bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides
Authors: Ma Wenting , Peng Donghai , Walker Sharon L. , Cao Bin , Gao Chun-Hui , Huang Qiaoyun , Cai Peng
Published: January 2017

Clay minerals and metal oxides, as important parts of the soil matrix, play crucial roles in the development of microbial communities. However, the mechanism underlying such a process, particularly on the formation of soil biofilm, remains poorly understood. Here, we investigated the effects of montmorillonite, kaolinite, and goethite on the biofilm formation of the representative soil bacteria Bacillus subtilis. The bacterial biofilm formation in goethite was found to be impaired in the initial 24 h but burst at 48 h in the liquid–air interface. Confocal laser scanning microscopy showed that the biofilm biomass in goethite was 3–16 times that of the control, montmorillonite, and kaolinite at 48 h. Live/Dead staining showed that cells had the highest death rate of 60% after 4 h of contact with goethite, followed by kaolinite and montmorillonite. Atomic force microscopy showed that the interaction between goethite and bacteria may injure bacterial cells by puncturing cell wall, leading to the swarming of bacteria toward the liquid–air interface. Additionally, the expressions of abrB and sinR, key players in regulating the biofilm formation, were upregulated at 24 h and downregulated at 48 h in goethite, indicating the initial adaptation of the cells to minerals. A model was proposed to describe the effects of goethite on the biofilm formation. Our findings may facilitate a better understanding of the roles of soil clays in biofilm development and the manipulation of bacterial compositions through controlling the biofilm in soils.
Erratum: Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors
Authors: Orsini Luisa , Gilbert Donald , Podicheti Ram , Jansen Mieke , Brown James B. , Solari Omid Shams , Spanier Katina I. , Colbourne John K. , Rusch Douglas B. , Decaestecker Ellen , Asselman Jana , De Schamphelaere Karel A.C. , Ebert Dieter , Haag Christoph R. , Kvist Jouni , Laforsch Christian , Petrusek Adam , Beckerman Andrew P. , Little Tom J. , Chaturvedi Anurag , Pfrender Michael E. , De Meester Luc , Frilander Mikko J.
Published: January 2017

Scientific Data 3:160030 doi:10.1038/sdata.2016.30 (2016); Published 10 May 2016; Updated 31 Jan 2017 The original version of this Data Descriptor contained a typographical error in the spelling of the author Douglas B. Rusch, which was incorrectly given as Douglas Rush. This has now been corrected in the PDF and HTML versions of the Data Descriptor.
Spheroid arrays for high-throughput single-cell analysis of spatial patterns and biomarker expression in 3D
Authors: Ivanov Delyan P. , Grabowska Anna M.
Published: January 2017

We describe and share a device, methodology and image analysis algorithms, which allow up to 66 spheroids to be arranged into a gel-based array directly from a culture plate for downstream processing and analysis. Compared to processing individual samples, the technique uses 11-fold less reagents, saves time and enables automated imaging. To illustrate the power of the technology, we showcase applications of the methodology for investigating 3D spheroid morphology and marker expression and for in vitro safety and efficacy screens. First, spheroid arrays of 11 cell-lines were rapidly assessed for differences in spheroid morphology. Second, highly-positive (SOX-2), moderately-positive (Ki-67) and weakly-positive (βIII-tubulin) protein targets were detected and quantified. Third, the arrays enabled screening of ten media compositions for inducing differentiation in human neurospheres. Last, the application of spheroid microarrays for spheroid-based drug screens was demonstrated by quantifying the dose-dependent drop in proliferation and increase in differentiation in etoposide-treated neurospheres.
A novel HDAC inhibitor, CG200745, inhibits pancreatic cancer cell growth and overcomes gemcitabine resistance
Authors: Lee Hee Seung , Park Soo Been , Kim Sun A , Kwon Sool Ki , Cha Hyunju , Lee Do Young , Ro Seonggu , Cho Joong Myung , Song Si Young
Published: January 2017

Pancreatic cancer is predominantly lethal, and is primarily treated using gemcitabine, with increasing resistance. Therefore, novel agents that increase tumor sensitivity to gemcitabine are needed. Histone deacetylase (HDAC) inhibitors are emerging therapeutic agents, since HDAC plays an important role in cancer initiation and progression. We evaluated the antitumor effect of a novel HDAC inhibitor, CG200745, combined with gemcitabine/erlotinib on pancreatic cancer cells and gemcitabine-resistant pancreatic cancer cells. Three pancreatic cancer-cell lines were used to evaluate the antitumor effect of CG200745 combined with gemcitabine/erlotinib. CG200745 induced the expression of apoptotic proteins (PARP and caspase-3) and increased the levels of acetylated histone H3. CG200745 with gemcitabine/erlotinib showed significant growth inhibition and synergistic antitumor effects in vitro. In vivo, gemcitabine/erlotinib and CG200745 reduced tumor size up to 50%. CG200745 enhanced the sensitivity of gemcitabine-resistant pancreatic cancer cells to gemcitabine, and decreased the level of ATP-binding cassette-transporter genes, especially multidrug resistance protein 3 (MRP3) and MRP4. The novel HDAC inhibitor, CG200745, with gemcitabine/erlotinib had a synergistic anti-tumor effect on pancreatic cancer cells. CG200745 significantly improved pancreatic cancer sensitivity to gemcitabine, with a prominent antitumor effect on gemcitabine-resistant pancreatic cancer cells. Therefore, improved clinical outcome is expected in the future.
The anti-tumor activities of Neferine on cell invasion and oxaliplatin sensitivity regulated by EMT via Snail signaling in hepatocellular carcinoma
Authors: Deng Ganlu , Zeng Shan , Ma Junli , Zhang Yan , Qu Yanling , Han Ying , Yin Ling , Cai Changjing , Guo Cao , Shen Hong
Published: January 2017

