bluuebunny/crossref_metadata_2025 huggingface dataset:
The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)
Authors: Gao Feng , Warren Alan , Zhang Qianqian , Gong Jun , Miao Miao , Sun Ping , Xu Dapeng , Huang Jie , Yi Zhenzhen , Song Weibo
Published: April 2016

The phylum Ciliophora plays important roles in a wide range of biological studies. However, the evolutionary relationships of many groups remain unclear due to a lack of sufficient molecular data. In this study, molecular dataset was expanded with representatives from 55 orders and all major lineages. The main findings are: (1) 14 classes were recovered including one new class, Protocruziea n. cl.; (2) in addition to the two main branches, Postciliodesmatophora and Intramacronucleata, a third branch, the Mesodiniea, is identified as being basal to the other two subphyla; (3) the newly defined order Discocephalida is revealed to be a sister clade to the euplotids, strongly suggesting the separation of discocephalids from the hypotrichs; (4) the separation of mobilids from the peritrichs is not supported; (5) Loxocephalida is basal to the main scuticociliate assemblage, whereas the thigmotrichs are placed within the order Pleuronematida; (6) the monophyly of classes Phyllopharyngea, Karyorelictea, Armophorea, Prostomatea, Plagiopylea, Colpodea and Heterotrichea are confirmed; (7) ambiguous generaAskenasia,CyclotrichiumParaspathidiumandPlagiocampashow close affiliation to the well known plagiopyleans; (8) validity of the subclass Rhynchostomatia is supported and (9) the systematic positions of Halteriida and Linconophoria remain unresolved and are thus regarded asincertae sediswithin Spirotrichea.
High activity of the stress promoter contributes to susceptibility to stress in the tree shrew
Authors: Fang Hui , Sun Yun-Jun , Lv Yan-Hong , Ni Rong-Jun , Shu Yu-Mian , Feng Xiu-Yu , Wang Yu , Shan Qing-Hong , Zu Ya-Nan , Zhou Jiang-Ning
Published: April 2016

Stress is increasingly present in everyday life in our fast-paced society and involved in the pathogenesis of many psychiatric diseases. Corticotrophin-releasing-hormone (CRH) plays a pivotal role in regulating the stress responses. The tree shrews are highly vulnerable to stress which makes them the promising animal models for studying stress responses. However, the mechanisms underlying their high stress-susceptibility remained unknown. Here we confirmed that cortisol was the dominate corticosteroid in tree shrew and was significantly increased after acute stress. Our study showed that the function of tree shrew CRH - hypothalamic-pituitary-adrenal (HPA) axis was nearly identical to human that contributed little to their hyper-responsiveness to stress. Using CRH transcriptional regulation analysis we discovered a peculiar active glucocorticoid receptor response element (aGRE) site within the tree shrew CRH promoter, which continued to recruit co-activators including SRC-1 (steroid receptor co-activator-1) to promote CRH transcription under basal or forskolin/dexamethasone treatment conditions. Basal CRH mRNA increased when the aGRE was knocked into the CRH promoter in human HeLa cells using CAS9/CRISPR. The aGRE functioned critically to form the “Stress promoter” that contributed to the higher CRH expression and susceptibility to stress. These findings implicated novel molecular bases of the stress-related diseases in specific populations.
Ecological restoration alters microbial communities in mine tailings profiles
Authors: Li Yang , Jia Zhongjun , Sun Qingye , Zhan Jing , Yang Yang , Wang Dan
Published: April 2016

Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.
Somatic genomic alterations in retinoblastoma beyond RB1 are rare and limited to copy number changes
Authors: Kooi Irsan E. , Mol Berber M. , Massink Maarten P. G. , Ameziane Najim , Meijers-Heijboer Hanne , Dommering Charlotte J. , van Mil Saskia E. , de Vries Yne , van der Hout Annemarie H. , Kaspers Gertjan J. L. , Moll Annette C. , te Riele Hein , Cloos Jacqueline , Dorsman Josephine C.
Published: April 2016

Retinoblastoma is a rare childhood cancer initiated by RB1 mutation or MYCN amplification, while additional alterations may be required for tumor development. However, the view on single nucleotide variants is very limited. To better understand oncogenesis, we determined the genomic landscape of retinoblastoma. We performed exome sequencing of 71 retinoblastomas and matched blood DNA. Next, we determined the presence of single nucleotide variants, copy number alterations and viruses. Aside from RB1, recurrent gene mutations were very rare. Only a limited fraction of tumors showed BCOR (7/71, 10%) or CREBBP alterations (3/71, 4%). No evidence was found for the presence of viruses. Instead, specific somatic copy number alterations were more common, particularly in patients diagnosed at later age. Recurrent alterations of chromosomal arms often involved less than one copy, also in highly pure tumor samples, suggesting within-tumor heterogeneity. Our results show that retinoblastoma is among the least mutated cancers and signify the extreme sensitivity of the childhood retina for RB1 loss. We hypothesize that retinoblastomas arising later in retinal development benefit more from subclonal secondary alterations and therefore, these alterations are more selected for in these tumors. Targeted therapy based on these subclonal events might be insufficient for complete tumor control.
Single-wall carbon nanotubes and graphene oxide-based saturable absorbers for low phase noise mode-locked fiber lasers
Authors: Li Xiaohui , Wu Kan , Sun Zhipei , Meng Bo , Wang Yonggang , Wang Yishan , Yu Xuechao , Yu Xia , Zhang Ying , Shum Perry Ping , Wang Qi Jie
Published: April 2016

