bluuebunny/crossref_metadata_2025 huggingface dataset:
Developmental Reprogramming in Mesenchymal Stromal Cells of Human Subjects with Idiopathic Pulmonary Fibrosis
Authors: Chanda Diptiman , Kurundkar Ashish , Rangarajan Sunad , Locy Morgan , Bernard Karen , Sharma Nirmal S. , Logsdon Naomi J. , Liu Hui , Crossman David K. , Horowitz Jeffrey C. , De Langhe Stijn , Thannickal Victor J.
Published: November 2016

Cellular plasticity and de-differentiation are hallmarks of tissue/organ regenerative capacity in diverse species. Despite a more restricted capacity for regeneration, humans with age-related chronic diseases, such as cancer and fibrosis, show evidence of a recapitulation of developmental gene programs. We have previously identified a resident population of mesenchymal stromal cells (MSCs) in the terminal airways-alveoli by bronchoalveolar lavage (BAL) of human adult lungs. In this study, we characterized MSCs from BAL of patients with stable and progressive idiopathic pulmonary fibrosis (IPF), defined as <5% and ≥10% decline, respectively, in forced vital capacity over the preceding 6-month period. Gene expression profiles of MSCs from IPF subjects with progressive disease were enriched for genes regulating lung development. Most notably, genes regulating early tissue patterning and branching morphogenesis were differentially regulated. Network interactive modeling of a set of these genes indicated central roles for TGF-β and SHH signaling. Importantly, fibroblast growth factor-10 (FGF-10) was markedly suppressed in IPF subjects with progressive disease, and both TGF-β1 and SHH signaling were identified as critical mediators of this effect in MSCs. These findings support the concept of developmental gene re-activation in IPF, and FGF-10 deficiency as a potentially critical factor in disease progression.
Catalytic conversion of lignin pyrolysis model compound- guaiacol and its kinetic model including coke formation
Authors: Zhang Huiyan , Wang Yun , Shao Shanshan , Xiao Rui
Published: November 2016

Lignin is the most difficult to be converted and most easy coking component in biomass catalytic pyrolysis to high-value liquid fuels and chemicals. Catalytic conversion of guaiacol as a lignin model compound was conducted in a fixed-bed reactor over ZSM-5 to investigate its conversion and coking behaviors. The effects of temperature, weight hourly space velocity (WHSV) and partial pressure on product distribution were studied. The results show the maximum aromatic carbon yield of 28.55% was obtained at temperature of 650 °C, WHSV of 8 h−1 and partial pressure of 2.38 kPa, while the coke carbon yield was 19.55%. The reaction pathway was speculated to be removing methoxy group to form phenols with further aromatization to form aromatics. The amount of coke increased with increasing reaction time. The surface area and acidity of catalysts declined as coke formed on the acid sites and blocked the pore channels, which led to the decrease of aromatic yields. Finally, a kinetic model of guaiacol catalytic conversion considering coke deposition was built based on the above reaction pathway to properly predict product distribution. The experimental and model predicting data agreed well. The correlation coefficient of all equations were all higher than 0.90.
The effects of manganese oxide octahedral molecular sieve chitosan microspheres on sludge bacterial community structures during sewage biological treatment
Authors: Pan Fei , Liu Wen , Yu Yang , Yin Xianze , Wang Qingrong , Zheng Ziyan , Wu Min , Zhao Dongye , Zhang Qiu , Lei Xiaoman , Xia Dongsheng
Published: November 2016

This study examines the effects of manganese oxide octahedral molecular sieve chitosan microspheres (Fe3O4@OMS-2@CTS) on anaerobic and aerobic microbial communities during sewage biological treatment. The addition of Fe3O4@OMS-2@CTS (0.25 g/L) resulted in enhanced levels of operational performance for decolourization dye X-3B. However, degradation dye X-3B inhibition in the presence of Fe3O4@OMS-2@CTS was recorded as greater than or equal to 1.00 g/L. Illumina MiSeq high throughput sequencing of the 16 S rRNA gene showed that 108 genera were observed during the anaerobic process, while only 71 genera were observed during the aerobic process. The largest genera (Aequorivita) decreased from 21.14% to 12.65% and the Pseudomonas genera increased from 10.57% to 12.96% according to the abundance in the presence of 0.25 g/L Fe3O4@OMS-2@CTS during the anaerobic process. The largest Gemmatimonas genera decreased from 21.46% to 11.68% and the Isosphaerae genera increased from 5.8% to 11.98% according to the abundance in the presence of 0.25 g/L Fe3O4@OMS-2@CTS during the aerobic process. Moreover, the X-ray photoelectron spectroscopy results show that the valence states of Mn and Fe in Fe3O4@OMS-2@CTS changed during sewage biological treatment.
Investigation of AlGaN/GaN high electron mobility transistor structures on 200-mm silicon (111) substrates employing different buffer layer configurations
Authors: Lee H.-P. , Perozek J. , Rosario L. D. , Bayram C.
Published: November 2016