Tumor invasion and chemotherapy resistance, which are associated with epithelial-mesenchymal transition (EMT), remain as major challenges in hepatocellular carcinoma (HCC) treatment. Neferine, a natural component of Nelumbo nucifera, have been proven the antitumor efficiency in cancer, but the effects of Neferine on HCC invasion and chemosensitivity need to be elucidated. Applying multiple assays of cell proliferation, flow cytometry, immunofluorescence staining, qRT-PCR, Western blot, fluorescence molecular tomography imaging, the influences of Neferine on EMT-regulated viability, apoptosis, invasion, and oxaliplatin (OXA) sensitivity were assessed in HCC cells of HepG2 and Bel-7402, as well as in xenograft animal models in vivo. Here, we reported that Neferine had no obvious effects on HCC cells proliferation, but significantly enhanced cytotoxicity and apoptosis caused by OXA in vitro and in vivo. Through an upregulation of E-cadherin and downregulation of Vimentin, Snail and N-cadherin, Neferine suppressed EMT-induced migration and invasion abilities of HCC cells. TGF-β1 cancelled the effects of Neferine on the migration and invasion of HCC cells. Snail overexpression or TGF-β1-induced EMT attenuated Neferine-mediated OXA sensitization in HCC. Together, our data suggest that Neferine enhances oxaliplatin sensitivity through an inhibition of EMT in HCC cells. Neferine may be used as an OXA sensitizer in HCC chemotherapy.
Effects of light on quantum phases and topological properties of two-dimensional Metal-organic frameworks
Authors: Wang Yunhua , Liu Yulan , Wang Biao
Published: January 2017

Periodically driven nontrivial quantum states open another door to engineer topological phases in solid systems by light. Here we show, based on the Floquet-Bloch theory, that the on-resonant linearly and circularly polarized infrared light brings in the exotic Floquet quantum spin Hall state and half-metal in two-dimensional Metal-organic frameworks (2D MOFs) because of the unbroken and broken time-reversal symmetry, respectively. We also observe that the off-resonant light triggers topological quantum phase transitions and induces semimetals with pseudospin-1 Dirac-Weyl fermions via the photon-dressed topological band structures of 2D MOFs. This work paves a way to design light-controlled spintronics and optoelectronics based on 2D MOFs.
Construction of 2D covalent organic frameworks by taking advantage of the variable orientation of imine bonds
Authors: Xu Shun-Qi , Liang Rong-Ran , Zhan Tian-Guang , Qi Qiao-Yan , Zhao Xin
Published: January 2017

A model has been established to construct covalent organic frameworks (COFs) by taking advantage of the variable orientation of imine bonds, from which an unprecedented heterodromous orientation of CN linkages in the COFs was observed.
Mechanistic investigation of the NH-sulfoximination of sulfide. Evidence for λ6-sulfanenitrile intermediates
Authors: Lohier Jean-François , Glachet Thomas , Marzag Hamid , Gaumont Annie-Claude , Reboul Vincent
Published: January 2017

One-pot synthesis of NH-sulfoximines from sulfides was reported through fully described acetoxy- and methoxy-λ6-sulfanenitrile intermediates (1H, 13C, 15N NMR and HRMS).
Comparison of tetrel bonds in neutral and protonated complexes of pyridineTF3and furanTF3(T = C, Si, and Ge) with NH3
Authors: Liu Mingxiu , Li Qingzhong , Scheiner Steve
Published: January 2017

Protonation not only changes the primary interaction mode between α/β-furanCF3/p-PyCF3and NH3but also prominently enhances the strength of the Si/Ge⋯N tetrel bond.
Simulated photoelectron intensities at the aqueous solution–air interface for flat and cylindrical (microjet) geometries
Authors: Olivieri Giorgia , Parry Krista M. , Powell Cedric J. , Tobias Douglas J. , Brown Matthew A.
Published: January 2017

The average emission angle and information depth of a photoelectron spectroscopy experiment that employs a liquid microjet is determined using SESSA and the predicted photoelectron intensities are compared with those from a flat aqueous interface.
On the twinning in ZnPd
Authors: Ivarsson Dennis C. A. , Burkhardt Ulrich , Heggen Marc , Ormeci Alim , Armbrüster Marc
Published: January 2017

Twinning in ZnPd characterised from the macroscopic to the atomic scale.
A luminescent Pt2Fe spin crossover complex
Authors: Schäfer Bernhard , Bauer Thomas , Faus Isabelle , Wolny Juliusz A. , Dahms Fabian , Fuhr Olaf , Lebedkin Sergei , Wille Hans-Christian , Schlage Kai , Chevalier Katharina , Rupp Fabian , Diller Rolf , Schünemann Volker , Kappes Manfred M. , Ruben Mario
Published: January 2017

A heterotrinuclear luminescent [Pt2Fe] spin crossover (SCO) complex was developed, synthesized, and investigated.
Mixing Li and Cs in the reduction of corannulene for the assembly of a cesium-capped sandwich with a hexanuclear heterometallic core
Authors: Spisak Sarah N. , Wei Zheng , Petrukhina Marina A.
Published: January 2017