Low phase noise mode-locked fiber laser finds important applications in telecommunication, ultrafast sciences, material science, and biology, etc. In this paper, two types of carbon nano-materials, i.e. single-wall carbon nanotube (SWNT) and graphene oxide (GO), are investigated as efficient saturable absorbers (SAs) to achieve low phase noise mode-locked fiber lasers. Various properties of these wall-paper SAs, such as saturable intensity, optical absorption and degree of purity, are found to be key factors determining the performance of the ultrafast pulses. Reduced-noise femtosecond fiber lasers based on such carbon-based SAs are experimentally demonstrated, for which the phase noise has been reduced by more than 10 dB for SWNT SAs and 8 dB for GO SAs at 10 kHz. To the best of our knowledge, this is the first investigation on the relationship between different carbon material based SAs and the phase noise of mode-locked lasers. This work paves the way to generate high-quality low phase noise ultrashort pulses in passively mode-locked fiber lasers.
A study of organic acid production in contrasts between two phosphate solubilizing fungi: Penicillium oxalicum and Aspergillus niger
Authors: Li Zhen , Bai Tongshuo , Dai Letian , Wang Fuwei , Tao Jinjin , Meng Shiting , Hu Yunxiao , Wang Shimei , Hu Shuijin
Published: April 2016

Phosphate solubilizing fungi (PSF) have huge potentials in enhancing release of phosphorus from fertilizer. Two PSF (NJDL-03 and NJDL-12) were isolated and identified asPenicillium oxalicumandAspergillus nigerrespectively in this study. The quantification and identification of organic acids were performed by HPLC. Total concentrations of organic acids secreted by NJDL-03 and NJDL-12 are ~4000 and ~10,000 mg/L with pH values of 3.6 and 2.4 respectively after five-days culture. Oxalic acid dominates acidity in the medium due to its high concentration and high acidity constant. The two fungi were also cultured for five days with the initial pH values of the medium varied from 6.5 to 1.5. The biomass reached the maximum when the initial pH values are 4.5 for NJDL-03 and 2.5 for NJDL-12. The organic acids for NJDL-12 reach the maximum at the initial pH = 5.5. However, the acids by NJDL-03 continue to decrease and proliferation of the fungus terminates at pH = 2.5. The citric acid production increases significantly for NJDL-12 at acidic environment, whereas formic and oxalic acids decrease sharply for both two fungi. This study shows that NJDL-12 has higher ability in acid production and has stronger adaptability to acidic environment than NJDL-03.
Smartphone spectrometer for colorimetric biosensing
Authors: Wang Yi , Liu Xiaohu , Chen Peng , Tran Nhung Thi , Zhang Jinling , Chia Wei Sheng , Boujday Souhir , Liedberg Bo
Published: April 2016

We report on a smartphone spectrometer for colorimetric detection of glucose and cardiac troponin I.
Two-channel image analysis method for the screening of OBOC libraries
Authors: Helmer Dorothea , Brahm Kevin , Helmer Christian , Wack Julia Susanne , Brenner-Weiss Gerald , Schmitz Katja
Published: April 2016

Compound libraries obtained by the split synthesis approach can be easily screened for novel protein ligands exploiting false-colour visualization in two-channel fluorescence microscopy.
Synthesis and fluorescence study of conjugated polymers based on 2,4,6-triphenylpyridine moieties
Authors: Ran Qianping , Ma Jianfeng , Wang Tao , Fan Shimin , Yang Yong , Qi Shuai , Cheng Yixiang , Song Fengyan
Published: April 2016

Three novel 2,4,6-triphenylpyridine-based conjugated polymers showed strong fluorescence emission with large Stokes' shifts, tunable band gaps and high quantum yields.
Selectivity engineering of the diazotization reaction in a continuous flow reactor
Authors: Shukla C. A. , Kulkarni A. A. , Ranade V. V.
Published: April 2016

In situ generated diazonium salts are useful intermediates for the synthesis of fine chemicals and active pharmaceutical ingredients. This paper presents a methodology for selectivity engineering of the diazotization reaction in continuous reactors.
Investigating the effect of Ag nanocube polydispersity on gap-mode SERS enhancement factors
Authors: Dill Tyler J. , Rozin Matthew J. , Brown Eric R. , Palani Stephen , Tao Andrea R.
Published: April 2016

Colloidal polydispersity has a significant impact on the high Raman enhancement factors (EFs) for nanoparticle-based surface-enhanced Raman spectroscopy (SERS) substrates.
Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry
Authors: Lippens Jennifer L. , Ranganathan Srivathsan V. , D'Esposito Rebecca J. , Fabris Daniele
Published: April 2016

This study explored the use of modular nucleic acid (NA) standards to generate calibration curves capable of translating primary ion mobility readouts into corresponding collision cross section (CCS) data.
Multi-scale silica structures for improved HIV-1 Capsid (p24) antigen detection
Authors: Lin Sophia , Hedde Per Niklas , Venugopalan Vasan , Gratton Enrico , Khine Michelle
Published: April 2016

