bluuebunny/crossref_metadata_2025 huggingface dataset:
Anthropogenic noise increases fish mortality by predation
Authors: Simpson Stephen D. , Radford Andrew N. , Nedelec Sophie L. , Ferrari Maud C. O. , Chivers Douglas P. , McCormick Mark I. , Meekan Mark G.
Published: February 2016

Noise-generating human activities affect hearing, communication and movement in terrestrial and aquatic animals, but direct evidence for impacts on survival is rare. We examined effects of motorboat noise on post-settlement survival and physiology of a prey fish species and its performance when exposed to predators. Both playback of motorboat noise and direct disturbance by motorboats elevated metabolic rate in Ambon damselfish (Pomacentrus amboinensis), which when stressed by motorboat noise responded less often and less rapidly to simulated predatory strikes. Prey were captured more readily by their natural predator (dusky dottyback, Pseudochromis fuscus) during exposure to motorboat noise compared with ambient conditions, and more than twice as many prey were consumed by the predator in field experiments when motorboats were passing. Our study suggests that a common source of noise in the marine environment has the potential to impact fish demography, highlighting the need to include anthropogenic noise in management plans.
Macrospin dynamics in antiferromagnets triggered by sub-20 femtosecond injection of nanomagnons
Authors: Bossini D. , Dal Conte S. , Hashimoto Y. , Secchi A. , Pisarev R. V. , Rasing Th. , Cerullo G. , Kimel A. V.
Published: February 2016

The understanding of how the sub-nanoscale exchange interaction evolves in macroscale correlations and ordered phases of matter, such as magnetism and superconductivity, requires to bridging the quantum and classical worlds. This monumental challenge has so far only been achieved for systems close to their thermodynamical equilibrium. Here we follow in real time the ultrafast dynamics of the macroscale magnetic order parameter in the Heisenberg antiferromagnet KNiF3 triggered by the impulsive optical generation of spin excitations with the shortest possible nanometre wavelength and femtosecond period. Our magneto-optical pump–probe experiments also demonstrate the coherent manipulation of the phase and amplitude of these femtosecond nanomagnons, whose frequencies are defined by the exchange energy. These findings open up opportunities for fundamental research on the role of short-wavelength spin excitations in magnetism and strongly correlated materials; they also suggest that nanospintronics and nanomagnonics can employ coherently controllable spin waves with frequencies in the 20 THz domain.
Correction: Corrigendum: Glycan complexity dictates microbial resource allocation in the large intestine
Authors: Rogowski Artur , Briggs Jonathon A. , Mortimer Jennifer C. , Tryfona Theodora , Terrapon Nicolas , Lowe Elisabeth C. , Baslé Arnaud , Morland Carl , Day Alison M. , Zheng Hongjun , Rogers Theresa E. , Thompson Paul , Hawkins Alastair R. , Yadav Madhav P. , Henrissat Bernard , Martens Eric C. , Dupree Paul , Gilbert Harry J. , Bolam David N.
Published: February 2016

Nature Communications 6 Article number: 7481 (2015); Published 26 June 2015; Updated 5 February 2016 The financial support for the work described in this Article was not fully acknowledged. The Acknowledgements should have included the following: This work was supported in part by a grant to H.J.G.,B.
Novel quantum description for nonadiabatic evolution of light wave propagation in time-dependent linear media
Authors: Lakehal Halim , Maamache Mustapha , Choi Jeong Ryeol
Published: February 2016

A simple elegant expression of nonadiabatic light wave evolution is necessary in order to have a deeper insight for complicated optical phenomena in light science as well as in everyday life. Light wave propagation in linear media which have time-dependent electromagnetic parameters is investigated by utilizing a quadratic invariant of the system. The time behavior of the nonadiabatic geometric phase of the waves that yield a cyclic nonadiabatic evolution is analyzed in detail. Various quantum properties of light waves in this situation, such as variances of electric and magnetic fields, uncertainty product, coherent and squeezed states and their classical limits, are developed. For better understanding of our research, we applied our analysis in a particular case. The variances of the fields D and B are illustrated and their time behaviors are addressed. Equivalent results for the corresponding classical systems are deduced from the study of the time evolution of the appropriate coherent and squeezed states.
Lysing bloom-causing alga Phaeocystis globosa with microbial algicide: An efficient process that decreases the toxicity of algal exudates
Authors: Cai Guanjing , Yang Xujun , Lai Qiliang , Yu Xiaoqi , Zhang Huajun , Li Yi , Chen Zhangran , Lei Xueqian , Zheng Wei , Xu Hong , Zheng Tianling
Published: February 2016

Algicidal microbes could effectively remove the harmful algae from the waters. In this study, we were concerned with the ecological influence of an algicide extracted from Streptomyces alboflavus RPS, which could completely lyse the Phaeocystis globosa cells within two days. In microcosms, 4 μg/mL of the microbial algicide could efficiently remove P. globosa cells without suppressing other aquatic organisms. Bioluminescent assays confirmed that the toxicity of microbial algicide at this concentration was negligible. Interestingly, the toxicity of P. globosa exudates was also significantly reduced after being treated with the algicide. Further experiments revealed that the microbial algicide could instantly increase the permeability of the plasma membrane and disturb the photosynthetic system, followed by the deformation of organelles, vacuolization and increasing oxidative stress. The pre-incubation of N-acetyl cysteine (NAC) verified that the rapid damages to the plasma membrane and photosynthetic system caused the algal death in the early phase and the increasing oxidative stress killed the rest. The late accumulation and possible release of CAT also explained the decreasing toxicity of the algal culture. These results indicated that this microbial algicide has great potential in controlling the growth of P. globosa on site.
Self-organization of frozen light in near-zero-index media with cubic nonlinearity
Authors: Marini A. , García de Abajo F. J.
Published: February 2016

