bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resource limitation drives spatial organization in microbial groups
Authors: Mitri Sara , Clarke Ellen , Foster Kevin R 
Published: November 2015

Abstract
Dense microbial groups such as bacterial biofilms commonly contain a diversity of cell types that define their functioning. However, we have a limited understanding of what maintains, or purges, this diversity. Theory suggests that resource levels are key to understanding diversity and the spatial arrangement of genotypes in microbial groups, but we need empirical tests. Here we use theory and experiments to study the effects of nutrient level on spatio-genetic structuring and diversity in bacterial colonies. Well-fed colonies maintain larger well-mixed areas, but they also expand more rapidly compared with poorly-fed ones. Given enough space to expand, therefore, well-fed colonies lose diversity and separate in space over a similar timescale to poorly fed ones. In sum, as long as there is some degree of nutrient limitation, we observe the emergence of structured communities. We conclude that resource-driven structuring is central to understanding both pattern and process in diverse microbial communities.
Janus-faced Sestrin2 controls ROS and mTOR signalling through two separate functional domains
Authors: Kim Hanseong , An Sojin , Ro Seung-Hyun , Teixeira Filipa , Jin Park Gyeong , Kim Cheal , Cho Chun-Seok , Kim Jeong-Sig , Jakob Ursula , Hee Lee Jun , Cho Uhn-Soo 
Published: November 2015

AbstractSestrins are stress-inducible metabolic regulators with two seemingly unrelated but physiologically important functions: reduction of reactive oxygen species (ROS) and inhibition of the mechanistic target of rapamycin complex 1 (mTORC1). How Sestrins fulfil this dual role has remained elusive so far. Here we report the crystal structure of human Sestrin2 (hSesn2), and show that hSesn2 is twofold pseudo-symmetric with two globular subdomains, which are structurally similar but functionally distinct from each other. While the N-terminal domain (Sesn-A) reduces alkylhydroperoxide radicals through its helix–turn–helix oxidoreductase motif, the C-terminal domain (Sesn-C) modified this motif to accommodate physical interaction with GATOR2 and subsequent inhibition of mTORC1. These findings clarify the molecular mechanism of how Sestrins can attenuate degenerative processes such as aging and diabetes by acting as a simultaneous inhibitor of ROS accumulation and mTORC1 activation.
Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion
Authors: Nguyen Van T. M. , Barozzi Iros , Faronato Monica , Lombardo Ylenia , Steel Jennifer H. , Patel Naina , Darbre Philippa , Castellano Leandro , Győrffy Balázs , Woodley Laura , Meira Alba , Patten Darren K. , Vircillo Valentina , Periyasamy Manikandan , Ali Simak , Frige Gianmaria , Minucci Saverio , Coombes R. Charles , Magnani Luca 
Published: November 2015

AbstractEndocrine therapies target the activation of the oestrogen receptor alpha (ERα) via distinct mechanisms, but it is not clear whether breast cancer cells can adapt to treatment using drug-specific mechanisms. Here we demonstrate that resistance emerges via drug-specific epigenetic reprogramming. Resistant cells display a spectrum of phenotypical changes with invasive phenotypes evolving in lines resistant to the aromatase inhibitor (AI). Orthogonal genomics analysis of reprogrammed regulatory regions identifies individual drug-induced epigenetic states involving large topologically associating domains (TADs) and the activation of super-enhancers. AI-resistant cells activate endogenous cholesterol biosynthesis (CB) through stable epigenetic activation in vitro and in vivo. Mechanistically, CB sparks the constitutive activation of oestrogen receptors alpha (ERα) in AI-resistant cells, partly via the biosynthesis of 27-hydroxycholesterol. By targeting CB using statins, ERα binding is reduced and cell invasion is prevented. Epigenomic-led stratification can predict resistance to AI in a subset of ERα-positive patients.
Boron nitride colloidal solutions, ultralight aerogels and freestanding membranes through one-step exfoliation and functionalization
Authors: Lei Weiwei , Mochalin Vadym N. , Liu Dan , Qin Si , Gogotsi Yury , Chen Ying 
Published: November 2015

AbstractManufacturing of aerogels and membranes from hexagonal boron nitride (h-BN) is much more difficult than from graphene or graphene oxides because of the poor dispersibility of h-BN in water, which limits its exfoliation and preparation of colloidal solutions. Here, a simple, one-step mechano-chemical process to exfoliate and functionalize h-BN into highly water-dispersible, few-layer h-BN containing amino groups is presented. The colloidal solutions of few-layer h-BN can have unprecedentedly high concentrations, up to 30 mg ml−1, and are stable for up to several months. They can be used to produce ultralight aerogels with a density of 1.4 mg cm−3, which is ∼1,500 times less than bulk h-BN, and freestanding membranes simply by cryodrying and filtration, respectively. The material shows strong blue light emission under ultraviolet excitation, in both dispersed and dry state.
Magnetic moments induce strong phonon renormalization in FeSi
Authors: Krannich S. , Sidis Y. , Lamago D. , Heid R. , Mignot J.-M. , Löhneysen H. v. , Ivanov A. , Steffens P. , Keller T. , Wang L. , Goering E. , Weber F. 
Published: November 2015