Silica (SiO2) micro- and nanostructures fabricated with pre-stressed thermoplastic shrink wrap film have been shown to yield far-field fluorescence signal enhancements over their planar or wrinkled counterparts.
UV-induced epitaxial attachment of TiO2 nanocrystals in molecularly mediated 1D and 2D alignments
Authors: Hiraide Tomoyuki , Kageyama Hiroyuki , Nakagawa Yoshitaka , Oaki Yuya , Imai Hiroaki
Published: April 2016

Molecularly mediated anatase nanocrystals were crystallographically connected via crystal bridges after UV irradiation.
Regioselective construction of diverse and multifunctionalized 2-hydroxybenzophenones for sun protection by indium(iii)-catalyzed benzannulation
Authors: Cai Hongyun , Xia Likai , Lee Yong Rok
Published: April 2016

Highly regioselective synthesis of 2-hydroxybenzophenones via the In(OTf)3-catalyzed formal [2+2+2] and [4+2] benzannulations has been successfully developed and their application as sun protection materials was also evaluated.
Aligning self-assembled gelators by drying under shear
Authors: Draper Emily R. , Mykhaylyk Oleksandr O. , Adams Dave J.
Published: April 2016

Here, we show how drying under shear can be used to prepare aligned fibres and worm-like micelles from perylene bisimide gelators.
Fractional electron number, temperature, and perturbations in chemical reactions
Authors: Miranda-Quintana Ramón Alain , Ayers Paul W.
Published: April 2016

The mathematical framework of conceptual density functional theory is extended to use the eigenstates and eigenvalues of perturbed subsystems. This unites, justifies, and extends, several previously proposed models.
Controlling particle deposit morphologies in drying nano-particle laden sessile droplets using substrate oscillations
Authors: Sanyal Apratim , Basu Saptarshi , Chaudhuri Swetaprovo
Published: April 2016

Sessile water droplets containing nano-silica particles are allowed to evaporate in the presence of driven substrate oscillations at chosen frequencies.
An efficient bifunctional two-component catalyst for oxygen reduction and oxygen evolution in reversible fuel cells, electrolyzers and rechargeable air electrodes
Authors: Dresp Sören , Luo Fang , Schmack Roman , Kühl Stefanie , Gliech Manuel , Strasser Peter
Published: April 2016

We report RDE and MEA performance of an active and stable non-precious, two-phase bifunctional oxygen reduction and evolution (ORR and OER) electrocatalyst for use in unitized reversible fuel cell/electrolyzers or rechargeable metal–air batteries.
The cyclopropylimine rearrangement/Povarov reaction cascade for the assembly of pyrrolo[3,2-c]quinoline derivatives
Authors: Cai Jinhui , Li Feifei , Deng Guo-Jun , Ji Xiaochen , Huang Huawen
Published: April 2016

Simple combination makes complexity. An efficient assembly of pyrrolo[3,2-c]quinoline derivatives from anilines and cyclopropyl aldehyde is disclosed.
Depolymerization of cellulose to processable glucans by non-thermal technologies
Authors: Jérôme F. , Chatel G. , De Oliveira Vigier K.
Published: April 2016

This review describes the contribution of non-thermal technologies to the conversion of cellulose to processable glucans. Whenever possible, the synergy of these technologies with catalysis, their impact on the cellulose structure and reactivity are discussed on the basis of recent reports on mechanocatalysis, non-thermal atmospheric plasma and sonochemistry.
Copper catalysed alkynylation of tertiary amines with CaC2via sp3 C–H activation
Authors: Teong Siew Ping , Yu Dingyi , Sum Yin Ngai , Zhang Yugen
Published: April 2016

A mild and easy-to-handle protocol to produce propargylamines with a terminal alkyne through sp3 C–H bond activation and C–C coupling of tertiary amines and calcium carbide has been developed.
Docetaxel-loaded SiO2@Au@GO core–shell nanoparticles for chemo-photothermal therapy of cancer cells
Authors: Li Xiaolin , Yang Zhi , Hu Nantao , Zhang Liying , Zhang Yafei , Yin Lei
Published: April 2016

The multifunctional antitumor SiO2@Au@GO core–shell nanoparticles (NPs) have been fabricated for serving as drug nanocarrier and photothermal inducer to have a treatment on human prostate cancer cell DU 145.
Chromosulfine, a novel cyclopentachromone sulfide produced by a marine-derived fungus after introduction of neomycin resistance
Authors: Yi Le , Cui Cheng-Bin , Li Chang-Wei , Peng Ji-Xing , Gu Qian-Qun
Published: April 2016

The discovery of chromosulfine, a novel cyclopentachromone sulfide generated by activating silent fungal pathways in a marine-derived fungus, was reported.
Improving the surface-enhanced Raman scattering activity of carbon nitride by two-step calcining
Authors: Jiang Jizhou
Published: April 2016

The modified g-C3N4 substrates were prepared by a two-step calcining method. The morphologies and microstructures of modified g-C3N4 were successfully controlled. The modified g-C3N4-2 h + Ag substrate exhibited superior SERS activity.
An in situ confinement strategy to porous poly(3,4-ethylenedioxythiophene)/sulfur composites for lithium–sulfur batteries
Authors: Ding Bing , Chang Zhi , Wang Jie , Dou Hui , Zhang Xiaogang
Published: April 2016