In the first Li/Cs organometallic self-assembly, the tetrareduced corannulene decks are angled up to keep the highly-charged (Li3Cs3)6+ unit in between, with two external Cs+ ions capping the sandwich from outside.
Extended germa[N]pericyclynes: synthesis and characterization
Authors: Tanimoto Hiroki , Fujiwara Taro , Mori Junta , Nagao Tomohiko , Nishiyama Yasuhiro , Morimoto Tsumoru , Ito Shunichiro , Tanaka Kazuo , Chujo Yoshiki , Kakiuchi Kiyomi
Published: January 2017

We herein describe the syntheses and characterization of extended germa[N]pericyclynes, which are macrocycles composed of germanium–butadiyne units.
Synthesis of silicon carbide nanocrystals from waste polytetrafluoroethylene
Authors: Wang Liangbiao , Cheng Qinglin , Qin Hengfei , Li Zhongchun , Lou Zhengsong , Lu Juanjuan , Zhang Junhao , Zhou Quanfa
Published: January 2017

Resource utilization of waste plastic could solve the problem of environmental pollution and simultaneously relieve energy shortages, achieving sustainable development.
Magnetic, recyclable PtyCo1−y/Ti3C2X2 (X = O, F) catalyst: a facile synthesis and enhanced catalytic activity for hydrogen generation from the hydrolysis of ammonia borane
Authors: Fan Guangyin , Li Xiaojing , Ma Yuling , Zhang Yun , Wu Jiangtao , Xu Bin , Sun Ting , Gao Daojiang , Bi Jian
Published: January 2017

Magnetic recyclable PtyCo1−y/Ti3C2X2 (X = O, F) catalyst exhibits excellent catalytic performance for the hydrolysis of AB at room temperature.
Design and structural characterization of the all-metal aromatic sandwich species [Bi3Au3Bi3]3−: insight from density functional theory
Authors: Tang Li-Hong , Zhu Ting-Ting , Ning Ping , Li Kai , Bao Shuang-You , Jin Xu , Zhang Xiu-Ying
Published: January 2017

The [Bi3Au3Bi3]3− species, with hollow features, has a unique all-metal sandwich aromatic structure.
Synthesis, photophysical and concentration-dependent tunable lasing behavior of 2,6-diacetylenyl-functionalized BODIPY dyes
Authors: Maity Apurba , Sarkar Anirban , Sil Amit , B. N. Shivakiran Bhaktha , Patra Sanjib K.
Published: January 2017

Extended π-conjugation through the 2- and 6-positions of the BODIPY core induces tunable yellow-red lasing with excellent efficiency of up to 41% in toluene.
Synthesis of pyrazole (hemi)aminals via the cleavage of saturated aliphatic ether C–O bonds in the presence of ferric halides
Authors: Govor Evgen V. , Sanakis Yiannis , Raptis Raphael G.
Published: January 2017

The discovery of reactions utilizing previously considered inert functional groups opens up new paths towards the synthesis of desired products.
Imidazo[1,5-a]pyridin-3-ylidenes as π-accepting carbene ligands: substituent effects on properties of N-heterocyclic carbenes
Authors: Koto Yuma , Shibahara Fumitoshi , Murai Toshiaki
Published: January 2017

Imidazo[1,5-a]pyridine-derived NHCs gained strong π-accepting character due to their structural features.
Ion-pair coordination driven stimuli-responsive one-dimensional supramolecular helicate
Authors: Naskar Sourenjit , Dalal Chumki , Ghosh Pradyut
Published: January 2017

A new self-assembled ion-pair coordination driven one-dimensional (1D) smart supramolecular helical assembly is reported. Moreover, thermo- and chemo-responsive transformation/disassembly/reassembly of the helical superstructure was also demonstrated.
SANS investigation of water adsorption in tunable cyclodextrin-based polymeric hydrogels
Authors: Rossi B. , Paciaroni A. , Venuti V. , Fadda G. C. , Melone L. , Punta C. , Crupi V. , Majolino D. , Mele A.
Published: January 2017

A quantitative law for the hydration-dependence of pore size in cyclodextrin-based hydrogels is provided by SANS experiments.
Cavity enhanced spectroscopy for measurement of nitrogen oxides in the Anthropocene: results from the Seoul tower during MAPS 2015
Authors: Brown Steven S. , An Hyunjin , Lee Meehye , Park Jeong-Hoo , Lee Sang-Deok , Fibiger Dorothy L. , McDuffie Erin E. , Dubé William P. , Wagner Nicholas L. , Min Kyung-Eun
Published: January 2017