AlGaN/GaN high electron mobility transistor (HEMT) structures are grown on 200-mm diameter Si(111) substrates by using three different buffer layer configurations: (a) Thick-GaN/3 × {AlxGa1−xN}/AlN, (b) Thin-GaN/3 × {AlxGa1−xN}/AlN, and (c) Thin-GaN/AlN, so as to have crack-free and low-bow (<50 μm) wafer. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, high resolution-cross section transmission electron microscopy, optical microscopy, atomic-force microscopy, cathodoluminescence, Raman spectroscopy, X-ray diffraction (ω/2θ scan and symmetric/asymmetric ω scan (rocking curve scan), reciprocal space mapping) and Hall effect measurements are employed to study the structural, optical, and electrical properties of these AlGaN/GaN HEMT structures. The effects of buffer layer stacks (i.e. thickness and content) on defectivity, stress, and two-dimensional electron gas (2DEG) mobility and 2DEG concentration are reported. It is shown that 2DEG characteristics are heavily affected by the employed buffer layers between AlGaN/GaN HEMT structures and Si(111) substrates. Particularly, we report that in-plane stress in the GaN layer affects the 2DEG mobility and 2DEG carrier concentration significantly. Buffer layer engineering is shown to be essential for achieving high 2DEG mobility (>1800 cm2/V∙s) and 2DEG carrier concentration (>1.0 × 1013 cm−2) on Si(111) substrates.
Peritoneal adhesion prevention with a biodegradable and injectable N,O-carboxymethyl chitosan-aldehyde hyaluronic acid hydrogel in a rat repeated-injury model
Authors: Song Linjiang , Li Ling , He Tao , Wang Ning , Yang Suleixin , Yang Xi , Zeng Yan , Zhang Wenli , Yang Li , Wu Qinjie , Gong Changyang
Published: November 2016

Postoperative peritoneal adhesion is one of the serious issues because it induces severe clinical disorders. In this study, we prepared biodegradable and injectable hydrogel composed of N,O-carboxymethyl chitosan (NOCC) and aldehyde hyaluronic acid (AHA), and assessed its anti-adhesion effect in a rigorous and severe recurrent adhesion model which is closer to clinical conditions. The flexible hydrogel, which gelated in 66 seconds at 37 °C, was cross-linked by the schiff base derived from the amino groups of NOCC and aldehyde groups in AHA. In vitro cytotoxicity test showed the hydrogel was non-toxic. In vitro and in vivo degradation examinations demonstrated the biodegradable and biocompatibility properties of the hydrogel. The hydrogel discs could prevent the invasion of fibroblasts, whereas fibroblasts encapsulated in the porous 3-dimensional hydrogels could grow and proliferate well. Furthermore, the hydrogel was applied to evaluate the anti-adhesion efficacy in a more rigorous recurrent adhesion model. Compared with normal saline group and commercial hyaluronic acid (HA) hydrogel, the NOCC-AHA hydrogel exhibited significant reduction of peritoneal adhesion. Compared to control group, the blood and abdominal lavage level of tPA was increased in NOCC-AHA hydrogel group. These findings suggested that NOCC-AHA hydrogel had a great potential to serve as an anti-adhesion candidate.
Towards ‘smart lasers’: self-optimisation of an ultrafast pulse source using a genetic algorithm
Authors: Woodward R. I. , Kelleher E. J. R.
Published: November 2016

Short-pulse fibre lasers are a complex dynamical system possessing a broad space of operating states that can be accessed through control of cavity parameters. Determination of target regimes is a multi-parameter global optimisation problem. Here, we report the implementation of a genetic algorithm to intelligently locate optimum parameters for stable single-pulse mode- locking in a Figure-8 fibre laser, and fully automate the system turn-on procedure. Stable ultrashort pulses are repeatably achieved by employing a compound fitness function that monitors both temporal and spectral output properties of the laser. Our method of encoding photonics expertise into an algorithm and applying machine-learning principles paves the way to self-optimising ‘smart’ optical technologies.
Nitrogen-doped carbon nanotubes as efficient catalysts for isobutane dehydrogenation
Authors: Mu Jiali , France Liam John , Liu Baoan , Shi Junjun , Long Jinxing , Lv LuFeng , Li Xuehui
Published: November 2016

Large-scale production of isobutene from isobutane requires high-performance and cost-effective catalysts.
A novel Ag(i)-calix[4]arene coordination polymer for the sensitive detection and efficient photodegradation of nitrobenzene in aqueous solution
Authors: Liu Lei-Lei , Chen Jing , Yu Cai-Xia , Lv Wen-Xing , Yu Hui-Ying , Cui Xiao-Qing , Liu Lin
Published: November 2016

A bi-functional coordination polymer for the detection and photodegradation of NB was designed and synthesized from AgNO3 and tetra-pyridyl calix[4]arene.
Ultra-fast preparation of high-performance thermoelectric bulk TiNiSb0.05Sn0.95 by microwave synthesis
Authors: Li Y. , Cheng C. , Lei Y. , Wang M. , Wan R. D.
Published: November 2016

The antimony-doped half-Heusler thermoelectric bulk TiNiSb0.05Sn0.95 with power factor of 4042 μW m−1 K−2 was prepared via ultra-fast 4.5 min microwave synthesis, cold-press forming and 20 min microwave pressureless sintering.
Pincer-plus-one ligands in self-assembly with palladium(ii): a molecular square and a molecular tetrahedron
Authors: Behnia Ava , Boyle Paul D. , Fard Mahmood A. , Blacquiere Johanna M. , Puddephatt Richard J.
Published: November 2016

Self-assembly with pincer-plus-one ligands can give tetramers as either a molecular square or tetrahedron.
Structural insight into inhibition of human Class II PI3K isoforms: homology modeling, binding site characterization, docking and molecular dynamics studies
Authors: Kumar Vikash , Siddiqi Mohammad Imran
Published: November 2016

Phosphoinositide-3-kinases (PI3Ks) are family of lipid kinases, involved in cell survival, growth and proliferation. Role of Class II PI3Ks in cancer is emerging and gaining importance for the therapeutic intervention.
Simultaneous encapsulation and stabilization of Aloe vera extract on cotton fabric for wound dressing application
Authors: Ghayempour S. , Montazer M. , Mahmoudi Rad M.
Published: November 2016