Optical beams are generally unbound in bulk media and propagate with a velocity approximately amounting to the speed of light in free-space. Guidance and full spatial confinement of light are usually achieved by means of waveguides, mirrors, resonators and photonic crystals. Here we theoretically demonstrate that nonlinear self-organization can be exploited to freeze optical beams in bulk near-zero-index media, thus enabling three-dimensional self-trapping of still light without the need of optical resonators. Light is stopped to a standstill owing to the divergent wavelength and the vanishing group velocity, effectively rendering, through nonlinearity, a positive-epsilon trapping cavity carved in an otherwise slightly-negative-epsilon medium. By numerically solving Maxwell’s equations, we find a soliton-like family of still azimuthal doughnuts, which we further study through an adiabatic perturbative theory that describes soliton evaporation in lossy media or condensation in actively pumped materials. Our results suggest applications in optical data processing and storage, quantum optical memories and soliton-based lasers without cavities. Additionally, near-zero-index conditions can also be found in the interplanetary medium and in the atmosphere, where we provide a complementary explanation to the rare phenomenon of ball-lightning.
Nutrient allocation strategies of woody plants: an approach from the scaling of nitrogen and phosphorus between twig stems and leaves
Authors: Yan Zhengbing , Li Peng , Chen Yahan , Han Wenxuan , Fang Jingyun
Published: February 2016

Allocation of limited nutrients, such as nitrogen (N) and phosphorus (P), among plant organs reflects the influences of evolutionary and ecological processes on functional traits of plants and thus is related to functional groups and environmental conditions. In this study, we tested this hypothesis by exploring the stoichiometric scaling of N and P concentrations between twig stems and leaves of 335 woody species from 12 forest sites across eastern China. Scaling exponents of twig stem N (or P) to leaf N (or P) varied among functional groups. With increasing latitude, these scaling exponents significantly decreased from >1 at low latitude to <1 at high latitude across the study area. These results suggested that, as plant nutrient concentration increased, plants at low latitudes showed a faster increase in twig stem nutrient concentration, whereas plants at high latitudes presented a faster increase in leaf nutrient concentration. Such shifts in nutrient allocation strategy from low to high latitudes may be controlled by temperature. Overall, our findings provide a new approach to explore plant nutrient allocation strategies by analysing the stoichiometric scaling of nutrients among organs, which could broaden our understanding of the interactions between plants and their environments.
SOX2 suppresses CDKN1A to sustain growth of lung squamous cell carcinoma
Authors: Fukazawa Takuya , Guo Minzhe , Ishida Naomasa , Yamatsuji Tomoki , Takaoka Munenori , Yokota Etsuko , Haisa Minoru , Miyake Noriko , Ikeda Tomoko , Okui Tatsuo , Takigawa Nagio , Maeda Yutaka , Naomoto Yoshio
Published: February 2016

Since the SOX2 amplification was identified in lung squamous cell carcinoma (lung SCC), SOX2 transcriptional downstream targets have been actively investigated; however, such targets are often cell line specific. Here, in order to identify highly consensus SOX2 downstream genes in lung SCC cells, we used RNA-seq data from 178 lung SCC specimens (containing tumor and tumor-associated cells) and analyzed the correlation between SOX2 and previously-reported SOX2-controlled genes in lung SCC. In addition, we used another RNA-seq dataset from 105 non-small cell lung cancer cell lines (NSCLC; including 4 lung SCC cell lines) and again analyzed the correlation between SOX2 and the reported SOX2-controlled genes in the NSCLC cell lines (no tumor-associated cells). We combined the two analyses and identified genes commonly correlated with SOX2 in both datasets. Among the 99 genes reported as SOX2 downstream and/or correlated genes, we found 4 negatively-correlated (e.g., CDKN1A) and 11 positively-correlated genes with SOX2. We used biological studies to demonstrate that CDKN1A was suppressed by SOX2 in lung SCC cells. G1 cell cycle arrest induced by SOX2 siRNA was rescued by CDKN1A siRNA. These results indicate that the tumorigenic effect of SOX2 in lung SCC cells is mediated in part by suppression of CDKN1A.
Structures and Electronic Properties of Different CH3NH3PbI3/TiO2 Interface: A First-Principles Study
Authors: Geng Wei , Tong Chuan-Jia , Liu Jiang , Zhu Wenjun , Lau Woon-Ming , Liu Li-Min
Published: February 2016

Methylammonium lead iodide perovskite, CH3NH3PbI3, has attracted particular attention due to its fast increase in efficiency in dye sensitization TiO2 solid-state solar cells. We performed first-principles calculations to investigate several different types of CH3NH3PbI3/TiO2 interfaces. The interfacial structures between the different terminated CH3NH3PbI3 and phase TiO2 are thoroughly explored and the calculated results suggest that the interfacial Pb atoms play important roles in the structure stability and electronic properties. A charge transfer from Pb atoms to the O atoms of TiO2 lead to the band edge alignment of Pb-p above Ti-d about 0.4 eV, suggesting a better carries separation. On the other hand, for TiO2, rutile (001) is the better candidate due to the better lattice and atoms arrangement match with CH3NH3PbI3.
Visualising inter-subject variability in fMRI using threshold-weighted overlap maps
Authors: Seghier Mohamed L. , Price Cathy J.
Published: February 2016