Cavity enhanced spectroscopy, CES, is a high sensitivity direct absorption method that has seen increasing utility in the last decade, a period also marked by increasing requirements for understanding human impacts on atmospheric composition. This paper describes the current NOAA six channel cavity ring-down spectrometer (CRDS, the most common form of CES) for measurement of nitrogen oxides and O3. It further describes the results from measurements from a tower 300 m above the urban area of Seoul in late spring of 2015. The campaign demonstrates the performance of the CRDS instrument and provides new data on both photochemistry and nighttime chemistry in a major Asian megacity. The instrument provided accurate, high time resolution data for N2O5, NO, NO2, NOyand O3, but suffered from large wall loss in the sampling of NO3, illustrating the requirement for calibration of the NO3inlet transmission. Both the photochemistry and nighttime chemistry of nitrogen oxides and O3were rapid in this megacity. Sustained average rates of O3buildup of 10 ppbv h−1during recurring morning and early afternoon sea breezes led to a 50 ppbv average daily O3rise. Nitrate radical production rates,P(NO3), averaged 3–4 ppbv h−1in late afternoon and early evening, much greater than contemporary data from Los Angeles, a comparable U. S. megacity. TheseP(NO3) were much smaller than historical data from Los Angeles, however. Nighttime data at 300 m above ground showed considerable variability in high time resolution nitrogen oxide and O3, likely resulting from sampling within gradients in the nighttime boundary layer structure. Apparent nighttime biogenic VOC oxidation rates of several ppbv h−1were also likely influenced by vertical gradients. Finally, daytime N2O5mixing ratios of 3–35 pptv were associated with rapid daytimeP(NO3) and agreed well with a photochemical steady state calculation.
Total synthesis of (+)-herboxidiene/GEX 1A
Authors: Gómez-Palomino Alejandro , Pellicena Miquel , Krämer Katrina , Romea Pedro , Urpí Fèlix , Aullón Gabriel , Padrón José M.
Published: January 2017

An efficient synthesis of herboxidiene is granted from highly stereoselective aldol reactions from two lactate-derived ketones and an oxa-Michael cyclization.
Enantioselective synthesis of 1,2,3,4-tetrahydroquinoline-4-ols and 2,3-dihydroquinolin-4(1H)-ones via a sequential asymmetric hydroxylation/diastereoselective oxidation process using Rhodococcus equi ZMU-LK19
Authors: Li Ke , Wang Juxiang , Wu Kailin , Zheng Daijun , Zhou Xiaojian , Han Wenyong , Wan Nanwei , Cui Baodong , Chen Yongzheng
Published: January 2017

A cascade biocatalysis system involving asymmetric hydroxylation and diastereoselective oxidation was developed giving the title compounds in good yields.
Correction: Novel metal chelators thiosemicarbazones with activity at the σ2 receptors and P-glycoprotein: an innovative strategy for resistant tumor treatment
Authors: Pati Maria Laura , Niso Mauro , Ferorelli Savina , Abate Carmen , Berardi Francesco
Published: January 2017

Correction for ‘Novel metal chelators thiosemicarbazones with activity at the σ2 receptors and P-glycoprotein: an innovative strategy for resistant tumor treatment’ by Maria Laura Pati et al., RSC Adv., 2015, 5, 103131–103146.
Kolmogorov parameter for the method of entropy polarisation
Authors: Zhuo Li , Lijuan Xing
Published: January 2017

A new parameter is introduced to the method of polarisation which is dual to the Bhattacharyya parameter in some sense. Through this parameter, the authors give an alternative proof on the result about the speed of the entropy polarising to 1.
Pruned non‐local means
Authors: Ghosh Sanjay , Mandal Amit K. , Chaudhury Kunal N.
Published: January 2017

In non‐local means (NLM), each pixel is denoised by performing a weighted averaging of its neighbouring pixels, where the weights are computed using image patches. The authors demonstrate that the denoising performance of NLM can be improved by pruning the neighbouring pixels, namely, by rejecting neighbouring pixels whose weights are below a certain threshold . While pruning can potentially reduce pixel averaging in uniform‐intensity regions, they demonstrate that there is generally an overall improvement in the denoising performance. In particular, the improvement comes from pixels situated close to edges and corners. The success of the proposed method strongly depends on the choice of the global threshold , which in turn depends on the noise level and the image characteristics. They show how Stein's unbiased estimator of the mean‐squared error can be used to optimally tune , at a marginal computational overhead. They present some representative denoising results to demonstrate the superior performance of the proposed method over NLM and its variants.
Cortical Brain Functions – The Brodmann Legacy in the 21st Century
Authors: Damiani Daniel , Nascimento Anna Maria , Pereira Leticia Kühl
Published: January 2017

In 1909, Korbinian Brodmann described 52 functional brain areas, 43 of them found in the human brain. More than a century later, his devoted functional map was incremented by Glasser et al in 2016, using functional nuclear magnetic resonance imaging techniques to propose the existence of 180 functional areas in each hemisphere, based on their cortical thickness, degree of myelination (cortical myelin content), neuronal interconnection, topographic organization, multitask answers, and assessment in their resting state. This opens a huge possibility, through functional neuroanatomy, to understand a little more about normal brain function and its functional impairment in the presence of a disease.
A Simplified Technique for Drainage of Chronic Calcified Pleural Empyema
Authors: Younssa Hama , Didier James , Ibrahim Magagi , Harissou Adamou , Adakal Ousseini , Sani Rachid , Rabiou Sani
Published: January 2017

Chronic pleural pocket has well-known diagnosis and treatment principles since first described by Hippocrates 2,400 years ago. However, its treatment remains constant even though its causes, severity during management, and terrain vary considerably. In well-structured health care systems, posttuberculous empyema has become rare; its well-codified medical treatment relies on early diagnosis and adapted antibiotherapy, punctures/drainage, and appropriate intrapleural antifibrinolytics. In developing countries, a poor health organizational system increases the incidence of pleural pocket, which can progress until surgery is indicated. In such a context, the general principles of treatment include pleural decortication along with pulmonary resection. This technique remains difficult, risky, and, sometimes, impossible due to the chronicity of the lesion. In patients debilitated by several months of septic evolution, a simplified thoracostomy technique permits complete resection of the pocket.
Velocity measurement by coherent x-ray heterodyning
Authors: Lhermitte Julien R. M. , Rogers Michael C. , Manet Sabine , Sutton Mark
Published: January 2017