AbstractThe interactions of electronic, spin and lattice degrees of freedom in solids result in complex phase diagrams, new emergent phenomena and technical applications. While electron–phonon coupling is well understood, and interactions between spin and electronic excitations are intensely investigated, only little is known about the dynamic interactions between spin and lattice excitations. Noncentrosymmetric FeSi is known to undergo with increasing temperature a crossover from insulating to metallic behaviour with concomitant magnetic fluctuations, and exhibits strongly temperature-dependent phonon energies. Here we show by detailed inelastic neutron-scattering measurements and ab initio calculations that the phonon renormalization in FeSi is linked to its unconventional magnetic properties. Electronic states mediating conventional electron–phonon coupling are only activated in the presence of strong magnetic fluctuations. Furthermore, phonons entailing strongly varying Fe–Fe distances are damped via dynamic coupling to the temperature-induced magnetic moments, highlighting FeSi as a material with direct spin–phonon coupling and multiple interaction paths.
Characterizing entanglement of an artificial atom and a cavity cat state with Bell’s inequality
Authors: Vlastakis Brian , Petrenko Andrei , Ofek Nissim , Sun Luyan , Leghtas Zaki , Sliwa Katrina , Liu Yehan , Hatridge Michael , Blumoff Jacob , Frunzio Luigi , Mirrahimi Mazyar , Jiang Liang , Devoret M. H. , Schoelkopf R. J. 
Published: November 2015

AbstractThe Schrodinger’s cat thought experiment highlights the counterintuitive concept of entanglement in macroscopically distinguishable systems. The hallmark of entanglement is the detection of strong correlations between systems, most starkly demonstrated by the violation of a Bell inequality. No violation of a Bell inequality has been observed for a system entangled with a superposition of coherent states, known as a cat state. Here we use the Clauser–Horne–Shimony–Holt formulation of a Bell test to characterize entanglement between an artificial atom and a cat state, or a Bell-cat. Using superconducting circuits with high-fidelity measurements and real-time feedback, we detect correlations that surpass the classical maximum of the Bell inequality. We investigate the influence of decoherence with states up to 16 photons in size and characterize the system by introducing joint Wigner tomography. Such techniques demonstrate that information stored in superpositions of coherent states can be extracted efficiently, a crucial requirement for quantum computing with resonators.
Satisfying the Einstein–Podolsky–Rosen criterion with massive particles
Authors: Peise J. , Kruse I. , Lange K. , Lücke B. , Pezzè L. , Arlt J. , Ertmer W. , Hammerer K. , Santos L. , Smerzi A. , Klempt C. 
Published: November 2015

AbstractIn 1935, Einstein, Podolsky and Rosen (EPR) questioned the completeness of quantum mechanics by devising a quantum state of two massive particles with maximally correlated space and momentum coordinates. The EPR criterion qualifies such continuous-variable entangled states, where a measurement of one subsystem seemingly allows for a prediction of the second subsystem beyond the Heisenberg uncertainty relation. Up to now, continuous-variable EPR correlations have only been created with photons, while the demonstration of such strongly correlated states with massive particles is still outstanding. Here we report on the creation of an EPR-correlated two-mode squeezed state in an ultracold atomic ensemble. The state shows an EPR entanglement parameter of 0.18(3), which is 2.4 s.d. below the threshold 1/4 of the EPR criterion. We also present a full tomographic reconstruction of the underlying many-particle quantum state. The state presents a resource for tests of quantum nonlocality and a wide variety of applications in the field of continuous-variable quantum information and metrology.
Photogenerated Intrinsic Free Carriers in Small-molecule Organic Semiconductors Visualized by Ultrafast Spectroscopy
Authors: He Xiaochuan , Zhu Gangbei , Yang Jianbing , Chang Hao , Meng Qingyu , Zhao Hongwu , Zhou Xin , Yue Shuai , Wang Zhuan , Shi Jinan , Gu Lin , Yan Donghang , Weng Yuxiang 
Published: November 2015