Porous poly(3,4-ethylenedioxythiophene)/sulfur composite was prepared throughin situautocatalytic polymerization of dibromized 3,4-ethylenedioxythiophene for lithium–sulfur batteries.
Electronic and transport properties of [V(Bz)2]n@SWCNT and [V(Bz)2]n@DWCNT nanocables
Authors: Shang Yan , Sun Cuicui , Zhang Guiling , Yang Zhaodi , Wang Xin
Published: April 2016

Novel nanocables with [V(Bz)2]n inside SWCNT and DWCNT.
Superior gas-sensing performance of amorphous CdO nanoflake arrays prepared at room temperature
Authors: Zhang Ye-Qing , Li Zhe , Ling Tao , Kulinich Sergei A. , Du Xi-Wen
Published: April 2016

Highly sensitive and selective detection of volatile organic compounds (VOCs) with fast response time is imperative based on safety requirements, yet often remains a challenge.
High voltage and high current density vertical GaN power diodes
Authors: Armstrong A.M. , Allerman A.A. , Fischer A.J. , King M.P. , van Heukelom M.S. , Moseley M.W. , Kaplar R.J. , Wierer J.J. , Crawford M.H. , Dickerson J.R.
Published: April 2016

The realisation of a GaN high voltage vertical p–n diode operating at >3.9 kV breakdown with a specific on‐resistance <0.9 mΩ cm2 is reported. Diodes achieved a forward current of 1 A for on‐wafer, DC measurements, corresponding to a current density >1.4 kA/cm2. An effective critical electric field of 3.9 MV/cm was estimated for the devices from analysis of the forward and reverse current–voltage characteristics. This suggests that the fundamental limit to the GaN critical electric field is significantly greater than previously believed.
Nonradiative lifetime extraction using power-dependent relative photoluminescence of III-V semiconductor double-heterostructures
Authors: Walker A. W. , Heckelmann S. , Karcher C. , Höhn O. , Went C. , Niemeyer M. , Bett A. W. , Lackner D.
Published: April 2016

A power-dependent relative photoluminescence measurement method is developed for double-heterostructures composed of III-V semiconductors. Analyzing the data yields insight into the radiative efficiency of the absorbing layer as a function of laser intensity. Four GaAs samples of different thicknesses are characterized, and the measured data are corrected for dependencies of carrier concentration and photon recycling. This correction procedure is described and discussed in detail in order to determine the material's Shockley-Read-Hall lifetime as a function of excitation intensity. The procedure assumes 100% internal radiative efficiency under the highest injection conditions, and we show this leads to less than 0.5% uncertainty. The resulting GaAs material demonstrates a 5.7 ± 0.5 ns nonradiative lifetime across all samples of similar doping (2–3 × 1017 cm−3) for an injected excess carrier concentration below 4 × 1012 cm−3. This increases considerably up to longer than 1 μs under high injection levels due to a trap saturation effect. The method is also shown to give insight into bulk and interface recombination.
Accumulation rate of bound states of dipoles in graphene
Authors: Rademacher Simone , Siedentop Heinz
Published: April 2016

We prove that the bound state energies of the two-dimensional massive Dirac operator with dipole type potentials accumulate with exponential rate at the band edge. In fact we prove a corresponding formula of De Martino et al. [Phys. Rev. Lett. 112(18), 186603 (2014)].
Spontaneous polarization induced electric field in zinc oxide nanowires and nanostars
Authors: Farid S. , Choi M. , Datta D. , Stroscio M. A. , Dutta M.
Published: April 2016

We report on the detection mechanism of spontaneous polarization using electrostatic force microscopy in zinc oxide nanowires and nanostars grown by vapor-liquid-solid technique. Optical and structural properties are investigated in detail to understand the complex ZnO nanostructures comprehensively. Calculations are carried out to estimate the electric field from the change in interleave amplitude induced by the electrostatic force due to the spontaneous polarization effects. Attraction of the probe between the tip and the sample varies for different structures with a stronger attraction for nanostars as compared to nanowires. Strength of electric field is dependent on the orientation of nanowires and nanostars c-axis with measured magnitude of electric field to be ∼107 V/m and 108 V/m respectively. This technique presents a unique detection mechanism of built-in spontaneous polarization and electric field from polar ZnO nanowires with applications in voltage gated ion channels, nano-bio interfaces, optoelectronic and photonic devices.
Novel focal point multipass cell for absorption spectroscopy on small sized atmospheric pressure plasmas
Authors: Winter Jörn , Hänel Mattis , Reuter Stephan
Published: April 2016

A novel focal point multipass cell (FPMPC) was developed, in which all laser beams propagate through a common focal point. It is exclusively constructed from standard optical elements. Main functional elements are two 90∘ off-axis parabolic mirrors and two retroreflectors. Up to 17 laser passes are demonstrated with a near-infrared laser beam. The number of laser passes is precisely adjustable by changing the retroreflector distance. At the focal point beams are constricted to fit through an aperture of 0.8 mm. This is shown for 11 beam passes. Moreover, the fast temporal response of the cell permits investigation of transient processes with frequencies up to 10 MHz. In order to demonstrate the applicability of the FPMPC for atmospheric pressure plasma jets, laser absorption spectroscopy on the lowest excited argon state (1s5) was performed on a 1 MHz argon atmospheric pressure plasma jet. From the obtained optical depth profiles, the signal-to-noise ratio was deduced. It is shown that an elevation of the laser pass number results in an proportional increase of the signal-to-noise ratio making the FPMPC an appropriate tool for absorption spectroscopy on plasmas of small dimensions.
New experimental perspectives for soft x-ray absorption spectroscopies at ultra-low temperatures below 50 mK and in high magnetic fields up to 7 T
Authors: Beeck T. , Baev I. , Gieschen S. , Meyer H. , Meyer S. , Palutke S. , Feulner P. , Uhlig K. , Martins M. , Wurth W.
Published: April 2016