We present a small-angle coherent x-ray scattering technique used for measuring flow velocities in slow moving materials. The technique is an extension of X-ray Photon Correlation Spectroscopy (XPCS): It involves mixing the scattering from moving tracer particles with a static reference that heterodynes the signal. This acts to elongate temporal effects caused by flow in homodyne measurements, allowing for a more robust measurement of flow properties. Using coherent x-ray heterodyning, velocities ranging from 0.1 to 10 μm/s were measured for a viscous fluid pushed through a rectangular channel. We describe experimental protocols and theory for making these Poiseuille flow profile measurements and also develop the relevant theory for using heterodyne XPCS to measure velocities in uniform and Couette flows.
Harmonium atoms at weak confinements: The formation of the Wigner molecules
Authors: Cioslowski Jerzy , Strasburger Krzysztof
Published: January 2017

The formation of the Wigner molecules in three-dimensional assemblies of equicharged particles upon weakening of harmonic confinements with spherical symmetry is investigated using five electronic states of the four-electron harmonium atom as a representative example. Numerical results of accurate explicitly-correlated calculations, carried out for a wide range of confinement strengths ω, reveal nonmonotonic convergence of the total energies and one-electron densities to those predicted by the formalism asymptotically exact at the ω→0 limit. The convergence rates are strongly state- and property-dependent, which implies the nonexistence of a single measure quantifying the extent of the formation of the Wigner molecule in a particular state of the harmonium atom. In light of these observations, it is concluded that, like in two dimensions, the emergence of the Wigner molecules in Coulombic systems confined by spherically symmetric harmonic potentials is a complex and gradual process that takes place over a range of confinement strengths spanning several orders of magnitude.
Stabilizing potentials in bound state analytic continuation methods for electronic resonances in polyatomic molecules
Authors: White Alec F. , Head-Gordon Martin , McCurdy C. William
Published: January 2017

The computation of Siegert energies by analytic continuation of bound state energies has recently been applied to shape resonances in polyatomic molecules by several authors. We critically evaluate a recently proposed analytic continuation method based on low order (type III) Padé approximants as well as an analytic continuation method based on high order (type II) Padé approximants. We compare three classes of stabilizing potentials: Coulomb potentials, Gaussian potentials, and attenuated Coulomb potentials. These methods are applied to a model potential where the correct answer is known exactly and to the Πg2 shape resonance of N2− which has been studied extensively by other methods. Both the choice of stabilizing potential and method of analytic continuation prove to be important to the accuracy of the results. We conclude that an attenuated Coulomb potential is the most effective of the three for bound state analytic continuation methods. With the proper potential, such methods show promise for algorithmic determination of the positions and widths of molecular shape resonances.
Evaluation of DFT-D3 dispersion corrections for various structural benchmark sets
Authors: Schröder Heiner , Hühnert Jens , Schwabe Tobias
Published: January 2017

We present an evaluation of our newly developed density functional theory (DFT)-D3 dispersion correction D3(CSO) in comparison to its predecessor D3(BJ) for geometry optimizations. Therefore, various benchmark sets covering bond lengths, rotational constants, and center of mass distances of supramolecular complexes have been chosen. Overall both corrections give accurate structures and show no systematic differences. Additionally, we present an optimized algorithm for the computation of the DFT-D3 gradient, which reduces the formal scaling of the gradient calculation from O(N3) to O(N2).
Effect of graphene-oxide on the microstructure and charge carrier transport of polyaniline nanocomposites under low applied electric fields
Authors: Mombrú Dominique , Romero Mariano , Faccio Ricardo , Mombrú Álvaro W.
Published: January 2017

We report a study on the preparation and characterization of polyaniline-graphene oxide (PANI-GO-X) nanocomposites focusing in the study of its structure, microstructure, and correlations with electrical transport properties under low applied electric fields. X-ray diffraction analysis showed evidence of graphene oxide (GO) blending between polyaniline fibers, and according to small angle X-ray scattering, the fractal dimensionality was quasi-one dimensional for all nanocomposites. Confocal Raman spectroscopy revealed that the addition of GO leads to a notorious decrease of the polaron population of polyaniline. A significant increase in resistivity was observed for PANI-GO-X nanocomposites with respect to pure polyaniline, in agreement with the decrease in the polaron population. The electrical transport mechanism could be explained by an Arrhenius behavior at high temperatures (T > 255 K) and a broad transition with a logarithmic dependence of the activation energy with temperature for the low temperature regime (T < 255 K). Additionally, an increase in the hopping transport dimensionality from quasi-1D to quasi-3D was observed for X = 7% GO nanocomposites. The transport properties, studied after the polarization using low applied electric fields, revealed the modification of the electrical transport at low temperatures. In addition, the electrical transport of PANI-GO-X nanocomposites followed a typical ln(σ) vs E1/2 Poole-Frenkel type dependence in the presence of low applied electric fields. At low temperatures, X = 7% GO nanocomposites showed a notorious increase in the Poole-Frenkel slope at low applied electric fields with respect to pure polyaniline. The enhancement on the electric response using low applied electric fields (E ∼ 2 V/cm) could be of great interest for the development of new organic electronic devices.
Crystallinity dependent thermal degradation in organic solar cell
Authors: Lee Hyunho , Sohn Jiho , Tyagi Priyanka , Lee Changhee
Published: January 2017