Functional neuroimaging studies are revealing the neural systems sustaining many sensory, motor and cognitive abilities. A proper understanding of these systems requires an appreciation of the degree to which they vary across subjects. Some sources of inter-subject variability might be easy to measure (demographics, behavioural scores, or experimental factors), while others are more difficult (cognitive strategies, learning effects and other hidden sources). Here, we introduce a simple way of visualising whole-brain consistency and variability in brain responses across subjects using threshold-weighted voxel-based overlap maps. The output quantifies the proportion of subjects activating a particular voxel or region over a wide range of statistical thresholds. The sensitivity of our approach was assessed in 30 healthy adults performing a matching task with their dominant hand. We show how overlap maps revealed many effects that were only present in a subsample of our group; we discuss how overlap maps can provide information that may be missed or misrepresented by standard group analysis and how this information can help users to understand their data. In particular, we emphasize that functional overlap maps can be particularly useful when it comes to explaining typical (or atypical) compensatory mechanisms used by patients following brain damage.
Identification of (2S,3S)-β-Methyltryptophan as the Real Biosynthetic Intermediate of Antitumor Agent Streptonigrin
Authors: Kong Dekun , Zou Yi , Zhang Zhang , Xu Fei , Brock Nelson L. , Zhang Liping , Deng Zixin , Lin Shuangjun
Published: February 2016

Streptonigrin is a potent antitumor antibiotic, active against a wide range of mammalian tumor cells. It was reported that its biosynthesis relies on (2S,3R)-β-methyltryptophan as an intermediate. In this study, the biosynthesis of (2S,3R)-β-methyltryptophan and its isomer (2S,3S)-β-methyltryptophan by enzymes from the streptonigrin biosynthetic pathway is demonstrated. StnR is a pyridoxal 5′-phosphate (PLP)-dependent aminotransferase that catalyzes a transamination between L-tryptophan and β-methyl indolepyruvate. StnQ1 is an S-adenosylmethionine (SAM)-dependent C-methyltransferase and catalyzes β-methylation of indolepyruvate to generate (R)-β-methyl indolepyruvate. Although StnR exhibited a significant preference for (S)-β-methyl indolepyruvate over the (R)-epimer, StnQ1 and StnR together catalyze (2S,3R)-β-methyltryptophan formation from L-tryptophan. StnK3 is a cupin superfamily protein responsible for conversion of (R)-β-methyl indolepyruvate to its (S)-epimer and enables (2S,3S)-β-methyltryptophan biosynthesis from L-tryptophan when combined with StnQ1 and StnR. Most importantly, (2S,3S)-β-methyltryptophan was established as the biosynthetic intermediate of the streptonigrin pathway by feeding experiments with a knockout mutant, contradicting the previous proposal that stated (2S,3R)-β-methyltryptophan as the intermediate. These data set the stage for the complete elucidation of the streptonigrin biosynthetic pathway, which would unlock the potential of creating new streptonigrin analogues by genetic manipulation of the biosynthetic machinery.
Non-adiabatic holonomic quantum computation in linear system-bath coupling
Authors: Sun Chunfang , Wang Gangcheng , Wu Chunfeng , Liu Haodi , Feng Xun-Li , Chen Jing-Ling , Xue Kang
Published: February 2016

Non-adiabatic holonomic quantum computation in decoherence-free subspaces protects quantum information from control imprecisions and decoherence. For the non-collective decoherence that each qubit has its own bath, we show the implementations of two non-commutable holonomic single-qubit gates and one holonomic nontrivial two-qubit gate that compose a universal set of non-adiabatic holonomic quantum gates in decoherence-free-subspaces of the decoupling group, with an encoding rate of "Equation missing". The proposed scheme is robust against control imprecisions and the non-collective decoherence and its non-adiabatic property ensures less operation time. We demonstrate that our proposed scheme can be realized by utilizing only two-qubit interactions rather than many-qubit interactions. Our results reduce the complexity of practical implementation of holonomic quantum computation in experiments. We also discuss the physical implementation of our scheme in coupled microcavities.
Tunable ultrasensitivity: functional decoupling and biological insights
Authors: Wang Guanyu , Zhang Mengshi
Published: February 2016

Sensitivity has become a basic concept in biology, but much less is known about its tuning, probably because allosteric cooperativity, the best known mechanism of sensitivity, is determined by rigid conformations of interacting molecules and is thus difficult to tune. Reversible covalent modification (RCM), owing to its systems-level ingenuity, can generate concentration based, tunable sensitivity. Using a mathematical model of regulated RCM, we find sensitivity tuning can be decomposed into two orthogonal modes, which provide great insights into vital biological processes such as tissue development and cell cycle progression. We find that decoupling of the two modes of sensitivity tuning is critical to fidelity of cell fate decision; the decoupling is thus important in development. The decomposition also allows us to solve the ‘wasteful degradation conundrum’ in budding yeast cell cycle checkpoint, which further leads to discovery of a subtle but essential difference between positive feedback and double negative feedback. The latter guarantees revocability of stress-induced cell cycle arrest; while the former does not. By studying concentration conditions in the system, we extend applicability of ultrasensitivity and explain the ubiquity of reversible covalent modification.
Skyrmion motion driven by oscillating magnetic field
Authors: Moon Kyoung-Woong , Kim Duck-Ho , Je Soong-Geun , Chun Byong Sun , Kim Wondong , Qiu Z.Q. , Choe Sug-Bong , Hwang Chanyong
Published: February 2016