A new ultra-low temperature experiment including a superconducting vector magnet has been developed for soft x-ray absorption spectroscopy experiments at third generation synchrotron light sources. The sample is cooled below 50 mK by a cryogen free 3He-4He dilution refrigerator. At the same time, magnetic fields of up to ±7 T in the horizontal direction and ±0.5 T in the vertical direction can be applied by a superconducting vector magnet. The setup allows to study ex situ and in situ prepared samples, offered by an attached UHV preparation chamber with load lock. The transfer of the prepared samples between the preparation section and the dilution refrigerator is carried out under cryogenic temperatures. First commissioning studies have been carried out at the Variable Polarization XUV Beamline P04 at PETRA III and the influence of the incident photon beam to the sample temperature has been studied.
Electron and hole drift mobility measurements on methylammonium lead iodide perovskite solar cells
Authors: Maynard Brian , Long Qi , Schiff Eric A. , Yang Mengjin , Zhu Kai , Kottokkaran Ranjith , Abbas Hisham , Dalal Vikram L.
Published: April 2016

We report nanosecond domain time-of-flight measurements of electron and hole photocarriers in methylammonium lead iodide perovskite solar cells. The mobilities ranged from 0.06 to 1.4 cm2/Vs at room temperature, but there is little systematic difference between the two carriers. We also find that the drift mobilities are dispersive (time-dependent). The dispersion parameters are in the range of 0.4–0.7, and they imply that terahertz domain mobilities will be much larger than nanosecond domain mobilities. The temperature-dependences of the dispersion parameters are consistent with confinement of electron and hole transport to fractal-like spatial networks within nanoseconds of their photogeneration.
Dynamical freezing, magnetic ordering, and the magnetocaloric effect in nanostructured Fe/Cu thin films
Authors: Desautels R. D. , Shueh C. , Lin K.-W. , Freeland J. W. , van Lierop J.
Published: April 2016

Dynamical freezing of Fe nanocrystallites in a Cu matrix with magnetic ordering of an FeCu interfacial phase provides a unique window into the magnetocaloric effect. The FeCu alloy altered the Fe nanocrystallite surface atoms, and with a magnetic ordering temperature comparable to the dynamical freezing temperature of the nanocrystallites enabled Fe surface atoms to contribute to the overall magnetization. Tuning the amount of interfacial alloy resulted in the control of the magnetic ordering temperature and the magnetocaloric properties.
Optical detection of strain and doping inhomogeneities in single layer MoS2
Authors: Michail A. , Delikoukos N. , Parthenios J. , Galiotis C. , Papagelis K.
Published: April 2016

Van der Waals single-layer materials are characterized by an inherent extremely low bending rigidity and therefore are prone to nanoscale structural modifications due to substrate interactions. Such interactions can induce excess charge concentration, conformational ripples, and residual mechanical strain. In this work, we employed spatially resolved Raman and photoluminescence (PL) images to investigate strain and doping inhomogeneities in a single layer exfoliated molybdenum disulphide crystal. We have found that correlations between the spectral parameters of the most prominent Raman bands A1′ and E′ enable us to decouple and quantify strain and charge doping effects. In comparison with Atomic Force Microscopy (AFM) topography, we show that the spatial distribution of the position of the A− -trion PL peak is strain sensitive and its linewidth can capture features smaller than the laser spot size. The presented optical analysis may have implications in the development of high-quality devices based on two-dimensional materials since structural and electronic modifications affect considerably their carrier mobility and conductivity.
Enhanced emission of quantum dots embedded within the high-index dielectric regions of photonic crystal slabs
Authors: See Gloria G. , Naughton Matt S. , Xu Lu , Nuzzo Ralph G. , Kenis Paul J. A. , Cunningham Brian T.
Published: April 2016

We demonstrate a method for combining sputtered TiO2 deposition with liquid phase dip-coating of a quantum dot (QD) layer that enables precise depth placement of QD emitters within a high-index dielectric film, using a photonic crystal (PC) slab resonator to demonstrate enhanced emission from the QDs when they are located at a specific depth within the film. The depth of the QDs within the PC is found to modulate the resonant wavelength of the PC as well as the emission enhancement efficiency, as the semiconducting material embedded within the dielectric changes its spatial overlap with the resonant mode.
Frequency selective tunable spin wave channeling in the magnonic network
Authors: Sadovnikov A. V. , Beginin E. N. , Odincov S. A. , Sheshukova S. E. , Sharaevskii Yu. P. , Stognij A. I. , Nikitov S. A.
Published: April 2016