An operating solar cell undergoes solar heating; thus, the degradation study of organic photo-voltaic (OPV) with a thermal stress is required for their practical applications. We present a thermal degradation study on OPVs fabricated with photo-active polymers having different crystalline phase. Light intensity dependent analysis for different thermal stress duration is performed. In crystalline, the degradation majorly occurs due to drop in open-circuit voltage while in amorphous one it is due to drop in short-circuit current. Physical mechanism in both systems is explained and supported by the X-ray diffraction, morphological and optical characterization.
Modification of far-field radiation pattern by shaping InGaN/GaN nanorods
Authors: Jiao Q. Q. , Chen Z. Z. , Feng Y. L. , Zhang S. , Li S. F. , Jiang S. X. , Li J. Z. , Chen Y. F. , Yu T. J. , Kang X. N. , Gu E. , Shen B. , Zhang G. Y.
Published: January 2017

In this work, we report on the fabrication of “golftee,” “castle,” and “pillar” shaped InGaN/GaN nanorod light-emitting diode (LED) arrays with a typical rod diameter of 200 nm based on nanoimprint lithography, dry etching, and wet etching. The photoluminescence (PL) integral intensities per active region area for “golftee,” “castle,” and “pillar” shaped nanorod samples were found to be 2.6, 1.9, and 2.2 times stronger than that of a conventional planar LED. Additionally, the far-field radiation patterns of the three different shaped nanorod samples were investigated based on angular resolved PL (ARPL) measurements. It was found that the sharp lobes appeared at certain angles in the ARPL curve of the “golftee” sample, while broad lobes were observed in the ARPL curves of the “castle” and “pillar” samples. Further analysis suggests that the shorter PL lifetime and smaller spectral width of the “golftee” sample were due to the coupling of photon modes with excitons, which also led to the observed high efficiency and directional emission pattern of the “golftee” sample. Finally, three dimensional finite difference time domain simulations were carried out to study the near-field distribution of the “golftee,” “castle,” and “pillar” shaped nanorods. The simulation results showed not only a strong enhancement of the electric field in the nanocavities of the three nanorod structures but also a reduction of the guided modes into the nanorod substrate for the “golftee” shaped structure.
Inductance and resistance measurement method for vessel detection and coil powering in all-surface inductive heating systems composed of outer squircle coils
Authors: Kilic Veli Tayfun , Unal Emre , Demir Hilmi Volkan
Published: January 2017

In this work, we investigate a method proposed for vessel detection and coil powering in an all-surface inductive heating system composed of outer squircle coils. Besides conventional circular coils, coils with different shapes such as outer squircle coils are used for and enable efficient all-surface inductive heating. Validity of the method, which relies on measuring inductance and resistance values of a loaded coil at different frequencies, is experimentally demonstrated for a coil with shape different from conventional circular coil. Simple setup was constructed with a small coil to model an all-surface inductive heating system. Inductance and resistance maps were generated by measuring coil’s inductance and resistance values at different frequencies loaded by a plate made of different materials and located at various positions. Results show that in an induction hob for various coil geometries it is possible to detect a vessel’s presence, to identify its material type and to specify its position on the hob surface by considering inductance and resistance of the coil measured on at least two different frequencies. The studied method is important in terms of enabling safe, efficient and user flexible heating in an all-surface inductive heating system by automatically detecting the vessel’s presence and powering on only the coils that are loaded by the vessel with predetermined current levels.
Response of Digitaria insularis seed germination to environmental factors
Authors: Oreja F. H. , de la Fuente E. B. , Fernandez-Duvivier M. E.
Published: January 2017

Digitaria insularis (sourgrass) is a weed problem emerging in importance in agricultural fields from the north of Argentina and has recently been reported as resistant to glyphosate. Understanding the germination of local biotypes of D. insularis could help to reduce invasion and improve the long-term management strategies for this weed. The objective of this work was to study the effect of environmental factors on germination of D. insularis seeds from two different populations of Argentina. Three experiments were performed in germination chambers by using recently dispersed seeds. Seeds with or without pre-chilling treatments had 95% germination, suggesting the absence of dormancy in freshly harvested seed. Germination at constant temperature of 25°C was ~55% lower than germination at fluctuating temperature of 20°−35°C. At constant 25°C, germination was higher for seeds from Santiago del Estero than seeds from Córdoba, and as the number of hydration–dehydration cycles increased. Germination was reduced with exposure to far-red light for 1 h. Any crop management decision that reduces soil thermal fluctuations and/or far-red : red ratio (such as stubble or cover crops) could reduce seedling field emergence for this species.
Malus domestica ADF1 severs actin filaments in growing pollen tubes
Authors: Yang Qing , Wang ShengNan , Wu ChuanBao , Zhang QiuLei , Zhang Yi , Chen QiuJu , Li Yang , Hao Li , Gu Zhaoyu , Li Wei , Li Tianzhong
Published: January 2017