The one-dimensional magnetic skyrmion motion induced by an electric current has attracted much interest because of its application potential in next-generation magnetic memory devices. Recently, the unidirectional motion of large (20 μm in diameter) magnetic bubbles with two-dimensional skyrmion topology, driven by an oscillating magnetic field, has also been demonstrated. For application in high-density memory devices, it is preferable to reduce the size of skyrmion. Here we show by numerical simulation that a skyrmion of a few tens of nanometres can also be driven by high-frequency field oscillations, but with a different direction of motion from the in-plane component of the tilted oscillating field. We found that a high-frequency field for small skyrmions can excite skyrmion resonant modes and that a combination of different modes results in a final skyrmion motion with a helical trajectory. Because this helical motion depends on the frequency of the field, we can control both the speed and the direction of the skyrmion motion, which is a distinguishable characteristic compared with other methods.
Electric stimulation of the ears ameliorated learning and memory impairment in rats with cerebral ischemia-reperfusion injury
Authors: Kuo Ching-Tung , Lin Yi-Wen , Tang Nou-Ying , Cheng Chin-Yi , Hsieh Ching-Liang
Published: February 2016

Ear acupuncture enhances the secretion of acetylcholine, which has anti-inflammatory effects. Here we want to investigate the effect of electric stimulation (ES) of the ears on learning and memory impairment in rats with cerebral ischemia-reperfusion injury. At 24 h after reperfusion, 2-Hz ES was applied to the ears for 20 min/day (10 min for each ear) for 7 days continuously. The step-through time of the passive avoidance test was greater in the ES group than in the control group (300.0 ± 0.0 s vs 45.0 ± 26.7 s,p < 0.05). Our results showed that neither neurological deficit score nor motor functions were improved after 2-Hz ES (4.0 ± 0 vs 4.5 ± 0.8,p > 0.05). The numbers of nicotinic acetylcholine receptor α4 positively stained cells in the CA2 and dentate gyrus of the hippocampus were 19.0 ± 11.5 and 269.2 ± 79.3, respectively, in the ES group, which were greater than those in the control group (7.0 ± 5.9 and 165.5 ± 30.8, respectively) (bothp < 0.05). These results suggested that 2-Hz ES of the ears ameliorated learning and memory impairment in rats with ischemia-reperfusion injury. ES of the ears has neuroprotective effects, which are related to acetylcholine release.
Maternal transcription of non-protein coding RNAs from the PWS-critical region rescues growth retardation in mice
Authors: Rozhdestvensky Timofey S. , Robeck Thomas , Galiveti Chenna R. , Raabe Carsten A. , Seeger Birte , Wolters Anna , Gubar Leonid V. , Brosius Jürgen , Skryabin Boris V.
Published: February 2016

Prader-Willi syndrome (PWS) is a neurogenetic disorder caused by loss of paternally expressed genes on chromosome 15q11-q13. The PWS-critical region (PWScr) contains an array of non-protein coding IPW-A exons hosting intronic SNORD116 snoRNA genes. Deletion of PWScr is associated with PWS in humans and growth retardation in mice exhibiting ~15% postnatal lethality in C57BL/6 background. Here we analysed a knock-in mouse containing a 5′HPRT-LoxP-NeoR cassette (5′LoxP) inserted upstream of the PWScr. When the insertion was inherited maternally in a paternal PWScr-deletion mouse model (PWScrp−/m5′LoxP), we observed compensation of growth retardation and postnatal lethality. Genomic methylation pattern and expression of protein-coding genes remained unaltered at the PWS-locus of PWScrp−/m5′LoxP mice. Interestingly, ubiquitous Snord116 and IPW-A exon transcription from the originally silent maternal chromosome was detected. In situ hybridization indicated that PWScrp−/m5′LoxP mice expressed Snord116 in brain areas similar to wild type animals. Our results suggest that the lack of PWScr RNA expression in certain brain areas could be a primary cause of the growth retardation phenotype in mice. We propose that activation of disease-associated genes on imprinted regions could lead to general therapeutic strategies in associated diseases.
Exploration of multiple Sortase A protein conformations in virtual screening
Authors: Gao Chunxia , Uzelac Ivana , Gottfries Johan , Eriksson Leif A.
Published: February 2016

Methicillin resistant Staphylococcus aureus (MRSA) has become a major health concern which has brought about an urgent need for new therapeutic agents. As the S. aureus Sortase A (SrtA) enzyme contributes to the adherence of the bacteria to the host cells, inhibition thereof by small molecules could be employed as potential antivirulence agents, also towards resistant strains. Albeit several virtual docking SrtA campaigns have been reported, no strongly inhibitatory non-covalent binders have as yet emerged therefrom. In order to better understand the binding modes of small molecules and the effect of different receptor structures employed in the screening, we herein report on an exploratory study employing 10 known binders and 500 decoys on 100 SrtA structures generated from regular or steered molecular dynamics simulations on four different SrtA crystal/NMR structures. The results suggest a correlation between the protein structural flexibility and the virtual screening performance and confirm the noted immobilization of the β6/β7 loop upon substrate binding. The NMR structures reported appear to perform slightly better than the Xray-crystal structures, but the binding modes fluctuate tremendously and it might be suspected that the catalytic site is not necessarily the preferred site of binding for some of the reported active compounds.
Tetherin/BST-2 promotes dendritic cell activation and function during acute retrovirus infection
Authors: Li Sam X. , Barrett Bradley S. , Guo Kejun , Kassiotis George , Hasenkrug Kim J. , Dittmer Ulf , Gibbert Kathrin , Santiago Mario L.
Published: February 2016

