: May 2018

A novel approach to synthesize enantiomerically pure α-hydroxy carboxylic derivatives is reported. A highly stereoselective oxidation of titanium(IV) enolates from chiral N-acyloxazolidinones is performed with oxygen under simple experimental conditions that do not require any reducing steps. The success of this approach depends on the biradical character of titanium(IV) enolates.
ZnO-Nanoparticles-Catalyzed Synthesis of Poly(tetrahydrobenzimidazo[2,1-b]quinazolin-1(2H)-ones) as Novel Multi-armed Molecules
Authors: Abdelhamid Ismail , Elwahy Ahmed , Diab Hadeer
Published: May 2018

A new series of poly(tetrahydrobenzimidazo[2,1-b]-quinazolin-1(2H)-ones) was synthesized in good yields using a multicomponent reaction of poly(aldehydes), dimedone, and 2-aminobenzimidazole in DMF under conventional heating as well as under microwave irradiation.
Mechanistic Basis for the Differential Effects of Rivaroxaban and Apixaban on Global Tests of Coagulation
Authors: Kim Paul , Yeh Calvin , Dale Brian , Leslie Beverly , Stafford Alan , Fredenburgh James , Hirsh Jack , Weitz Jeffrey
Published: May 2018

Rivaroxaban and apixaban are both small molecules that reversibly inhibit factor Xa. Compared with rivaroxaban, apixaban has minimal effects on the prothrombin time and activated partial thromboplastin time. To investigate this phenomenon, we used a factor Xa-directed substrate in a buffer system. Although rivaroxaban and apixaban inhibited factor Xa with similar Ki values at equilibrium, kinetic measurements revealed that rivaroxaban inhibited factor Xa up to 4-fold faster than apixaban (p < 0.001). Using a discontinuous chromogenic assay to monitor thrombin production by prothrombinase in a purified system, rivaroxaban was 4-fold more potent than apixaban (Ki values of 0.7 ± 0.3 and 2.9 ± 0.5 nM, respectively; p = 0.02). Likewise, in thrombin generation assays in plasma, rivaroxaban prolonged the lag time and suppressed endogenous thrombin potential to a greater extent than apixaban. To characterize how the two inhibitors differ in recognizing factor Xa, inhibition of prothrombinase was monitored in real-time using a fluorescent probe for thrombin. The data were fit using a mixed-inhibition model and the individual association and dissociation rate constants were determined. The association rates for the binding of rivaroxaban to either free factor Xa or factor Xa incorporated into the prothrombinase complex were 10- and 1,193-fold faster than those for apixaban, respectively, whereas dissociation rates were about 3-fold faster. Collectively, these findings suggest that rivaroxaban and apixaban differ in their capacity to inhibit factor Xa and provide a plausible explanation for the observation that rivaroxaban has a greater effect on global tests of coagulation than apixaban.
Comparing Part-Solid and Pure-Solid Tumors in the TNM Classification of Lung Cancer (Eighth Edition)
Authors: Yamanashi Keiji , Okumura Norihito , Yamamoto Yoshiharu , Takahashi Ayuko , Nakashima Takashi , Matsuoka Tomoaki
Published: May 2018

Background In the eighth edition of the TNM classification, the lung tumors that have the same solid components are categorized either as part-solid or pure-solid tumors. However, this is debatable since the tumors in the same T component categories were evaluated without considering this categorization, and was based on a more malignant behavior and a poorer prognosis of pure-solid tumors. The aim of this study was to investigate and compare the prognosis between part-solid and pure-solid tumors.

Methods We retrospectively analyzed 530 patients who were diagnosed with clinical-T1a-cN0M0 non–small-cell lung cancer (NSCLC) and were treated surgically. The subjects were divided into part-solid and pure-solid tumor groups using thin-section computed tomography. The prognosis was compared between the groups.

Results Although relapse-free survival (RFS) was significantly shorter in the pure-solid tumor group (p = 0.016), no significant differences were observed in the overall survival (OS) between the two groups (p = 0.247). In 137 propensity score–matched pairs, including variables such as age, gender, Brinkman index, body mass index, forced expiratory volume in 1 second/forced vital capacity, Charlson comorbidity index, carcinoembryonic antigen levels, clinical-T status, surgical procedure, and extent of surgery, no significant differences were seen in the RFS and OS between the two groups (p = 0.709 and p = 0.517, respectively).

Conclusion In the eighth edition of the TNM classification of clinical-T1a-cN0M0 NSCLC, the prognosis of part-solid and pure-solid tumors showed no significant differences. Solid component size of the tumor is considered important prognostic factor in early-stage NSCLC.
Shock wave boundary layer interaction controlled by surface arc plasma actuators
Authors: Gan Tian , Wu Yun , Sun Zhengzhong , Jin Di , Song Huimin , Jia Min
Published: May 2018

An array of 16 surface arc plasma actuators (SAPAs) is employed to control the shock wave boundary layer interaction (SWBLI) at a 26° compression ramp in a Mach 2.0 flow. A new electrical circuit is used to actuate all 16 SAPAs. The electrical measurement reveals significant augmentation in peak current (200 A) and an energy deposition of 1.05 J, which are the nominal characteristics of the setup. The SAPA array is later applied for SWBLI control. The actuator array is placed upstream of the SWBLI and operates at four different frequencies, namely, 500 Hz, 1 kHz, 2 kHz, and 5 kHz. In the wind tunnel experiment, high-speed schlieren at 25 000 frames per second is used for flow visualization. The shock wave system is modified significantly by the controlling gas blobs (CGBs) or controlling gas bulbs (CGBUs) generated by SAPAs. The foot portion of the separation shock wave disappears, and the oblique shock wave bifurcates when the CGBs pass through the interaction region. The shock weakening effect is further verified through the rms of the schlieren intensity of the same phase.
Boundary control of laminated beams with interfacial slip
Authors: Mustafa Muhammad I.
Published: May 2018

In this paper, we consider a laminated beam model. This structure is given by two identical uniform layers on top of each other, taking into account that an adhesive of small thickness is bonding the two surfaces and produces an interfacial slip. We use boundary feedback control and establish an exponential energy decay result. Our result improves the earlier related results in the literature.
Temporal and spatial evolution of nanosecond microwave-driven plasma
Authors: Chang C. , Chen X. Q. , Zhu M. , Pu Y. K.
Published: May 2018

In this paper, a method for simultaneously acquiring the temporal and spatial evolution of characteristic plasma spectra in a single microwave pulse is proposed and studied. By using multi-sub-beam fiber bundles coupled with a spectrometer and EMICCD (Electron-multiplying intensified charge-coupled device), the spatial distribution and time evolution of characteristic spectra of desorbed gases at the dielectric/vacuum interface during nanosecond microwave-driven plasma discharge are observed. Arrays of small align tubes punctured with metal walls of feed horn are filled with separate fibers of matched sizes and equal lengths. The output ends of fibers arranged in a single longitudinal column are connected to the entrance slit of a spectrometer, where the optical spectrum inputs to a high-speed EMICCD, to detect the rapid-varying time and space spectra of nanosecond giga-watt microwave discharges. The evolution of spectral clusters of N2 (C-B), N2+ (B-X), and the hydrogen atoms is discovered and monitored. The whole duration of light emission is much longer than the microwave pulse, and the intensities of ion N2+ (B-X) spectra increase after microwave pulses with rise times of 25–50 ns. The brightness distribution of plasma spectra in different space is observed and approximately consistent with the simulated E-field distribution.