Utilization of some herbal products in wound dressing for rapid healing with no side effects is a highly interesting task.
Simultaneous determination of paeoniflorin-6′-O-benzene sulfonate (CP-25) and its active paeoniflorin (Pae) metabolite in rat plasma using UPLC-MS/MS: an application for pharmacokinetic studies
Authors: Yu Jun , Xiao Feng , Asenso James , Zhou Peng , Yang Xiao-Dan , Wang Chun , Wei Wei
Published: November 2016

Paeoniflorin (Pae), a water-soluble monoterpene glucoside, is the main effective component of total glucoside of paeony (TGP) paeoniflorin-6′-O-benzene sulfonate (CP-25), an acylated derivative of Pae, was synthesized via esterification.
Effect of nitrogen substitution on the structural and magnetic ordering transitions of NiCr2O4
Authors: Liu Xin , Yin Nan , Thomas Tiju , Yang Minghui , Wang Junhu , Shi Quan
Published: November 2016

The nitrogen (N) doped spinel NiCr2O4 has been synthesized at 773 K (N500) and 873 K (N600) by ammonolysis of NiCr2O4 powders to study the effect of anion doping on its structural and magnetic properties.
In situ mass spectrometry analysis of chemical vapour deposition of TiO2thin films to study gas phase mechanisms
Authors: Blackburn Ben J. , Drosos Charalampos , Brett Dean B. , Parkes Michael A. , Carmalt Claire J. , Parkin Ivan. P.
Published: November 2016

In situmass spectrometry measurements has been used to study as phase intermediates in CVD of TiO2thin films.
Experimental research on the thermal decomposition of pentafluoroethane (HFC-125) extinguishing agent with n-heptane/air pool fire in confined space
Authors: Ting Wang , Kuang Qin , Hua Wang , Renming Pan
Published: November 2016

We studied the thermal decomposition of pentafluoroethane (HFC-125) with the flame in confined space and the thermolysis gaseous products are hydrogen fluoride (HF) and other organic gases, such as CF3CHCF2, CF3CH2CF3, and so on.
Benzothiazole based multi-analyte sensor for selective sensing of Zn2+and Cd2+and subsequent sensing of inorganic phosphates (Pi) in mixed aqueous medium
Authors: Singh Rupinder , Gogoi Abhijit , Das Gopal
Published: November 2016

A multi-analyte sensor selectively senses Zn2+and Cd2+ions and subsequently responds to phosphates in mixed aqueous medium.
Probing the role of electrostatics of polypeptide main-chain in protein folding by perturbing N-terminal residue stereochemistry: DFT study with oligoalanine models
Authors: Goyal Bhupesh , Srivastava Kinshuk Raj , Kumar Anil , Patwari G. Naresh , Durani Susheel
Published: November 2016

Energetics of folding (ΔHE→F, in kcal mol−1) from the extended (E) structure to the folded (F) structure for Ia and Ib critically depend on the geometrical relationship between the backbone peptide units of the polypeptide structure.
Stable nickel-substituted spinel cathode material (LiMn1.9Ni0.1O4) for lithium-ion batteries obtained by using a low temperature aqueous reduction technique
Authors: Kunjuzwa Niki , Kebede Mesfin A. , Ozoemena Kenneth I. , Mathe Mkhulu K.
Published: November 2016

Nickel-doping of spinel LiMn2O4cathode material provides physico-chemical properties that allow for enhanced electrochemistry for lithium-ion battery.
Towards the electrochemical diagnosis of cancer: nanomaterial-based immunosensors and cytosensors
Authors: Anik Ülkü , Timur Suna
Published: November 2016

In this review, nanomaterial based electrochemical biosensors including electrochemical immunosensors and cytosensors towards cancer detection are covered.
Structural effects of amphiphilic protein/gold nanoparticle hybrid based nanozyme on peroxidase-like activity and silver-mediated inhibition
Authors: Liu Yan , Xiang Yinping , Ding Ding , Guo Rong
Published: November 2016

Structural effects of amphiphilic protein/gold nanoparticle hybrid based nanozyme on peroxidase-like activity and silver-mediated inhibition.
The influence of citrate on surface dissolution and alteration of the micro- and nano-structure of biotite
Authors: Li Jifu , Zhang Wenjun , Zhu Jianqiang , Lu Jianwei
Published: November 2016

Unraveling the kinetics and mechanisms of K-bearing mineral dissolution in the presence of organic acids on the nanometer scale is important for understanding the effectiveness of organic acids present in most soil environments.
Retracted Article: Synthesis and characterization of Mn/Co/Ti LDH and its utilization as a photocatalyst in visible light assisted degradation of aqueous Rhodamine B
Authors: Chowdhury Priyadarshi Roy , Bhattacharyya Krishna G.
Published: November 2016

Mn/Co/Ti LDH, hydrothermally synthesized, has been found to be optically responsive and could be used as an efficient photocatalyst for destruction of the dye, Rhodamine B, in aqueous solution irradiated by visible light.
Effective conversion of biomass-derived ethyl levulinate into γ-valerolactone over commercial zeolite supported Pt catalysts
Authors: Chen Chu-Bai , Chen Meng-Yuan , Zada Bakht , Ma Ying-Jie , Yan Long , Xu Qing , Li Wen-zhi , Guo Qing-Xiang , Fu Yao
Published: November 2016

Selective hydrogenation of biomass-derived ethyl levulinate into γ-valerolactone over commercial zeolite supported catalysts was performed, and high yield was obtained.
Unique cation–cyclohexane interactions in tri- and hexa-fluorocyclohexane multidecker complexes in the gas phase: a DFT study
Authors: Sarma Dipshikha , Saha Bapan , Chandra Deka Bhabesh , Bhattacharyya Pradip Kr.
Published: November 2016