Tetherin/BST-2 is a host restriction factor that inhibits retrovirus release from infected cells in vitro by tethering nascent virions to the plasma membrane. However, contradictory data exists on whether Tetherin inhibits acute retrovirus infection in vivo. Previously, we reported that Tetherin-mediated inhibition of Friend retrovirus (FV) replication at 2 weeks post-infection correlated with stronger natural killer, CD4+ T and CD8+ T cell responses. Here, we further investigated the role of Tetherin in counteracting retrovirus replication in vivo. FV infection levels were similar between wild-type (WT) and Tetherin KO mice at 3 to 7 days post-infection despite removal of a potent restriction factor, Apobec3/Rfv3. However, during this phase of acute infection, Tetherin enhanced myeloid dendritic cell (DC) function. DCs from infected, but not uninfected, WT mice expressed significantly higher MHC class II and the co-stimulatory molecule CD80 compared to Tetherin KO DCs. Tetherin-associated DC activation during acute FV infection correlated with stronger NK cell responses. Furthermore, Tetherin+ DCs from FV-infected mice more strongly stimulated FV-specific CD4+ T cells ex vivo compared to Tetherin KO DCs. The results link the antiretroviral and immunomodulatory activity of Tetherin in vivo to improved DC activation and MHC class II antigen presentation.
Vector cavity solitons in broad area Vertical-Cavity Surface-Emitting Lasers
Authors: Averlant Etienne , Tlidi Mustapha , Thienpont Hugo , Ackemann Thorsten , Panajotov Krassimir
Published: February 2016

We report the experimental observation of two-dimensional vector cavity solitons in a Vertical-Cavity Surface-Emitting Laser (VCSEL) under linearly polarized optical injection when varying optical injection linear polarization direction. The polarization of the cavity soliton is not the one of the optical injection as it acquires a distinct ellipticity. These experimental results are qualitatively reproduced by the spin-flip VCSEL model. Our findings open the road to polarization multiplexing when using cavity solitons in broad-area lasers as pixels in information technology.
KCTD12 Regulates Colorectal Cancer Cell Stemness through the ERK Pathway
Authors: Li Liping , Duan Tingmei , Wang Xin , Zhang Ru-Hua , Zhang Meifang , Wang Suihai , Wang Fen , Wu Yuanzhong , Huang Haojie , Kang Tiebang
Published: February 2016

Targeting cancer stem cells (CSCs) in colorectal cancer (CRC) remains a difficult problem, as the regulation of CSCs in CRC is poorly understood. Here we demonstrated that KCTD12, potassium channel tetramerization domain containing 12, is down-regulated in the CSC-like cells of CRC. The silencing of endogenous KCTD12 and the overexpression of ectopic KCTD12 dramatically enhances and represses CRC cell stemness, respectively, as assessed in vitro and in vivo using a colony formation assay, a spheroid formation assay and a xenograft tumor model. Mechanistically, KCTD12 suppresses CRC cell stemness markers, such as CD44, CD133 and CD29, by inhibiting the ERK pathway, as the ERK1/2 inhibitor U0126 abolishes the increase in expression of CRC cell stemness markers induced by the down-regulation of KCTD12. Indeed, a decreased level of KCTD12 is detected in CRC tissues compared with their adjacent normal tissues and is an independent prognostic factor for poor overall and disease free survival in patients with CRC (p = 0.007). Taken together, this report reveals that KCTD12 is a novel regulator of CRC cell stemness and may serve as a novel prognostic marker and therapeutic target for patients with CRC.
From synchrotron radiation to lab source: advanced speckle-based X-ray imaging using abrasive paper
Authors: Wang Hongchang , Kashyap Yogesh , Sawhney Kawal
Published: February 2016

X-ray phase and dark-field imaging techniques provide complementary and inaccessible information compared to conventional X-ray absorption or visible light imaging. However, such methods typically require sophisticated experimental apparatus or X-ray beams with specific properties. Recently, an X-ray speckle-based technique has shown great potential for X-ray phase and dark-field imaging using a simple experimental arrangement. However, it still suffers from either poor resolution or the time consuming process of collecting a large number of images. To overcome these limitations, in this report we demonstrate that absorption, dark-field, phase contrast and two orthogonal differential phase contrast images can simultaneously be generated by scanning a piece of abrasive paper in only one direction. We propose a novel theoretical approach to quantitatively extract the above five images by utilising the remarkable properties of speckles. Importantly, the technique has been extended from a synchrotron light source to utilise a lab-based microfocus X-ray source and flat panel detector. Removing the need to raster the optics in two directions significantly reduces the acquisition time and absorbed dose, which can be of vital importance for many biological samples. This new imaging method could potentially provide a breakthrough for numerous practical imaging applications in biomedical research and materials science.
Localized Single Frequency Lasing States in a Finite Parity-Time Symmetric Resonator Chain
Authors: Phang Sendy , Vukovic Ana , Creagh Stephen C. , Sewell Phillip D. , Gradoni Gabriele , Benson Trevor M.
Published: February 2016

In this paper a practical case of a finite periodic Parity Time chain made of resonant dielectric cylinders is considered. The paper analyzes a more general case where PT symmetry is achieved by modulating both the real and imaginary part of the material refractive index along the resonator chain. The band-structure of the finite periodic PT resonator chains is compared to infinite chains in order to understand the complex interdependence of the Bloch phase and the amount of the gain/loss in the system that causes the PT symmetry to break. The results show that the type of the modulation along the unit cell can significantly affect the position of the threshold point of the PT system. In all cases the lowest threshold is achieved near the end of the Brillouin zone. In the case of finite PT-chains and for a particular type of modulation, early PT symmetry breaking is observed and shown to be caused by the presence of termination states localized at the edges of the finite chain resulting in localized lasing and dissipative modes at each end of the chain.
Chloroplast Phylogenomic Inference of Green Algae Relationships
Authors: Sun Linhua , Fang Ling , Zhang Zhenhua , Chang Xin , Penny David , Zhong Bojian
Published: February 2016