AbstractConfirmation of direct photogeneration of intrinsic delocalized free carriers in small-molecule organic semiconductors has been a long-sought but unsolved issue, which is of fundamental significance to its application in photo-electric devices. Although the excitonic description of photoexcitation in these materials has been widely accepted, this concept is challenged by recently reported phenomena. Here we report observation of direct delocalized free carrier generation upon interband photoexcitation in highly crystalline zinc phthalocyanine films prepared by the weak epitaxy growth method using ultrafast spectroscopy. Transient absorption spectra spanning the visible to mid-infrared region revealed the existence of short-lived free electrons and holes with a diffusion length estimated to cross at least 11 molecules along the π−π stacking direction that subsequently localize to form charge transfer excitons. The interband transition was evidenced by ultraviolet-visible absorption, photoluminescence and electroluminescence spectroscopy. Our results suggest that delocalized free carriers photogeneration can also be achieved in organic semiconductors when the molecules are packed properly.
Pericolactines A–C, a New Class of Diterpenoid Alkaloids with Unusual Tetracyclic Skeleton
Authors: Wu Yue-Hua , Chen Guo-Dong , He Rong-Rong , Wang Chuan-Xi , Hu Dan , Wang Gao-Qian , Guo Liang-Dong , Yao Xin-Sheng , Gao Hao 
Published: November 2015

AbstractFusicoccane diterpenoids usually possess a fused 5-8-5 tricyclic ring system, which are biogenetically generated from geranylgeranyl diphosphate (GGDP). In our report, three novel diterpenoid alkaloids with fusicoccane skeleton, pericolactines A–C (1–3), were isolated from Periconia sp.. Their structures with absolute configurations were determined by spectroscopic analyses and quantum chemical ECD calculation. Pericolactines A–C (1–3) are a new class of diterpenoid alkaloids with an unusual fused 5-5-8-5 tetracyclic ring system, which derive from a geranylgeranyl diphosphate (GGDP) and serine conjugated biosynthesis. They belong to the atypical diterpenoid alkaloids.
Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures
Authors: Wilkins Laetitia G. E. , Rogivue Aude , Schütz Frédéric , Fumagalli Luca , Wedekind Claus 
Published: November 2015

AbstractThe taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area.
Measuring Phonon Mean Free Path Distributions by Probing Quasiballistic Phonon Transport in Grating Nanostructures
Authors: Zeng Lingping , Collins Kimberlee C. , Hu Yongjie , Luckyanova Maria N. , Maznev Alexei A. , Huberman Samuel , Chiloyan Vazrik , Zhou Jiawei , Huang Xiaopeng , Nelson Keith A. , Chen Gang 
Published: November 2015

AbstractHeat conduction in semiconductors and dielectrics depends upon their phonon mean free paths that describe the average travelling distance between two consecutive phonon scattering events. Nondiffusive phonon transport is being exploited to extract phonon mean free path distributions. Here, we describe an implementation of a nanoscale thermal conductivity spectroscopy technique that allows for the study of mean free path distributions in optically absorbing materials with relatively simple fabrication and a straightforward analysis scheme. We pattern 1D metallic grating of various line widths but fixed gap size on sample surfaces. The metal lines serve as both heaters and thermometers in time-domain thermoreflectance measurements and simultaneously act as wire-grid polarizers that protect the underlying substrate from direct optical excitation and heating. We demonstrate the viability of this technique by studying length-dependent thermal conductivities of silicon at various temperatures. The thermal conductivities measured with different metal line widths are analyzed using suppression functions calculated from the Boltzmann transport equation to extract the phonon mean free path distributions with no calibration required. This table-top ultrafast thermal transport spectroscopy technique enables the study of mean free path spectra in a wide range of technologically important materials.
ω-Tbo-IT1–New Inhibitor of Insect Calcium Channels Isolated from Spider Venom
Authors: Mikov Alexander N. , Fedorova Irina M. , Potapieva Natalia N. , Maleeva Ekaterina E. , Andreev Yaroslav A. , Zaitsev Alexey V. , Kim Kira K. , Bocharov Eduard V. , Bozin Timur N. , Altukhov Dmitry A. , Lipkin Alexey V. , Kozlov Sergey A. , Tikhonov Denis B. , Grishin Eugene V. 
Published: November 2015

AbstractNovel disulfide-containing polypeptide toxin was discovered in the venom of the Tibellus oblongus spider. We report on isolation, spatial structure determination and electrophysiological characterization of this 41-residue toxin, called ω-Tbo-IT1. It has an insect-toxic effect with LD50 19 μg/g in experiments on house fly Musca domestica larvae and with LD50 20 μg/g on juvenile Gromphadorhina portentosa cockroaches. Electrophysiological experiments revealed a reversible inhibition of evoked excitatory postsynaptic currents in blow fly Calliphora vicina neuromuscular junctions, while parameters of spontaneous ones were not affected. The inhibition was concentration dependent, with IC50 value 40 ± 10 nM and Hill coefficient 3.4 ± 0.3. The toxin did not affect frog neuromuscular junctions or glutamatergic and GABAergic transmission in rat brains. Ca2+ currents in Calliphora vicina muscle were not inhibited, whereas in Periplaneta americana cockroach neurons at least one type of voltage gated Ca2+ current was inhibited by ω-Tbo-IT1. Thus, the toxin apparently acts as an inhibitor of presynaptic insect Ca2+ channels. Spatial structure analysis of the recombinant ω-Tbo-IT1 by NMR spectroscopy in aqueous solution revealed that the toxin comprises the conventional ICK fold containing an extended β-hairpin loop and short β-hairpin loop which are capable of making “scissors-like mutual motions”.
Lactic Acid Bacteria Protects Caenorhabditis elegans from Toxicity of Graphene Oxide by Maintaining Normal Intestinal Permeability under different Genetic Backgrounds
Authors: Zhao Yunli , Yu Xiaoming , Jia Ruhan , Yang Ruilong , Rui Qi , Wang Dayong 
Published: November 2015