Using the space-resolved Brillouin light scattering spectroscopy, we study the frequency and wavenumber selective spin-wave channeling. We demonstrate the frequency selective collimation of spin-wave in an array of magnonic waveguides, formed between the adjacent magnonic crystals on the surface of yttrium iron garnet film. We show the control over spin-wave propagation length by the orientation of an in-plane bias magnetic field. Fabricated array of magnonic crystal can be used as a magnonic platform for multidirectional frequency selective signal processing applications in magnonic networks.
The role of chemical structure on the magnetic and electronic properties of Co2FeAl0.5Si0.5/Si(111) interface
Authors: Kuerbanjiang Balati , Nedelkoski Zlatko , Kepaptsoglou Demie , Ghasemi Arsham , Glover Stephanie E. , Yamada Shinya , Saerbeck Thomas , Ramasse Quentin M. , Hasnip Philip J. , Hase Thomas P. A. , Bell Gavin R. , Hamaya Kohei , Hirohata Atsufumi , Lazarov Vlado K.
Published: April 2016

We show that Co2FeAl0.5Si0.5 film deposited on Si(111) has a single crystal structure and twin related epitaxial relationship with the substrate. Sub-nanometer electron energy loss spectroscopy shows that in a narrow interface region there is a mutual inter-diffusion dominated by Si and Co. Atomic resolution aberration-corrected scanning transmission electron microscopy reveals that the film has B2 ordering. The film lattice structure is unaltered even at the interface due to the substitutional nature of the intermixing. First-principles calculations performed using structural models based on the aberration corrected electron microscopy show that the increased Si incorporation in the film leads to a gradual decrease of the magnetic moment as well as significant spin-polarization reduction. These effects can have significant detrimental role on the spin injection from the Co2FeAl0.5Si0.5 film into the Si substrate, besides the structural integrity of this junction.
Femtosecond X-ray solution scattering reveals that bond formation mechanism of a gold trimer complex is independent of excitation wavelength
Authors: Kim Kyung Hwan , Kim Jong Goo , Oang Key Young , Kim Tae Wu , Ki Hosung , Jo Junbeom , Kim Jeongho , Sato Tokushi , Nozawa Shunsuke , Adachi Shin-ichi , Ihee Hyotcherl
Published: April 2016

The [Au(CN)2−]3 trimer in water experiences a strong van der Waals interaction between the d10 gold atoms due to large relativistic effect and can serve as an excellent model system to study the bond formation process in real time. The trimer in the ground state (S0) exists as a bent structure without the covalent bond between the gold atoms, and upon the laser excitation, one electron in the antibonding orbital goes to the bonding orbital, thereby inducing the formation of a covalent bond between gold atoms. This process has been studied by various time-resolved techniques, and most of the interpretation on the structure and dynamics converge except that the structure of the first intermediate (S1) has been debated due to different interpretations between femtosecond optical spectroscopy and femtosecond X-ray solution scattering. Recently, the excitation wavelength of 267 nm employed in our previous scattering experiment was suggested as the culprit for misinterpretation. Here, we revisited this issue by performing femtosecond X-ray solution scattering with 310 nm excitation and compared the results with our previous study employing 267 nm excitation. The data show that a linear S1 structure is formed within 500 fs regardless of excitation wavelength and the structural dynamics observed at both excitation wavelengths are identical to each other within experimental errors.
Loading of a Phenanthroline-Based Platinum(II) Complex onto the Surface of a Carbon Nanotube via π–π Stacking
Authors: Houston Stephanie A. , Venkataramanan Natarajan S. , Suvitha Ambigapathy , Wheate Nial J.
Published: April 2016

Stacking of the metal complex [(5,6-dimethyl-1,10-phenanthroline)(1S,2S-diaminocyclohexane)platinum(ii)]2+ (56MESS) onto the surface of two different fullerenes, a carbon nanotube (CNT), and a C60-buckyball was examined. The metal complex forms a supramolecular complex with multi-walled CNTs but not with buckyballs. Binding of 56MESS to the CNTs is highly efficient (90 %) but can be further stabilized by the addition of the surfactant, pluronic F-127, which resulted in a loading efficiency of 95 %. Molecular modelling shows that binding of 56MESS to the CNT is supported by the large surface area of the fullerene, whereas the more pronounced curvature and lack of a flat surface on the buckyball affects the ability of 56MESS to form bonds to its surface. The loading of 56MESS onto the CNT is via π–π stacking from the metal complex phenanthroline ligand and C–H···π bonding from the diaminocyclohexane ligand. 56MESS has 13 critical bonding points with the CNT, eight of which are π–π stacking bonds, but the metal complex forms only seven bonds with the buckyball. In addition, the loading of 56MESS onto the CNT results in a charge transfer of –0.111 eV; however, charge transfer is almost negligible for binding to the buckyball.
The role of ions in the self-healing behavior of soft particle suspensions
Authors: Scotti Andrea , Gasser Urs , Herman Emily S. , Pelaez-Fernandez Miguel , Han Jun , Menzel Andreas , Lyon L. Andrew , Fernández-Nieves Alberto
Published: April 2016

Significance

Understanding when a material crystallizes is of fundamental importance in condensed matter. In many materials, the presence of point defects suppresses crystallization. Surprisingly, colloidal hydrogels can overcome this limitation: A small number of large microgels can spontaneously deswell to fit in the crystal lattice of smaller microgels, thus avoiding the occurrence of point defects. We find that this unique particle deswelling is due to an osmotic pressure difference between the inside and the outside of the microgels resulting from the overlap of counterion clouds of neighboring particles. When this pressure difference exceeds the bulk modulus of the large microgels, these shrink, enabling crystallization without point defects.
In vivo metabolic labeling of sialoglycans in the mouse brain by using a liposome-assisted bioorthogonal reporter strategy
Authors: Xie Ran , Dong Lu , Du Yifei , Zhu Yuntao , Hua Rui , Zhang Chen , Chen Xing
Published: April 2016