The green algal phylum Chlorophyta has six diverse classes, but the phylogenetic relationship of the classes within Chlorophyta remains uncertain. In order to better understand the ancient Chlorophyta evolution, we have applied a site pattern sorting method to study compositional heterogeneity and the model fit in the green algal chloroplast genomic data. We show that the fastest-evolving sites are significantly correlated with among-site compositional heterogeneity and these sites have a much poorer fit to the evolutionary model. Our phylogenomic analyses suggest that the class Chlorophyceae is a monophyletic group and the classes Ulvophyceae, Trebouxiophyceae and Prasinophyceae are non-monophyletic groups. Our proposed phylogenetic tree of Chlorophyta will offer new insights to investigate ancient green algae evolution and our analytical framework will provide a useful approach for evaluating and mitigating the potential errors of phylogenomic inferences.
Load-dependent modulation of non-muscle myosin-2A function by tropomyosin 4.2
Authors: Hundt Nikolas , Steffen Walter , Pathan-Chhatbar Salma , Taft Manuel H. , Manstein Dietmar J.
Published: February 2016

Tropomyosin isoforms play an important role in the organisation of cytoplasmic actomyosin complexes in regard to function and cellular localisation. In particular, Tpm4.2 is upregulated in rapidly migrating cells and responsible for the specific recruitment of the cytoplasmic class-2 myosin NM-2A to actin filaments during the formation of stress fibres. Here, we investigate how the decoration of F-actin with Tpm4.2 affects the motor properties of NM-2A under conditions of low and high load. In the absence of external forces, decoration of actin filaments with Tpm4.2 does not affect the gated release of ADP from NM-2A and the transition from strong to weak actin-binding states. In the presence of resisting loads, our results reveal a marked increase in the mechanosensitive gating between the leading and trailing myosin head. Thereby, the processive behaviour of NM-2A is enhanced in the presence of resisting loads. The load- and Tpm4.2-induced changes in the functional behaviour of NM-2A are in good agreement with the role of this myosin in the context of stress fibres and the maintenance of cellular tension.
How does the foraging behavior of large herbivores cause different associational plant defenses?
Authors: Huang Yue , Wang Ling , Wang Deli , Zeng De-Hui , Liu Chen
Published: February 2016

The attractant-decoy hypothesis predicts that focal plants can defend against herbivory by neighboring with preferred plant species when herbivores make decisions at the plant species scale. The repellent-plant hypothesis assumes that focal plants will gain protection by associating with nonpreferred neighbors when herbivores are selective at the patch scale. However, herbivores usually make foraging decisions at these scales simultaneously. The net outcomes of the focal plant vulnerability could depend on the spatial scale at which the magnitude of selectivity by the herbivores is stronger. We quantified and compared the within- and between-patch overall selectivity index (OSI) of sheep to examine the relationships between associational plant effects and herbivore foraging selectivity. We found that the sheep OSI was stronger at the within- than the between-patch scale, but focal plant vulnerability followed both hypotheses. Focal plants defended herbivory with preferred neighbors when the OSI difference between the two scales was large. Focal plants gained protection with nonpreferred neighbors when the OSI difference was narrowed. Therefore, the difference in selectivity by the herbivores between the relevant scales results in different associational plant defenses. Our study suggests important implications for understanding plant-herbivore interactions and grassland management.
Nanoparticle Decorated Ultrathin Porous Nanosheets as Hierarchical Co3O4 Nanostructures for Lithium Ion Battery Anode Materials
Authors: Mujtaba Jawayria , Sun Hongyu , Huang Guoyong , Mølhave Kristian , Liu Yanguo , Zhao Yanyan , Wang Xun , Xu Shengming , Zhu Jing
Published: February 2016

We report a facile synthesis of a novel cobalt oxide (Co3O4) hierarchical nanostructure, in which crystalline core-amorphous shell Co3O4 nanoparticles with a bimodal size distribution are uniformly dispersed on ultrathin Co3O4 nanosheets. When tested as anode materials for lithium ion batteries, the as-prepared Co3O4 hierarchical electrodes delivered high lithium storage properties comparing to the other Co3O4 nanostructures, including a high reversible capacity of 1053.1 mAhg−1 after 50 cycles at a current density of 0.2 C (1 C = 890 mAg−1), good cycling stability and rate capability.
Silver nanoparticles disrupt germline stem cell maintenance in the Drosophila testis
Authors: Ong Cynthia , Lee Qian Ying , Cai Yu , Liu Xiaoli , Ding Jun , Yung Lin-Yue Lanry , Bay Boon-Huat , Baeg Gyeong-Hun
Published: February 2016

Silver nanoparticles (AgNPs), one of the most popular nanomaterials, are commonly used in consumer products and biomedical devices, despite their potential toxicity. Recently, AgNP exposure was reported to be associated with male reproductive toxicity in mammalian models. However, there is still a limited understanding of the effects of AgNPs on spermatogenesis. The fruit fly Drosophila testis is an excellent in vivo model to elucidate the mechanisms underlying AgNP-induced defects in spermatogenesis, as germ lineages can be easily identified and imaged. In this study, we evaluated AgNP-mediated toxicity on spermatogenesis by feeding Drosophila with AgNPs at various concentrations. We first observed a dose-dependent uptake of AgNPs in vivo. Concomitantly, AgNP exposure caused a significant decrease in the viability and delay in the development of Drosophila in a dose-dependent manner. Furthermore, AgNP-treated male flies showed a reduction in fecundity and the resulting testes contained a decreased number of germline stem cells (GSCs) compared to controls. Interestingly, testes exposed to AgNPs exhibited a dramatic increase in reactive oxygen species levels and showed precocious GSC differentiation. Taken together, our study suggests that AgNP exposure may increase ROS levels in the Drosophila testis, leading to a reduction of GSC number by promoting premature GSC differentiation.
A pathogenic IFNα, BLyS and IL-17 axis in Systemic Lupus Erythematosus patients
Authors: López Patricia , Rodríguez-Carrio Javier , Caminal-Montero Luis , Mozo Lourdes , Suárez Ana
Published: February 2016