AbstractLactic acid bacteria (LAB) is safe and useful for food and feed fermentation. We employed Caenorhabditis elegans to investigate the possible beneficial effect of LAB (Lactobacillus bulgaricus) pretreatment against toxicity of graphene oxide (GO) and the underlying mechanisms. LAB prevented GO toxicity on the functions of both primary and secondary targeted organs in wild-type nematodes. LAB blocked translocation of GO into secondary targeted organs through intestinal barrier by maintaining normal intestinal permeability in wild-type nematodes. Moreover, LAB prevented GO damage on the functions of both primary and secondary targeted organs in exposed nematodes with mutations of susceptible genes (sod-2, sod-3, gas-1 and aak-2) to GO toxicity by sustaining normal intestinal permeability. LAB also sustained the normal defecation behavior in both wild-type nematodes and nematodes with mutations of susceptible genes. Therefore, the beneficial role of LAB against GO toxicity under different genetic backgrounds may be due to the combinational effects on intestinal permeability and defecation behavior. Moreover, the beneficial effects of LAB against GO toxicity was dependent on the function of ACS-22, homologous to mammalian FATP4 to mammalian FATP4. Our study provides highlight on establishment of pharmacological strategy to protect intestinal barrier from toxicity of GO.
PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs
Authors: Cheng Zhongshan , Chu Hin , Fan Yanhui , Li Cun , Song You-Qiang , Zhou Jie , Yuen Kwok-Yung 
Published: November 2015

AbstractExpression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets.
Ubiquitous anaerobic ammonium oxidation in inland waters of China: an overlooked nitrous oxide mitigation process
Authors: Zhu Guibing , Wang Shanyun , Zhou Leiliu , Wang Yu , Zhao Siyan , Xia Chao , Wang Weidong , Zhou Rong , Wang Chaoxu , Jetten Mike S. M. , Hefting Mariet M. , Yin Chengqing , Qu Jiuhui 
Published: November 2015

AbstractDenitrification has long been regarded as the only pathway for terrestrial nitrogen (N) loss to the atmosphere. Here we demonstrate that large-scale anaerobic ammonium oxidation (anammox), an overlooked N loss process alternative to denitrification which bypasses nitrous oxide (N2O), is ubiquitous in inland waters of China and contributes significantly to N loss. Anammox rates in aquatic systems show different levels (1.0–975.9 μmol N m−2 h−1, n = 256) with hotspots occurring at oxic-anoxic interfaces and harboring distinct biogeochemical and biogeographical features. Extrapolation of these results to the China-national level shows that anammox could contribute about 2.0 Tg N yr−1, which equals averagely 11.4% of the total N loss from China’s inland waters. Our results indicate that a significant amount of the nitrogen lost from inland waters bypasses denitrification, which is important for constructing more accurate climate models and may significantly reduce potential N2O emission risk at a large scale.
Strong Geometrical Effects in Submillimeter Selective Area Growth and Light Extraction of GaN Light Emitting Diodes on Sapphire
Authors: Tanaka Atsunori , Chen Renjie , Jungjohann Katherine L. , Dayeh Shadi A. 
Published: November 2015

AbstractAdvanced semiconductor devices often utilize structural and geometrical effects to tailor their characteristics and improve their performance. We report here detailed understanding of such geometrical effects in the epitaxial selective area growth of GaN on sapphire substrates and utilize them to enhance light extraction from GaN light emitting diodes. Systematic size and spacing effects were performed side-by-side on a single 2” sapphire substrate to minimize experimental sampling errors for a set of 144 pattern arrays with circular mask opening windows in SiO2. We show that the mask opening diameter leads to as much as 4 times increase in the thickness of the grown layers for 20 μm spacings and that spacing effects can lead to as much as 3 times increase in thickness for a 350 μm dot diameter. We observed that the facet evolution in comparison with extracted Ga adatom diffusion lengths directly influences the vertical and lateral overgrowth rates and can be controlled with pattern geometry. Such control over the facet development led to 2.5 times stronger electroluminescence characteristics from well-faceted GaN/InGaN multiple quantum well LEDs compared to non-faceted structures.