A dynamic actin cytoskeleton is essential for pollen tube growth and germination. However, the molecular mechanism that determines the organisation of the actin cytoskeleton in pollen remains poorly understood. ADF modulates the structure and dynamics of actin filaments and influences the higher-order organisation of the actin cytoskeleton in eukaryotic cells. Members of the ADF family have been shown to have important functions in pollen tube growth. However, the role of this gene family remains largely unknown in apple (Malus domestica Borkh.). In this study, we identified seven ADFs in the apple genome. Phylogenetic analysis showed that MdADF1 clusters with Arabidopsis thaliana (L.) Heynh. AtADF7, ADF8, ADF10 and AtADF11. We performed sequence alignments and analysed the domain structures of the seven MdADF proteins and identified the chromosome locations of the encoding genes. We cloned the gene encoding MdADF1 from ‘Ralls Janet’ apple and found that it was strongly expressed in pollen. Biochemical assays revealed that MdADF1 directly bound to and severed F-actin under low Ca2+ conditions. We demonstrated that knockdown of MdADF1 inhibited pollen tube growth and reduced the pollen germination rate, but rendered the pollen insensitive to treatment with Latrunculin B, an actin depolymerising agent. Taken together, our results provide insight into the function of MdADF1 and serve as a reference for studies of ADF in other plants.
The impact of face systems on the pragmalinguistic features of academic e-mail requests
Authors: Aslan Erhan
Published: January 2017

This study investigates the impact of power/distance (PD) variables operationalized as face systems on the pragmalinguistic features of academic e-mail requests. A corpus of 90 academic e-mails was classified into four face system groups: hierarchical (sender +P), hierarchical (recipient +P), deference, and solidarity. Request perspectives, strategies, and mitigating supportive moves were analyzed. The analysis revealed that the speaker and hearer dominance were the most frequent request perspectives in the hierarchical (recipient+P) and deference groups. The impersonal perspective was more common in the hierarchical (sender+P) group. The preparatory was the dominant request strategy in all groups, relatively more frequent in the hierarchical (recipient+P) and deference groups. The most common supportive move was the grounder, which occurred more frequently than other supportive moves. The findings of the study indicate that face systems influence the request patterns in academic e-mail communication. The study has implications for future research on pragmatics of computer-mediated communication (CMC).
Association of Maternal Plasma Folate and Cardiometabolic Risk Factors in Pregnancy with Elevated Blood Pressure of Offspring in Childhood
Authors: Wang Hongjian , Mueller Noel T. , Li Jianping , Sun Ninglin , Huo Yong , Ren Fazheng , Wang Xiaobin
Published: January 2017

BACKGROUND

The prevalence of childhood elevated blood pressure (BP) has increased in the United States, particularly among African Americans. The influence of maternal plasma folate levels, alone or in combination with maternal cardiometabolic risk factors (hypertensive disorders, diabetes, and prepregnancy obesity), on child systolic BP (SBP) has not been examined in a prospective birth cohort. We hypothesize that adequate maternal folate levels can reduce the risk of elevated SBP in children born to mothers with cardiometabolic risk factors.

METHODS

This study included 1,290 mother–child dyads (875 African Americans (67.8%)) recruited at birth and followed prospectively up to age 9 years from 2003 to 2014 at the Boston Medical Center. Child SBP percentile was calculated according to US reference data and elevated SBP was defined as SBP ≥75th percentile.

RESULTS

Maternal folate levels, overall, were not associated with child SBP. However, we found a significant multiplicative interaction between maternal cardiometabolic risk factors and maternal folate levels (Pinteraction = 0.015) on childhood elevated SBP. Among children born to mothers with any cardiometabolic risk factors, those whose mothers had folate levels above (vs. below) the median had 40% lower odds of elevated childhood SBP (odds ratio = 0.60, 95% confidence interval: 0.40–0.90). The associations did not differ appreciably in analyses restricted to African Americans, and they were not explained by gestational age, size at birth, prenatal folate intake, or breastfeeding.

CONCLUSIONS

Findings from our urban minority birth cohort suggest that higher levels of maternal folate may help counteract the adverse associations of maternal cardiometabolic risk factors on child SBP.
Health Insurance Type and Control of Hypertension Among US Women Living With and Without HIV Infection in the Women’s Interagency HIV Study
Authors: Ludema Christina , Cole Stephen R. , Eron Joseph J. , Holmes G. Mark , Anastos Kathryn , Cocohoba Jennifer , Cohen Marge H. , Cooper Hannah L.F. , Golub Elizabeth T. , Kassaye Seble , Konkle-Parker Deborah , Metsch Lisa , Milam Joel , Wilson Tracey E. , Adimora Adaora A.
Published: January 2017

BACKGROUND

Health care access is an important determinant of health. We assessed the effect of health insurance status and type on blood pressure control among US women living with (WLWH) and without HIV.

METHODS

We used longitudinal cohort data from the Women’s Interagency HIV Study (WIHS). WIHS participants were included at their first study visit since 2001 with incident uncontrolled blood pressure (BP) (i.e., BP ≥140/90 and at which BP at the prior visit was controlled (i.e., <135/85). We assessed time to regained BP control using inverse Kaplan–Meier curves and Cox proportional hazard models. Confounding and selection bias were accounted for using inverse probability-of-exposure-and-censoring weights.

RESULTS

Most of the 1,130 WLWH and 422 HIV-uninfected WIHS participants who had an elevated systolic or diastolic measurement were insured via Medicaid, were African-American, and had a yearly income ≤$12,000. Among participants living with HIV, comparing the uninsured to those with Medicaid yielded an 18-month BP control risk difference of 0.16 (95% CI: 0.10, 0.23). This translates into a number-needed-to-treat (or insure) of 6; to reduce the caseload of WLWH with uncontrolled BP by one case, five individuals without insurance would need to be insured via Medicaid. Blood pressure control was similar among WLWH with private insurance and Medicaid. There were no differences observed by health insurance status on 18-month risk of BP control among the HIV-uninfected participants.

