bluuebunny/crossref_metadata_2025_split huggingface dataset:
A methodology of design for affordances using affordance feature repositories
Authors: Kim Yong Se 
Published: July 2015

AbstractPeople interact with artifacts, either products or services, in their lives. These interactions are based on two-way communication between people and artifacts. The characteristics of artifacts that induce natural activities of people, affordances, play critical roles in making interactions successful and meaningful. The notion of affordance features, structural elements of artifacts that provide affordances, has been proposed earlier. In this paper, a methodological framework for design for affordances is proposed where repositories of affordance features are used. Affordances are identified through function–task interaction matrices or use activity observations. Using an affordance feature repository where many alternative structural elements for a specific affordance are stored together with corresponding design constraints and contexts, affordance features for those identified affordances are retrieved considering similarities between the target design constraints and those of the affordance features in the repositories. Using the clues given by such affordance features, a new affordance feature is to be designed through analogical reasoning. We present this design for affordance framework together with illustrative cases where various designers designed affordance features using affordance feature repositories.
French future: Exploring the future ratification hypothesis
Authors: MARI ALDA 
Published: July 2015

ABSTRACTThe paper proposes a unified account of the systematic polysemy of French future (FUT) that does not uniquely rely on Aktionsart. It explains the predominant preference for the temporal interpretation of FUT, appealing to the ‘future ratification hypothesis’. This is a felicity condition that can be satisfied to different degrees and among competing interpretations the one that satisfies it to the highest degree is preferred. The paper also shows that FUT does not convey uncertainty at utterance time (tu), and can be used when the attitude holder knows attuthat the embedded proposition is true.
Fire-related cues and the germination of eight Conostylis (Haemodoraceae) taxa, when freshly collected, after burial and after laboratory storage
Authors: Downes Katherine S. , Light Marnie E. , Pošta Martin , van Staden Johannes 
Published: July 2015

AbstractThe genus Conostylis (Haemodoraceae) is endemic to fire-prone south-western Australia. To gain an understanding of the effect of some fire-related germination cues, eight Conostylis taxa were tested in response to water, nitrate, smoke water and karrikinolide (KAR1) under light and dark conditions, when seeds were freshly collected and after a year of burial. The germination of all taxa tested was higher in response to smoke water and KAR1 than in water alone, whereas nitrate did not stimulate germination. Germination was higher in all taxa following 1 year of burial than in fresh seeds. Recently, glyceronitrile has been identified as another chemical in smoke water, apart from KAR1, that can stimulate the germination of certain species. The relative response of eight Conostylis taxa to KAR1, glyceronitrile and smoke water was examined in laboratory-stored seeds. Germination of these taxa was promoted by both smoke water and KAR1, except for C. neocymosa, which had high germination regardless of treatment. Four of the other seven taxa germinated to higher levels in at least one of the glyceronitrile concentrations tested (10, 50 or 100 μM) than in water alone. However, in only two of these taxa, C. aculeata subsp. septentrionora and C. juncea, was germination in glyceronitrile as high as that in smoke water. Thus, the response to glyceronitrile is not uniform across Conostylis taxa. Generally, germination was higher with KAR1 than glyceronitrile, suggesting that although some Conostylis taxa have the capacity to respond to glyceronitrile, KAR1 is the more important germination stimulant for this genus.
Resting Plasma Lipids and Cardiovascular Reactivity to Acute	Psychological Stress
Authors: Austin Anthony W. , Kushnick Michael R. , Knutson Michael J. , McGlynn Mark L. , Patterson Stephen M. 
Published: July 2015

Abstract. Prior research suggests that hyperlipidemia is associated with elevated blood pressure responses to acute stress but whether lipid levels influence underlying cardiac and vascular determinants of blood pressure during stress is not known. Thus, we examined whether lipids were associated with stress-induced blood pressure responses and responses of stroke volume (SV), cardiac output (CO), and total peripheral resistance (TPR). In 19 healthy university students (15 men), blood was drawn to measure lipid levels (triglycerides, low-density lipoprotein cholesterol [LDL-c], high-density lipoprotein cholesterol [HDL-c], total cholesterol) after a 10-min rest period. Participants then completed a 6-min mental arithmetic stressor and a 3-min cold pressor (separated by a 10-min recovery). This procedure was repeated twice, approximately 6 weeks apart. Lipids and hemodynamic values were averaged across the two sessions. Multiple linear regression analyses revealed that a model including LDL-c, HDL-c, and triglycerides significantly predicted diastolic blood pressure (DBP), R2adj = .45, p = .007, and systolic blood pressure (SBP) cold pressor reactivity, R2adj = .35, p = .023. Individually, only LDL-c significantly predicted DBP, β = .64, p = .003, and SBP cold pressor reactivity, β = .64, p = .005. The same model marginally predicted CO, R2adj = .24, p = .069, and TPR, R2adj = 21, p = .091, reactivity to mental arithmetic, but only triglycerides were independently associated with CO, β = −.63, p = .012, and TPR, β = .54, p = .029 reactivity. Lipids were not associated with heart rate (HR) or SV reactivity. LDL-c was positively associated with the blood pressure response to the cold pressor, whereas triglycerides were positively and negatively associated with the TPR and CO responses, respectively, to mental arithmetic. Endothelial dysfunction and greater release of vasoconstrictors in those with high lipids may explain these relationships.
AF9 promotes hESC neural differentiation through recruiting TET2 to neurodevelopmental gene loci for methylcytosine hydroxylation
Authors: Qiao Yunbo , Wang Xiongjun , Wang Ran , Li Yuanyuan , Yu Fang , Yang Xianfa , Song Lu , Xu Guoliang , Chin Y Eugene , Jing Naihe 
Published: July 2015