The formation of stable sandwich and multidecker complexes through electrostatic interaction in tri- and hexa-fluorocyclohexane has been analyzed in the light of density functional theory.
Antimony-ligated dysprosium single-molecule magnets as catalysts for stibine dehydrocoupling
Authors: Pugh Thomas , Chilton Nicholas F. , Layfield Richard A.
Published: November 2016

The synthesis of antimony-ligated dysprosium SMMs is described in addition to the unexpected reactivity of the SMMs in stibine dehydrocoupling catalysis.
A metal–organic framework functionalized with piperazine exhibiting enhanced CH4 storage
Authors: Zhang Mingxing , Chen Cong , Wang Qian , Fu Wensheng , Huang Kunlin , Zhou Wei
Published: November 2016

NJU-Bai 19, the first cycloaliphatic ring (piperazine) functionalized MOF-505 analogue, exhibits a notably high methane storage capacity of 246 cm3 (STP) cm−3 (at room temperature and 65 bar) and a working capacity of 185 cm3 (STP) cm−3.
Mixing effects of Cr2O3–PrBaMn2O5 for increased redox cycling properties of Fe powder for a solid-oxide Fe–air rechargeable battery
Authors: Kim Hackho , Ida Shintaro , Ju Young-Wan , Matsuda Junko , Kim Guntae , Ishihara Tatsumi
Published: November 2016

Modifying Fe powder with an oxygen activated catalyst is useful for increasing the oxidation degree and cycling performance of Fe powder resulting in an increased capacity of a solid state Fe–air rechargeable battery.
In situ confined synthesis of molybdenum oxide decorated nickel–iron alloy nanosheets from MoO42− intercalated layered double hydroxides for the oxygen evolution reaction
Authors: Xie Chao , Wang Yanyong , Hu Kui , Tao Li , Huang Xiaobing , Huo Jia , Wang Shuangyin
Published: November 2016

This work reports molybdenum oxide decorated NiFe alloy nanosheets with high OER activity by reducing MoO42− intercalated nickel–iron layered double hydroxides (LDHs).
Three-dimensional NiCo2O4@NiWO4 core–shell nanowire arrays for high performance supercapacitors
Authors: Chen Sanming , Yang Guang , Jia Yi , Zheng Huajun
Published: November 2016

Self-supported NiCo2O4@NiWO4 core–shell nanowire arrays have been synthesized by a hydrothermal method for asymmetric supercapacitors.
Osteogenic activity and angiogenesis of a SrTiO3 nano-gridding structure on titanium surface
Authors: Gong Zheni , Cheng Haoyan , Zhang Meng , Liu Xi , Zeng Yan , Xiang Kaiwen , Xu Yuan , Wang Yinwei , Zhu Zhihong
Published: November 2016

Dual effect of alveolate double-layered SrTiO3 nano-gridding based on Ti substrate: osteogenic activity and angiogenesis.
LiRb2PO4: a new deep-ultraviolet nonlinear optical phosphate with a large SHG response
Authors: Li Lin , Wang Ying , Lei Bing-Hua , Han Shujuan , Yang Zhihua , Li Hongyi , Pan Shilie
Published: November 2016

LiRb2PO4(LRPO) possesses a very short UV cut-off edge (<170 nm), and a large SHG response (2.1 × KDP) and is phase-matchable.
Feasibility of Clinical Endoscopy and Stroboscopy in Children With Bilateral Vocal Fold Lesions
Authors: Zacharias Stephanie R. C. , Brehm Susan Baker , Weinrich Barbara , Kelchner Lisa , Tabangin Meredith , de Alarcon Alessandro
Published: November 2016

Purpose

The purpose of this study was to examine the utility of flexible and rigid endoscopy and stroboscopy for the identification of anatomical and physiological features in children with bilateral vocal fold lesions. The secondary purpose was to describe the age distribution of patients who could tolerate use of the different types of endoscopes.

Method

This cross-sectional clinic-based study included 38 children (ages 5 to 12 years) diagnosed with bilateral vocal fold lesions via videoendoscopy. Vocal fold vibratory characteristics (e.g., mucosal wave) were rated by 4 clinicians by consensus.

Results

Bilateral vocal fold lesions could be well described anatomically after visualization with both flexible and rigid endoscopes and were most commonly described as symmetrical and broad based. However, the clinicians' confidence in the accuracy of stroboscopy for rating vocal fold vibratory characteristics was limited for both flexible and rigid stroboscopes.

Conclusions

Videoendoscopy was adequate for viewing and characterizing anatomical structures of bilateral vocal fold lesions in pediatric patients; however, vibratory characteristics were often not fully visualized with videostroboscopy. In view of the importance of visualizing vocal fold vibration in the differential diagnosis and treatment of vocal fold lesions, other imaging modalities, such as high-speed videoendoscopy, may provide more accurate descriptions of vocal fold vibratory characteristics in this population.
Une cause inhabituelle d’hyperCKémie
Authors: Modrego Pedro J. , Gazulla José , Cobo Ana-Maria , Andoni Urtizberea J.
Published: November 2016

