bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactions between hydrology and water chemistry shape bacterioplankton biogeography across boreal freshwater networks
Authors: Niño-García Juan Pablo , Ruiz-González Clara , del Giorgio Paul A 
Published: February 2016

Abstract
Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S ribosomal RNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Québec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (that is, the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum.
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

AbstractNoise-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

AbstractThe 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

AbstractA 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

AbstractAlgicidal 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

AbstractOptical 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

AbstractAllocation 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

AbstractSince 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

AbstractMethylammonium 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

AbstractFunctional 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

AbstractStreptonigrin 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

AbstractNon-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

AbstractSensitivity 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

AbstractThe 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

AbstractEar 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.