Significance

In mammals, the brain is the organ with the highest level of sialic acids, a family of negatively charged monosaccharides that are commonly expressed as outer terminal residues of cell-surface glycans. Brain sialoglycans play essential roles in brain development, cognition, and disease progression; however, in vivo visualization of the sialoglycan biosynthesis in the mouse brain has been impossible. Here, we introduce a liposome-assisted bioorthogonal reporter (LABOR) strategy for metabolic labeling and visualization of brain sialoglycans in living mice. Applying LABOR, we visualized the biosynthesis of brain sialoglycans by in vivo fluorescence imaging and histological analysis, and identified important sialylated glycoproteins in the brain by glycoproteomics. We discovered that the turnover of sialoglycans is spatially regulated in distinct brain regions.
A single origin of Indo-European primary adpositions?
Authors: Reinöhl Uta
Published: April 2016

It has been widely assumed that the primary adpositions of modern Indo-European languages constitute a historically identical category, descending from the Proto-Indo-European ‘local particles’. I argue that this assumption needs to be revised, because a major branch of the language family, Indo-Aryan, possesses adpositions of unrelated origin. This is not only a question of different etyma, but the New Indo-Aryan adpositions descend from structurally different sources. The ancient local particles, as attested in early Indo-Aryan varieties, combine with local case forms and show a preference for the prenominal position. By contrast, the New Indo-Aryan adpositions descend from nominal and verbal forms heading genitives, and show a propensity for the postnominal slot. Thus, we are dealing with elements unrelated not only etymologically, but also with regard to their morphosyntactic distribution.
Summation Effects in Human Learning: Evidence from Patterning Discriminations in Goal-Tracking
Authors: Thorwart Anna , Uengoer Metin , Livesey Evan J. , Harris Justin A.
Published: April 2016

Participants in two human goal-tracking experiments were simultaneously trained with negative patterning (NP) and positive patterning (PP) discriminations (A+, B+, AB–, C–, D–, CD+). Both elemental and configural models of associative learning predict a PP advantage, such that NP is solved less readily than PP. However, elemental models like the unique cue approach additionally predict responding in AB– trials to be initially stronger than that in A+ and B+ trials due to summation of associative strength. Both experiments revealed a PP advantage and a strong summation effect in AB– trials in the first half of the experiments, irrespective of whether the same US was used for both discriminations (Experiment 1) or two different USs (Experiment 2). We discuss that the correct predictions of the unique cue approach are based on its assumptions of non-normalized and context-independent stimulus processing rather than elemental processing per se.
Combinatorics: A Very Short Introduction
Authors: Wilson Robin
Published: April 2016

Combinatorics is the branch of mathematics concerned with selecting, arranging, and listing or counting collections of objects. Dating back some 3000 years, and initially consisting mainly of the study of permutations and combinations, its scope has broadened to include topics such as graph theory, partitions of numbers, block designs, design of codes, and latin squares. Combinatorics: A Very Short Introduction provides an overview of the field and its applications in mathematics and computer theory, considering problems from the shortest routes covering certain stops to the minimum number of colours needed to draw a map with different colours for neighbouring countries.
Informed kmer selection for de novo transcriptome assembly
Authors: Durai Dilip A. , Schulz Marcel H.
Published: April 2016

Motivation:  De novo transcriptome assembly is an integral part for many RNA-seq workflows. Common applications include sequencing of non-model organisms, cancer or meta transcriptomes. Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure. The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k. As such no single kmer value leads to optimal results. Instead, DBGs over different kmer values are built and the assemblies are merged to improve sensitivity. However, no studies have investigated thoroughly the problem of automatically learning at which kmer value to stop the assembly. Instead a suboptimal selection of kmer values is often used in practice.

Results: Here we investigate the contribution of a single kmer value in a multi-kmer based assembly approach. We find that a comparative clustering of related assemblies can be used to estimate the importance of an additional kmer assembly. Using a model fit based algorithm we predict the kmer value at which no further assemblies are necessary. Our approach is tested with different de novo assemblers for datasets with different coverage values and read lengths. Further, we suggest a simple post processing step that significantly improves the quality of multi-kmer assemblies.

Conclusion: We provide an automatic method for limiting the number of kmer values without a significant loss in assembly quality but with savings in assembly time. This is a step forward to making multi-kmer methods more reliable and easier to use.

Availability and Implementation:A general implementation of our approach can be found under: https://github.com/SchulzLab/KREATION.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  mschulz@mmci.uni-saarland.de
Early life stages of the Arctic copepod Calanus glacialis are unaffected by increased seawater pCO2
Authors: Bailey Allison , Thor Peter , Browman Howard I. , Fields David M. , Runge Jeffrey , Vermont Alexander , Bjelland Reidun , Thompson Cameron , Shema Steven , Durif Caroline M. F. , Hop Haakon
Published: April 2016