CONCLUSIONS

These results underscore the importance of health insurance for hypertension control—especially for people living with HIV.
‘COV’COP’ allows to detect CNVs responsible for inherited diseases among amplicons sequencing data
Authors: Derouault P , Parfait B , Moulinas R , Barrot C.-C , Sturtz F , Merillou S , Lia A.-S
Published: January 2017

In order to help molecular geneticists to rapidly identify CNVs responsible for inherited diseases among amplicons sequencing data generated by NGS, we designed a user-friendly tool ‘Cov’Cop’. Using the run’s coverage file provided by the sequencer, Cov’Cop simultaneously analyzes all the patients of the run using a two-stage algorithm containing correction and normalization levels and provides an easily understandable output, showing with various colors, potentially deleted and duplicated amplicons.

Availability and Implementation

https://git.unilim.fr/merilp02/CovCop

Supplementary information

Supplementary data are available at Bioinformatics online.
Large-scale 16S gene assembly using metagenomics shotgun sequences
Authors: Zeng Feng , Wang Zicheng , Wang Ying , Zhou Jizhong , Chen Ting
Published: January 2017

Motivation

Combining a 16S rRNA (16S) gene database with metagenomic shotgun sequences promises unbiased identification of known and novel microbes.

Results

To achieve this, we herein report reference-based ribosome assembly (RAMBL), a computational pipeline, which integrates taxonomic tree search and Dirichlet process clustering to reconstruct full-length 16S gene sequences from metagenomic sequencing data with high accuracy. By benchmarking against the synthetic and real shotgun sequences, we demonstrated that full-length 16S gene assemblies of RAMBL were a good proxy for known and putative microbes, including Candidate Phyla Radiation. We found that 30–40% of bacteria genera in the terrestrial and intestinal biomes have no closely related genome sequences. We also observed that RAMBL was able to generate a more accurate determination of environmental microbial diversity and yield better disease classification, suggesting that full-length 16S gene assemblies are a powerful alternative to marker gene set and 16S short reads. RAMBL first realizes the access to full-length 16S gene sequences in the near-terabase-scale metagenomic shotgun sequences, which markedly improve metagenomic data analysis and interpretation.

Availability and Implementation

RAMBL is available at https://github.com/homopolymer/RAMBL for academic use.

Supplementary information

Supplementary data are available at Bioinformatics online.
LOCUST: a custom sequence locus typer for classifying microbial isolates
Authors: Brinkac Lauren M , Beck Erin , Inman Jason , Venepally Pratap , Fouts Derrick E , Sutton Granger
Published: January 2017

LOCUST is a custom sequence locus typer tool for classifying microbial genomes. It provides a fully automated opportunity to customize the classification of genome-wide nucleotide variant data most relevant to biological research.

Availability and Implementation

Source code, demo data, and detailed documentation are freely available at http://sourceforge.net/projects/locustyper.

Supplementary information

Supplementary data are available at Bioinformatics online.
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data
Authors: Kyle Jennifer E , Crowell Kevin L , Casey Cameron P , Fujimoto Grant M , Kim Sangtae , Dautel Sydney E , Smith Richard D , Payne Samuel H , Metz Thomas O
Published: January 2017

We introduce an open-source software, LIQUID, for semi-automated processing and visualization of LC-MS/MS-based lipidomics data. LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species. LIQUID was compared to other freely available software commonly used to identify lipids and other small molecules (e.g. CFM-ID, MetFrag, GNPS, LipidBlast and MS-DIAL), and was found to have a faster processing time to arrive at a higher number of validated lipid identifications.

Availability and Implementation

LIQUID is available at http://github.com/PNNL-Comp-Mass-Spec/LIQUID.

Supplementary information

Supplementary data are available at Bioinformatics online.
admixturegraph: an R package for admixture graph manipulation and fitting
Authors: Leppälä Kalle , Nielsen Svend V , Mailund Thomas
Published: January 2017

Admixture graphs generalize phylogenetic trees by allowing genetic lineages to merge as well as split. In this paper we present the R package admixturegraph containing tools for building and visualizing admixture graphs, for fitting graph parameters to genetic data, for visualizing goodness of fit and for evaluating the relative goodness of fit between different graphs.

Availability and Implementation

GitHub: https://github.com/mailund/admixture_graph and CRAN: https://cran.r-project.org/web/packages/admixturegraph.
Bayesian network–response regression
Authors: Wang Lu , Durante Daniele , Jung Rex E , Dunson David B
Published: January 2017

Motivation

There is increasing interest in learning how human brain networks vary as a function of a continuous trait, but flexible and efficient procedures to accomplish this goal are limited. We develop a Bayesian semiparametric model, which combines low-rank factorizations and flexible Gaussian process priors to learn changes in the conditional expectation of a network-valued random variable across the values of a continuous predictor, while including subject-specific random effects.

Results

The formulation leads to a general framework for inference on changes in brain network structures across human traits, facilitating borrowing of information and coherently characterizing uncertainty. We provide an efficient Gibbs sampler for posterior computation along with simple procedures for inference, prediction and goodness-of-fit assessments. The model is applied to learn how human brain networks vary across individuals with different intelligence scores. Results provide interesting insights on the association between intelligence and brain connectivity, while demonstrating good predictive performance.

Availability and Implementation

Source code implemented in R and data are available at https://github.com/wangronglu/BNRR

Supplementary information

Supplementary data are available at Bioinformatics online.