This study aims to analyze in depth the role of IFNα in the upregulation of BLyS in different leukocyte populations and the possible relationship of these molecules with IL-17 and other pathogenic cytokines in SLE. Thus, IFNAR1 and membrane BLyS (mBLyS) expression was upregulated on various blood cell types from patients and closely correlated in all individuals. Moreover, BLyS serum levels associated positively with IFNα and IL-17A amounts, as well as with mBLyS on B cells and neutrophils. Interestingly, mBLyS on neutrophils was also correlated with IL-17A levels. Additionally, intracellular IL-17A expression was increased in both CD4+ lymphocytes and neutrophils from patients and IL-17+CD4+ T cell frequency was associated with serum IFNα and IFNRA1 expression on B cells. Finally, in vitro assays support an IFNα role in the activation of Th17 cells in SLE. In conclusion, these data suggest that IFNα, BLyS and IL-17 could form a pathological axis in SLE, involving T and B lymphocytes, monocytes, DCs and neutrophils, which act in a vicious circle that encourage the preexisting inflammation and propagate the disease process.
Co-expression of Dorsal and Rel2 Negatively Regulates Antimicrobial Peptide Expression in the Tobacco Hornworm Manduca sexta
Authors: Zhong Xue , Rao Xiang-Jun , Yi Hui-Yu , Lin Xin-Yu , Huang Xiao-Hong , Yu Xiao-Qiang
Published: February 2016

Nuclear factor κB (NF-κB) plays an essential role in regulation of innate immunity. In mammals, NF-κB factors can form homodimers and heterodimers to activate gene expression. In insects, three NF-κB factors, Dorsal, Dif and Relish, have been identified to activate antimicrobial peptide (AMP) gene expression. However, it is not clear whether Dorsal (or Dif) and Relish can form heterodimers. Here we report the identification and functional analysis of a Dorsal homologue (MsDorsal) and two Relish short isoforms (MsRel2A and MsRel2B) from the tobacco hornworm, Manduca sexta. Both MsRel2A and MsRel2B contain only a Rel homology domain (RHD) and lack the ankyrin-repeat inhibitory domain. Overexpression of the RHD domains of MsDorsal and MsRel2 in Drosophila melanogaster S2 and Spodoptera frugiperda Sf9 cells can activate AMP gene promoters from M. sexta and D. melanogaster. We for the first time confirmed the interaction between MsDorsal-RHD and MsRel2-RHD, and suggesting that Dorsal and Rel2 may form heterodimers. More importantly, co-expression of MsDorsal-RHD with MsRel2-RHD suppressed activation of several M. sexta AMP gene promoters. Our results suggest that the short MsRel2 isoforms may form heterodimers with MsDorsal as a novel mechanism to prevent over-activation of antimicrobial peptides.
Effects of Obesity Related Genetic Variations on Visceral and Subcutaneous Fat Distribution in a Chinese Population
Authors: Wang Tao , Ma Xiaojing , Peng Danfeng , Zhang Rong , Sun Xue , Chen Miao , Yan Jing , Wang Shiyun , Yan Dandan , He Zhen , Jiang Feng , Bao Yuqian , Hu Cheng , Jia Weiping
Published: February 2016

Genome-wide association studies (GWAS) have uncovered numerous variants associated with body mass index (BMI), waist circumference, and waist-to-hip ratio. Our study aims to investigate how these variants are linked to fat distribution. We genotyped 56 validated variants of BMI, waist circumference, and waist-to-hip ratio in 2958 subjects from Chinese community-based populations and performed linear regression analyses to determine the association with visceral fat area (VFA) and subcutaneous fat area (SFA) imaged by magnetic resonance imaging (MRI). We found rs671 in ALDH2 exhibited the significant associations with VFA and the VFA-SFA ratio in all subjects (P = 9.64 × 10−5 and 6.54 × 10−4). rs17782313 near MC4R for VFA and rs4846567 near LYPLAL1 for SFA were found in females only (P = 2.93 × 10−4 and 0.0015), whereas rs671 in ALDH2 for VFA and the VFA-SFA ratio was restricted to males (P = 1.75 × 10−8 and 4.43 × 10−8). Given the robust association of rs671 with alcohol consumption, we next demonstrated the primary effects of rs671 on VFA and the VFA-SFA ratio were restricted to drinkers (P = 1.45 × 10−4 and 4.65 × 10−3). Our data implied that variants of MC4R and LYPLAL1 modulated body fat distribution with sexual dimorphism and that alcohol consumption may mediate the impact of the ALDH2 locus on visceral fat in a Chinese population.
Establishment of feeder-free culture system for human induced pluripotent stem cell on
DAS nanocrystalline graphene
Authors: Lee Hyunah , Nam Donggyu , Choi Jae-Kyung , Araúzo-Bravo Marcos J. , Kwon Soon-Yong , Zaehres Holm , Lee Taehee , Park Chan Young , Kang Hyun-Wook , Schöler Hans R. , Kim Jeong Beom
Published: February 2016