Les élévations du taux de créatine-phospho-kinase (CPK), ou hyperCKémies, constituent le lot quotidien de nombreux myologues. Leur grande diversité étiologique rend les choses difficiles en pratique clinique, plus encore lorsque l’hyperCKémie est isolée. Mis à part les élévations transitoires liées à certaines circonstances facilement identifiables (naissance, traumatisme, exercice musculaire extrême, exposition aux statines) ou certains facteurs ethniques, de nombreuses maladies neuromusculaires peuvent en être à l’origine. Il s’agit en premier lieu des dystrophies musculaires progressives et des myopathies métaboliques (glycogénoses surtout). Les progrès obtenus dans l’identification des causes des hyperCKémies ont sensiblement progressé ces dernières années grâce, notamment, à l’utilisation plus large du NGS. Dans l’observation ci-dessous, l’accent est mis sur une cause rare d’hyperCKémie pour laquelle un marqueur érythrocytaire simple permet d’évoquer le diagnostic.
PRKACA Mutations in Adrenal Adenomas: Genotype/Phenotype
Correlations
Authors: Dalmazi G. D. , Beuschlein F.
Published: November 2016

Untargeted, next generation sequencing approaches have provided deep insights
into genetic events that result in unopposed steroidogenesis from the adrenal
cortex. In particular, somatic mutations in the gene encoding the catalytic
subunit α of protein kinase A (PKA) (PRKACA) were identified
independently by several groups as the most frequently altered gene in
cortisol-producing adenomas. Detailed functional studies could explore the
molecular consequences of these hot-spot mutations and large international
cohorts have provided the basis to explore the clinical characteristics
associated with this mutation. Thereby, PRKACA mutations are highly
specific for cortisol over-secretion, while they are absent or very rare in the
context of other adrenal diseases. Patients carrying these somatic mutations are
affected by a more severe phenotype and are identified at a younger age. Thus,
these genotype/phenotype correlations provide further evidence for the
importance of PKA-dependent pathways for adrenal physiology and disease.
High pressure chemistry of thioaldehydes: A first-principles molecular dynamics study
Authors: Zhang Yaoting , Mosey Nicholas J.
Published: November 2016

First-principles molecular dynamics simulations are used to investigate the chemical behavior of bulk thioacetaldehyde (MeC(H)S) in response to changes in pressure, P. The simulations show that these molecules oligomerize in response to applied P. Oligomerization is initiated through C—S bond formation, with constrained dynamics simulations showing that the barrier to this reaction step is lowered significantly by applied P. Subsequent reactions involving the formation of additional C—S bonds or radical processes that lead to S—S and C—C bonds lengthen the oligomers. Oligomerization is terminated through proton transfer or the formation of rings. The mechanistic details of all reactions are examined. The results indicate that the P-induced reactivity of the MeC(H)S-based system differs significantly from that of analogous MeC(H)O-based systems, which have been reported previously. Comparison with the MeC(H)O study shows that replacing oxygen with sulfur significantly lowers the P required to initiate oligomerization (from 26 GPa to 5 GPa), increases the types of reactions in which systems of this type can take part, and increases the variety of products formed through these reactions. These differences can be explained in terms of the electronic structures of these systems, which may be useful for certain high P applications.
Preface: Special Topic on Nucleation: New Concepts and Discoveries
Authors: Kelton K. F. , Frenkel Daan
Published: November 2016

Many phenomena in the world around us depend on infrequent, yet short-lived, events that completely alter how a system subsequently develops in time. In the physical sciences, there are many examples of such crucial “rare events.” Among the most important of these are nucleation processes, in which, due to a rare fluctuation, a new phase forms spontaneously within a meta-stable parent phase. Because nucleation processes are both rare and rapid and happen on a microscopic spatial scale, their experimental study is challenging. In recent years, there have been major developments both in the experimental study of nucleation phenomena and in the numerical simulation of such processes. As the articles in this special issue demonstrate, these recent advances in the ability to probe nucleation phenomena have transformed our understanding of the field.
First order reversal curves (FORC) analysis of individual magnetic nanostructures using micro-Hall magnetometry
Authors: Pohlit Merlin , Eibisch Paul , Akbari Maryam , Porrati Fabrizio , Huth Michael , Müller Jens
Published: November 2016

Alongside the development of artificially created magnetic nanostructures, micro-Hall magnetometry has proven to be a versatile tool to obtain high-resolution hysteresis loop data and access dynamical properties. Here we explore the application of First Order Reversal Curves (FORC)—a technique well-established in the field of paleomagnetism for studying grain-size and interaction effects in magnetic rocks—to individual and dipolar-coupled arrays of magnetic nanostructures using micro-Hall sensors. A proof-of-principle experiment performed on a macroscopic piece of a floppy disk as a reference sample well known in the literature demonstrates that the FORC diagrams obtained by magnetic stray field measurements using home-built magnetometers are in good agreement with magnetization data obtained by a commercial vibrating sample magnetometer. We discuss in detail the FORC diagrams and their interpretation of three different representative magnetic systems, prepared by the direct-write Focused Electron Beam Induced Deposition (FEBID) technique: (1) an isolated Co-nanoisland showing a simple square-shaped hysteresis loop, (2) a more complex CoFe-alloy nanoisland exhibiting a wasp-waist-type hysteresis, and (3) a cluster of interacting Co-nanoislands. Our findings reveal that the combination of FORC and micro-Hall magnetometry is a promising tool to investigate complex magnetization reversal processes within individual or small ensembles of nanomagnets grown by FEBID or other fabrication methods. The method provides sub-μm spatial resolution and bridges the gap of FORC analysis, commonly used for studying macroscopic samples and rather large arrays, to studies of small ensembles of interacting nanoparticles with the high moment sensitivity inherent to micro-Hall magnetometry.
Physical investigation of electrophoretically deposited graphene oxide and reduced graphene oxide thin films
Authors: Politano Grazia Giuseppina , Versace Carlo , Vena Carlo , Castriota Marco , Ciuchi Federica , Fasanella Angela , Desiderio Giovanni , Cazzanelli Enzo
Published: November 2016