As the world's oceans continue to absorb anthropogenic CO2 from the atmosphere, the carbonate chemistry of seawater will change. This process, termed ocean acidification, may affect the physiology of marine organisms. Arctic seas are expected to experience the greatest decreases in pH in the future, as changing sea ice dynamics and naturally cold, brackish water, will accelerate ocean acidification. In this study, we investigated the effect of increased pCO2 on the early developmental stages of the key Arctic copepod Calanus glacialis. Eggs from wild-caught C. glacialis females from Svalbard, Norway (80°N), were cultured for 2 months to copepodite stage C1 in 2°C seawater under four pCO2 treatments (320, 530, 800, and 1700 μatm). Developmental rate, dry weight, and carbon and nitrogen mass were measured every other day throughout the experiment, and oxygen consumption rate was measured at stages N3, N6, and C1. All endpoints were unaffected by pCO2 levels projected for the year 2300. These results indicate that naupliar development in wild populations of C. glacialis is unlikely to be detrimentally affected in a future high CO2 ocean.
The effect of baryons on redshift space distortions and cosmic density and velocity fields in the EAGLE simulation
Authors: Hellwing Wojciech A. , Schaller Matthieu , Frenk Carlos S. , Theuns Tom , Schaye Joop , Bower Richard G. , Crain Robert A.
Published: April 2016

We use the Evolution and Assembly of GaLaxies and their Environments (EAGLE) galaxy formation simulation to study the effects of baryons on the power spectrum of the total matter and dark matter distributions and on the velocity fields of dark matter and galaxies. On scales k ≳ 4 h Mpc−1 the effect of baryons on the amplitude of the total matter power spectrum is greater than 1 per cent. The back-reaction of baryons affects the density field of the dark matter at the level of ∼3 per cent on scales of 1 ≤ k/( h Mpc−1) ≤ 5. The dark matter velocity divergence power spectrum at k ≲ 0.5 h Mpc−1 is changed by less than 1 per cent. The 2D redshift space power spectrum is affected at the level of ∼6 per cent at $|\boldsymbol {k}|\gtrsim 1\,h\,{\rm Mpc}^{-1}$ (for μ > 0.5), but for $|\boldsymbol {k}|\le 0.4\,h\,{\rm Mpc}^{-1}$ it differs by less than 1 per cent. We report vanishingly small baryonic velocity bias for haloes: the peculiar velocities of haloes with M200 > 3 × 1011 M⊙ (hosting galaxies with M* > 109 M⊙) are affected at the level of at most 1 km s−1, which is negligible for 1 per cent-precision cosmology. We caution that since EAGLE overestimates cluster gas fractions it may also underestimate the impact of baryons, particularly for the total matter power spectrum. Nevertheless, our findings suggest that for theoretical modelling of redshift space distortions and galaxy velocity-based statistics, baryons and their back-reaction can be safely ignored at the current level of observational accuracy. However, we confirm that the modelling of the total matter power spectrum in weak lensing studies needs to include realistic galaxy formation physics in order to achieve the accuracy required in the precision cosmology era.
Ipsilateral obturator type of hip dislocation with fracture shaft femur in a child: a case report and literature review
Authors: Arjun R.H.H. , Kumar Vishal , Saibaba Balaji , John Rakesh , Guled Uday , Aggarwal Sameer
Published: April 2016

The incidence of traumatic hip dislocations in children is rising in this fast developing world along with increasing numbers of high-velocity road traffic accidents. Anterior dislocation of the hip has a lower incidence compared with posterior dislocation of the hip. We encountered a rare case of the obturator type of anteriorly dislocated hip associated with ipsilateral fracture of the shaft femur in an 11-year-old child. This is a highly unusual injury combination and the mechanism of injury is obscure. Only two similar cases have been reported in the English literature to date. Closed reduction of the hip using a hitherto undescribed technique and an intramedullary interlocking nail was performed in this case. At 6 months of follow-up, the fracture shaft femur has united and the child is bearing full weight on the limb.
Side-effects of checkpoint inhibitor-based combination therapy
Authors: Kourie Hampig R. , Klastersky Jean A.
Published: April 2016

Purpose of review

After the dramatic and often long-standing response rates of checkpoint inhibitors as single agents, the new era for checkpoint inhibitors is combined therapy (either with other checkpoint inhibitors, chemotherapies, targeted therapies or immunotherapies) that is aiming to do even better. Although one can speculate that these combinations will result in improved results, high cost and potential toxicity are limiting factors for their use. In this review, we plan to report on the different side-effects of the checkpoint inhibitor-based combination therapies and to discuss the future perspectives of these new modalities.

Recent findings

Many checkpoint inhibitor-based combinations are associated with high response rates (>50%) in melanomas and nonsmall cell lung cancers (NSCLCs). As a result, the combination of nivolumab and ipilimumab for metastatic melanoma was recently approved by the Food and Drug Administration; however, 30% of the patients had to discontinue this combination because of high toxicity. In NSCLC, the combination of chemotherapy and anti-programmed cell death protein 1 or anti-programmed cell death protein ligand 1 agents is leading to high response rate (exceeding 65%) but with more than 40% of the patients presenting grade 3/4 toxicities. Despite the discouraging results with the combination of ipilimumab (anti-cytotoxic T-lymphocyte-associated protein 4) with vemurafenib (anti-proto-oncogene protein B-raf-targeted therapy) due to hepatotoxicity, more recent trials are showing less frequent and severe toxicities with other combinations of checkpoint inhibitors and targeted therapies.

Despite the high toxicity rates observed with some checkpoint inhibitor-based combination therapies, these combinations will likely become the new paradigm for the management of various malignancies, namely, melanomas, renal cell carcinomas and NSCLC, provided that their side-effects can be effectively managed.