The maintenance of undifferentiated human pluripotent stem cells (hPSC) under
xeno-free condition requires the use of human feeder cells or extracellular matrix
(ECM) coating. However, human-derived sources may cause human pathogen contamination
by viral or non-viral agents to the patients. Here we demonstrate feeder-free and
xeno-free culture system for hPSC expansion using diffusion assisted synthesis-grown
nanocrystalline graphene (DAS-NG), a synthetic non-biological nanomaterial which
completely rule out the concern of human pathogen contamination. DAS-NG exhibited
advanced biocompatibilities including surface nanoroughness, oxygen containing
functional groups and hydrophilicity. hPSC cultured on DAS-NG could maintain
pluripotency in vitro and in vivo and especially cell
adhesion-related gene expression profile was comparable to those of cultured on
feeders, while hPSC cultured without DAS-NG differentiated spontaneously with high
expression of somatic cell-enriched adhesion genes. This feeder-free and xeno-free
culture method using DAS-NG will facilitate the generation of clinical-grade
hPSC.
Myocardial Regional Interstitial Fibrosis is Associated With Left Intra-Ventricular Dyssynchrony in Patients With Heart Failure: A Cardiovascular Magnetic Resonance Study
Authors: Lin Lian-Yu , Wu Cho-Kai , Juang Jyh-Ming Jimmy , Wang Yi-Chih , Su Mao-Yuan Marine , Lai Ling-Ping , Hwang Juey-Jen , Chiang Fu-Tien , Tseng Wen-Yih Issac , Lin Jiunn-Lee
Published: February 2016

Left ventricular (LV) dyssynchrony is associated with poor prognosis in patients with heart failure (HF). The mechanisms leading to LV dyssynchrony are not fully elucidated. This study evaluates whether myocardium regional variation in interstitial fibrosis is associated with LV dyssynchrony. Forty-two patients with systolic heart failure (SHF), 76 patients with heart failure with preserved ejection fraction (HFpEF) and 20 patients without HF received cardiovascular magnetic resonance imaging (MRI) study. LV was divided into 18 segments by short-axis view. In each segment, regional extracellular volume fraction (ECV) and the time taken to reach minimum regional volume (Tmv) were derived. Intra-LV dyssynchrony were represented by maximum difference (Dysyn_max) and standard deviation (Dysyn_sd) of all Tmv. The results showed that among the covariates, only age (1.87, 95% CI: 0.61–3.13, p = 0.004) and ECV (3.77, 95% CI: 2.72–4.81, p < 0.001) were positively associated with Tmv. The results remained robust in certain subgroups. In conclusion, we demonstrated that LV myocardium regional variation in interstitial fibrosis is closely related to LV intra-ventricular dyssynchrony irrespective of the LV global function. These data might help explain the pathophysiology of LV dyssynchrony and it’s underlying mechanisms leading to poor prognosis.
Inhibition of airway surface fluid absorption by cholinergic stimulation
Authors: Joo Nam Soo , Krouse Mauri E. , Choi Jae Young , Cho Hyung-Ju , Wine Jeffrey J.
Published: February 2016

In upper airways airway surface liquid (ASL) depth and clearance rates are both increased by fluid secretion. Secretion is opposed by fluid absorption, mainly via the epithelial sodium channel, ENaC. In static systems, increased fluid depth activates ENaC and decreased depth inhibits it, suggesting that secretion indirectly activates ENaC to reduce ASL depth. We propose an alternate mechanism in which cholinergic input, which causes copious airway gland secretion, also inhibits ENaC-mediated absorption. The conjoint action accelerates clearance, and the increased transport of mucus out of the airways restores ASL depth while cleansing the airways. We were intrigued by early reports of cholinergic inhibition of absorption by airways in some species. To reinvestigate this phenomenon, we studied inward short-circuit currents (Isc) in tracheal mucosa from human, sheep, pig, ferret, and rabbit and in two types of cultured cells. Basal Isc was inhibited 20–70% by the ENaC inhibitor, benzamil. Long-lasting inhibition of ENaC-dependent Isc was also produced by basolateral carbachol in all preparations except rabbit and the H441 cell line. Atropine inhibition produced a slow recovery or prevented inhibition if added before carbachol. The mechanism for inhibition was not determined and is most likely multi-factorial. However, its physiological significance is expected to be increased mucus clearance rates in cholinergically stimulated airways.
Erratum: SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy
Authors: Ball Graeme , Demmerle Justin , Kaufmann Rainer , Davis Ilan , Dobbie Ian M. , Schermelleh Lothar
Published: February 2016

Scientific Reports 5: Article number: 15915; published online: 03 November 2015; updated: 05 February 2016 In the Supplementary Information file originally published with this Article, the details of the beta testers in Supplementary Table S11 were incorrect. These errors have been corrected in the Supplementary Information that now accompanies the Article.
Computational design of donor-bridge-acceptor systems exhibiting pronounced quantum interference effects
Authors: Gorczak Natalie , Renaud Nicolas , Galan Elena , Eelkema Rienk , Siebbeles Laurens D. A. , Grozema Ferdinand C.
Published: February 2016

Quantum interference is a well-known phenomenon that dictates charge transport properties of single molecule junctions.
An ARXPS and ERXPS study of quaternary ammonium and phosphonium ionic liquids: utilising a high energy Ag Lα′ X-ray source
Authors: Blundell Rebecca K. , Delorme Astrid E. , Smith Emily F. , Licence Peter
Published: February 2016

A series of ammonium- and phosphonium-based ionic liquids have been probed using X-ray photoelectron spectroscopy (XPS) with a high energy Ag Lα′ X-ray source.
A detailed assignment of NEXAFS resonances of imidazolium based ionic liquids
Authors: Ehlert Christopher , Holzweber Markus , Lippitz Andreas , Unger Wolfgang E. S. , Saalfrank Peter
Published: February 2016

Experimental and theoretical investigation of Near Edge Absorption Fine Structure (NEXAFS) resonances of two kinds of imidazolium based ionic Liquids.
Band engineering and improved thermoelectric performance in M-doped SnTe (M = Mg, Mn, Cd, and Hg)
Authors: Tan X. J. , Shao H. Z. , He J. , Liu G. Q. , Xu J. T. , Jiang J. , Jiang H. C.
Published: February 2016

Sn vacancy is found to play an important role in the band engineering and thermoelectric performance of SnTe.