Graphene oxide and reduced graphene oxide thin films are very promising materials because they can be used in optoelectronic devices and in a growing range of applications such as touch screens and flexible displays. In this work, graphene oxide (GO) and thermally reduced graphene oxide (rGO) thin films, deposited on Ti/glass substrates, have been obtained by electrophoretic deposition. The morphological and the structural properties of the samples have been investigated by micro-Raman technique, X-ray reflectometry, and SEM analysis. In order to study the optical and electrical properties, variable angle spectroscopic ellipsometry and impedance analysis have been performed. The thermal annealing changes strongly the structural, electrical, and optical properties, because during the thermal processes some amount of sp3 bonds originally present in GO were removed. In particular, the annealing enhances the Ohmic behavior of the rGO film increasing its conductivity and the estimated optical density. Moreover, using electrophoretic deposition, we have found a higher value of optical density for GO thin films, not observed in GO films obtained with other deposition methods.
Continuous monitoring of the bulk oxidation states in LixNi1/3Mn1/3Co1/3O2 during charging and discharging
Authors: Klinser G. , Topolovec S. , Kren H. , Koller S. , Goessler W. , Krenn H. , Würschum R.
Published: November 2016

Operando magnetic susceptibility measurements on the LixNi1/3Mn1/3Co1/3O2 cathode material during repetitive electrochemical cycling were performed, enabling a continuous and bulk sensitive monitoring of the charge compensation process. Upon charging and Li extraction down to the Li contents of x = 1/3, exclusively Ni undergoes oxidation in two consecutive steps, namely, Ni2+→Ni3+ for x > 2/3 and Ni3+→Ni4+ for 2/3 > x > 1/3 with a continuous transition in between. In the regime of low Li concentrations x < 1∕3, both Co- and O-ions contribute to the charge compensation. While the oxidation of Ni and O during charging is reversible, the Co oxidation is found to be irreversible.
Intrinsic electron mobility limits in β-Ga2O3
Authors: Ma Nan , Tanen Nicholas , Verma Amit , Guo Zhi , Luo Tengfei , Xing Huili (Grace) , Jena Debdeep
Published: November 2016

By systematically comparing experimental and theoretical transport properties, we identify the polar optical phonon scattering as the dominant mechanism limiting electron mobility in β–Ga2O3 to <200 cm2/V s at 300 K for donor doping densities lower than ∼1018 cm–3. Despite similar electron effective mass of β–Ga2O3 to GaN, the electron mobility is ∼10× lower because of a massive Fröhlich interaction, due to the low phonon energies stemming from the crystal structure and strong bond ionicity. Based on the theoretical and experimental analysis, we provide an empirical expression for electron mobility in β–Ga2O3 that should help calibrate its potential in high performance device design and applications.
Determination of spin polarization using an unconventional iron superconductor
Authors: Gifford J. A. , Chen B. B. , Zhang J. , Zhao G. J. , Kim D. R. , Li B. C. , Wu D. , Chen T. Y.
Published: November 2016

An unconventional iron superconductor, SmO0.7F0.3FeAs, has been utilized to determine the spin polarization and temperature dependence of a highly spin-polarized material, La0.67Sr0.33MnO3, with Andreev reflection spectroscopy. The polarization value obtained is the same as that determined using a conventional superconductor Pb but the temperature dependence of the spin polarization can be measured up to 52 K, a temperature range, which is several times wider than that using a typical conventional superconductor. The result excludes spin-parallel triplet pairing in the iron superconductor.
Breaking down scats: degradation of DNA from greater bilby (Macrotis lagotis) faecal pellets
Authors: Carpenter Fiona M. , Dziminski Martin A.
Published: November 2016

Isolating DNA from scats (faeces) of threatened species is a valuable, non-invasive method for identifying individuals. To establish whether genotyping of greater bilby (Macrotis lagotis) individuals from faecal pellets collected in the field can be useful for population monitoring, an understanding of the DNA degradation rates is necessary. To determine the relationship between time and degradation of bilby faecal DNA, and assess whether a two-step elution process during extraction results in better-quality DNA, faecal pellets were collected from captive individuals, maintained under seminatural conditions, then harvested at known periods. DNA was amplified from faecal pellets with a 99% success rate and error rates of less than 5% up to 14 days after deposition. The amplification rate decreases, and the rate of allelic dropout increases with time, but DNA can still be amplified at rates above 60% and error rates below 15% at 90–180 days. We found that a second elution step was unnecessary, with more DNA amplified over a longer period using the first eluate. Viable DNA exists on bilby faecal pellets for a long period after deposition, which is useful for obtaining genetic samples for population monitoring programs and studies on population genetics.
Loss of β-adrenergic–stimulated phosphorylation of Ca
V
1.2 channels on Ser1700 leads to heart failure
Authors: Yang Linghai , Dai Dao-Fu , Yuan Can , Westenbroek Ruth E. , Yu Haijie , West Nastassya , de la Iglesia Horacio O. , Catterall William A.
Published: November 2016

Significance

Calcium entry initiates contraction in cardiac myocytes, and altered expression of voltage-gated calcium channel 1.2 (Ca
V
1.2) causes heart failure in mice. Here we show that reducing β-adrenergic regulation of Ca
V
1.2 by mutation of a PKA site in the C-terminal domain causes age-related heart failure. Dual mutation of a nearby casein-kinase II phosphorylation site accelerated heart failure. The PKA level was increased; PKA-mediated phosphorylation of ryanodine receptor type-2, phospholamban, and troponin-I was increased; the calcium pool in the sarcoplasmic reticulum was increased; and the activity of the calcium-dependent phosphoprotein phosphatase calcineurin was persistently elevated. These changes in mice with a mutation at the PKA site Ser1700 (SA mice) suggest that compensatory mechanisms may initially enhance contractility but eventually cause increased sensitivity to cardiovascular stress and heart failure.
Skopos translation theory, text-types, and the African postcolonial text in intercultural postcolonial communication
Authors: Eke Joseph N.
Published: November 2016

The Postcolonial text is a political and ideological text that is differentiable in translation. This is because of its location in the dialogic and discursive communicative exchange between former coloniser and former colonised cultures and societies. This communicative exchange takes place in the situation and condition of asymmetrical relations and relations of inequality and involves the contestation of histories, cultures, meanings, identities and representations. The functionality of the postcolonial text with its message is fixated on this dialogue and discourse; and each postcolonial text is a single statement directly and specifically responding to this dialogue and discourse in some way. This paper examines the African postcolonial text* and its communicative location in the light of postcolonial theory and the possibility offered by the skopos functional theory in translation to set aside the purpose and function of the source text intended by the author. Using Chinua Achebe’s texts, It would conclude that the mediatory role of the translator in the dialogic and discursive exchange between former coloniser and former colonised cultures and societies need not become interference in the application of the skopos theory.
Comparative analysis of nonvolatile and volatile metabolites in Lichtheimia ramosa cultivated in different growth media
Authors: Chung Hyun , Lee NaKyeom , Seo Jeong-Ah , Kim Young-Suk
Published: November 2016

Lichtheimia ramosa is one of the predominant filamentous fungi in Korean traditional nuruk. The nonvolatile and volatile metabolites of L. ramosa cultivated in three growth media: complete medium (CM), potato dextrose broth (PDB), and sabouraud dextrose broth (SDB), were investigated and compared. Among nonvolatile metabolites, serine, lysine, and ornithine increased in CM and PDB cultivated with L. ramosa during the exponential phase. In addition, glucose level increased in CM whereas decreased in PDB and SDB. The major volatile metabolites in the extract samples were acetic acid, ethanol, 3-methyl-2-buten-1-ol, 2-phenylethanol, ethylacetate, 2-furaldehyde, 5-(hydroxymethyl)-2-furaldehyde, 2,3-dihydro-3,5,-dihydroxy-6-methyl-4H-pyran-4-one, and α-humulene. In particular, the levels of volatile metabolites related to makgeolli (e.g., acetic acid, ethanol, and ethyl acetate) were highest in extracts cultivated in CM. On the other hand, the level of 2-phenylethanol was relatively higher in PDB and SDB, possibly due to there being more phenylalanine present in the biomass sample in media.
Language choice for science education: policy and practice
Authors: Mifsud Jordan , Farrugia Josette
Published: November 2016

The Maltese National Minimum Curriculum published in 1999 sought to strengthen bilingualism by reinforcing the practice of teaching and assessing some subjects in English and others in Maltese. It also pointed out that code‐switching should only be used in cases of severe pedagogical difficulties. As a new National Curriculum Framework was being prepared some educators suggested language as a possible barrier to student progress and argued that the traditional practice of teaching subjects such as science in English should be reconsidered. This study investigated language choices, function and code‐switching in science lessons. Classroom observations, interviews and focus groups showed that in state schools 12–13 year old students were being taught science predominantly in Maltese while reading, writing and formal assessment were in English. Students who were more exposed to English, irrespective of class stream, used this language more frequently than those who were less exposed to the language. The findings seem to suggest that teachers may be overcautious. While code‐switching may initially provide technical terms and serve as a bridge between the two languages, eventually it can give way to a more precise and formal use of English thus ensuring both learning of science and development of bilingualism.
Axon degeneration: Linking axonal bioenergetics to myelin
Authors: Beirowski Bogdan , Babetto Elisabetta , Wrabetz Lawrence
Published: November 2016

The mechanisms by which axonal degeneration occurs, even in the presence of apparently normal myelin sheaths, remain unknown. In this issue, Yin et al. (2016. J. Cell Biol. https://doi.org/10.1083/jcb.201607099) study mutant mice in which proteolipid protein is replaced by the peripheral myelin protein P0 and describe a number of early axonal abnormalities, which together suggest that aberrant mitochondrial energy metabolism precedes axonal degeneration.
Free boundary minimal surfaces in the unit ball with low cohomogeneity
Authors: Freidin Brian , Gulian Mamikon , McGrath Peter
Published: November 2016

We study free boundary minimal surfaces in the unit ball of low cohomogeneity. For each pair of positive integers

(
m
,
n
)

(m,n)

such that

m
,
n
>
1

m, n >1

and

m
+
n
≥
8

m+n\geq 8

, we construct a free boundary minimal surface

Σ

m
,
n

⊂

B

m
+
n

\Sigma _{m, n} \subset B^{m+n}

(1) invariant under

O
(
m
)
×
O
(
n
)

O(m)\times O(n)

. When

m
+
n
>
8

m+n>8

, an instability of the resulting equation allows us to find an infinite family

{

Σ

m
,
n
,
k

}

k
∈

N

\{\Sigma _{m,n, k}\}_{k\in \mathbb {N}}

of such surfaces. In particular,

{

Σ

2
,
2
,
k

}

k
∈

N

\{\Sigma _{2, 2, k}\}_{k\in \mathbb {N}}

is a family of solid tori which converges to the cone over the Clifford torus as

k
k

goes to infinity. These examples indicate that a smooth compactness theorem for free boundary minimal surfaces due to Fraser and Li does not generally extend to higher dimensions.

For each

n
≥
3

n\geq 3

, we prove there is a unique nonplanar

S
O
(
n
)

SO(n)

-invariant free boundary minimal surface (a “catenoid”)

Σ
n

⊂

B
n

(
1
)

\Sigma _n \subset B^n(1)

. These surfaces generalize the “critical catenoid” in

B
3

(
1
)

B^3(1)

studied by Fraser and Schoen.
Linearity of network proximity measures: implications for set-based queries and significance testing
Authors: Maxwell Sean , Chance Mark R , Koyutürk Mehmet
Published: November 2016

Motivation

In recent years, various network proximity measures have been proposed to facilitate the use of biomolecular interaction data in a broad range of applications. These applications include functional annotation, disease gene prioritization, comparative analysis of biological systems and prediction of new interactions. In such applications, a major task is the scoring or ranking of the nodes in the network in terms of their proximity to a given set of ‘seed’ nodes (e.g. a group of proteins that are identified to be associated with a disease, or are deferentially expressed in a certain condition). Many different network proximity measures are utilized for this purpose, and these measures are quite diverse in terms of the benefits they offer.

Results

We propose a unifying framework for characterizing network proximity measures for set-based queries. We observe that many existing measures are linear, in that the proximity of a node to a set of nodes can be represented as an aggregation of its proximity to the individual nodes in the set. Based on this observation, we propose methods for processing of set-based proximity queries that take advantage of sparse local proximity information. In addition, we provide an analytical framework for characterizing the distribution of proximity scores based on reference models that accurately capture the characteristics of the seed set (e.g. degree distribution and biological function). The resulting framework facilitates computation of exact figures for the statistical significance of network proximity scores, enabling assessment of the accuracy of Monte Carlo simulation based estimation methods.

Availability and Implementation

Implementations of the methods in this paper are available at https://bioengine.case.edu/crosstalker which includes a robust visualization for results viewing.

Supplementary information

Supplementary data are available at Bioinformatics online.
Training alignment parameters for arbitrary sequencers with LAST-TRAIN
Authors: Hamada Michiaki , Ono Yukiteru , Asai Kiyoshi , Frith Martin C
Published: November 2016

LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads.

Availability and Implementation

the source code is freely available at http://last.cbrc.jp/

Supplementary information

Supplementary data are available at Bioinformatics online.
Exploring the predictive power of polygenic scores derived from genome-wide association studies: a study of 10 complex traits
Authors: So Hon-Cheong , Sham Pak C
Published: November 2016

Motivation

It is hoped that advances in our knowledge in disease genomics will contribute to personalized medicine such as individualized preventive strategies or early diagnoses of diseases. With the growth of genome-wide association studies (GWAS) in the past decade, how far have we reached this goal? In this study we explored the predictive ability of polygenic risk scores (PRSs) derived from GWAS for a range of complex disease and traits.

Results

We first proposed a new approach to evaluate predictive performances of PRS at arbitrary P-value thresholds. The method was based on corrected estimates of effect sizes, accounting for possible false positives and selection bias. This approach requires no distributional assumptions and only requires summary statistics as input. The validity of the approach was verified in simulations. We explored the predictive power of PRS for ten complex traits, including type 2 diabetes (DM), coronary artery disease (CAD), triglycerides, high- and low-density lipoprotein, total cholesterol, schizophrenia (SCZ), bipolar disorder (BD), major depressive disorder and anxiety disorders. We found that the predictive ability of PRS for CAD and DM were modest (best AUC = 0.608 and 0.607) while for lipid traits the prediction R-squared ranged from 16.1 to 29.8%. For psychiatric disorders, the predictive power for SCZ was estimated to be the highest (best AUC 0.820), followed by BD. Predictive performance of other psychiatric disorders ranged from 0.543 to 0.585. Psychiatric traits tend to have more gradual rise in AUC when significance thresholds increase and achieve the best predictive power at higher P-values than cardiometabolic traits.

Supplementary information

Supplementary data are available at Bioinformatics online.
Analysis of the mechanism of radiation-induced upregulation of mitochondrial abundance in mouse fibroblasts
Authors: Yamamori Tohru , Sasagawa Tomoya , Ichii Osamu , Hiyoshi Mie , Bo Tomoki , Yasui Hironobu , Kon Yasuhiro , Inanami Osamu
Published: November 2016

Mitochondria strongly contribute to the maintenance of cellular integrity through various mechanisms, including oxidative adenosine triphosphate production and calcium homeostasis regulation. Therefore, proper regulation of the abundance, distribution and activity of mitochondria is crucial for the maintenance of cellular homeostasis. Previous studies have shown that ionizing radiation (IR) alters mitochondrial functions, suggesting that mitochondria are likely to be an important target of IR. Though IR reportedly influences cellular mitochondrial abundance, the mechanism remains largely unknown. In this study, we examined how IR influences mitochondrial abundance in mouse fibroblasts. When mouse NIH/3T3 cells were exposed to X-rays, a time-dependent increase was observed in mitochondrial DNA (mtDNA) and mitochondrial mass, indicating radiation-induced upregulation of mitochondrial abundance. Meanwhile, not only did we not observe a significant change in autophagic activity after irradiation, but in addition, IR hardly influenced the expression of two mitochondrial proteins, cytochrome c oxidase subunit IV and cytochrome c, or the mRNA expression of Polg, a component of DNA polymerase γ. We also observed that the expression of transcription factors involved in mitochondrial biogenesis was only marginally affected by IR. These data imply that radiation-induced upregulation of mitochondrial abundance is an event independent of macroautophagy and mitochondrial biogenesis. Furthermore, we found evidence that IR induced long-term cell cycle arrest and cellular senescence, indicating that these events are involved in regulating mitochondrial abundance. Considering the growing significance of mitochondria in cellular radioresponses, we believe the present study provides novel insights into understanding the effects of IR on mitochondria.