AbstractAF9 mutations have been implicated in human neurodevelopmental diseases and murine Af9 mediates histone methylation during cortical neuron generation. However, AF9 function and related mechanisms in human neurodevelopment remain unknown. Here we show that AF9 is necessary and sufficient for human embryonic stem cell (hESC) neural differentiation and neurodevelopmental gene activation. The 5-methylcytosine (5mC) dioxygenase TET2, which was identified in an AF9-associated protein complex, physically interacted with AF9. Both AF9 and TET2 co-localized in 5-hydroxymethylcytosine (5hmC)-positive hESC-derived neurons and were required for appropriate hESC neural differentiation. Upon binding to AAC-containing motifs, AF9 recruited TET2 to occupy the common neurodevelopmental gene loci to direct 5mC-to-5hmC conversion, which was followed by sequential activation of neural target genes and hESC neural commitment. These findings define an AF9–TET2 regulatory complex for modulating human neural development and reveal a novel mechanism by which the AF9 recognition specificity and TET2 hydroxylation activity cooperate to control neurodevelopmental gene activation.
Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice
Authors: Hoffmann Thomas W , Pham Hang-Phuong , Bridonneau Chantal , Aubry Camille , Lamas Bruno , Martin-Gallausiaux Camille , Moroldo Marco , Rainteau Dominique , Lapaque Nicolas , Six Adrien , Richard Mathias L , Fargier Emilie , Le Guern Marie-Emmanuelle , Langella Philippe , Sokol Harry 
Published: July 2015

Abstract
Studying host–microbiota interactions are fundamental to understanding the mechanisms involved in intestinal homeostasis and inflammation. In this work, we analyzed these interactions in mice that were mono-associated with six microorganisms that are representative of inflammatory bowel disease (IBD)-associated dysbiosis: the bacteria Bacteroides thetaiotaomicron, adhesive-invasive Escherichia coli (AIEC), Ruminococcus gnavus and Roseburia intestinalis; a yeast used as a probiotic drug, Saccharomyces boulardii CNCM I-745; and another yeast, Candida albicans. Extensive ex vivo analyses including colon transcriptomics, histology, immune response, bile acid metabolism and short-chain fatty acid production were studied. We showed that B. thetaiotaomicron had the highest impact on the immune system because it was almost able to recapitulate the effects of the entire conventional microbiota and notably induced Treg pathways. Furthermore, these analyses uncovered the effects of E. coli AIEC LF82 on indoleamine 2,3-dioxygenase expression and of S. boulardii CNCM I-745 on angiogenesis. These results were confirmed in vitro in human cell lines. Finally, our results suggested that R. gnavus has major effects on metabolism, and notably on tryptophan metabolism. This work therefore reveals that microorganisms with a potential role in intestinal homeostasis and inflammation have specific impacts on the host, and it suggests several tracks to follow to understand intestinal homeostasis and IBD pathogenesis better, providing new insights to identify novel therapeutic targets.
Observation of non-Markovian micromechanical Brownian motion
Authors: Gröblacher S. , Trubarov A. , Prigge N. , Cole G. D. , Aspelmeyer M. , Eisert J. 
Published: July 2015

AbstractAll physical systems are to some extent open and interacting with their environment. This insight, basic as it may seem, gives rise to the necessity of protecting quantum systems from decoherence in quantum technologies and is at the heart of the emergence of classical properties in quantum physics. The precise decoherence mechanisms, however, are often unknown for a given system. In this work, we make use of an opto-mechanical resonator to obtain key information about spectral densities of its condensed-matter heat bath. In sharp contrast to what is commonly assumed in high-temperature quantum Brownian motion describing the dynamics of the mechanical degree of freedom, based on a statistical analysis of the emitted light, it is shown that this spectral density is highly non-Ohmic, reflected by non-Markovian dynamics, which we quantify. We conclude by elaborating on further applications of opto-mechanical systems in open system identification.
Stabilization of 4H hexagonal phase in gold nanoribbons
Authors: Fan Zhanxi , Bosman Michel , Huang Xiao , Huang Ding , Yu Yi , Ong Khuong P. , Akimov Yuriy A. , Wu Lin , Li Bing , Wu Jumiati , Huang Ying , Liu Qing , Eng Png Ching , Lip Gan Chee , Yang Peidong , Zhang Hua 
Published: July 2015

AbstractGold, silver, platinum and palladium typically crystallize with the face-centred cubic structure. Here we report the high-yield solution synthesis of gold nanoribbons in the 4H hexagonal polytype, a previously unreported metastable phase of gold. These gold nanoribbons undergo a phase transition from the original 4H hexagonal to face-centred cubic structure on ligand exchange under ambient conditions. Using monochromated electron energy-loss spectroscopy, the strong infrared plasmon absorption of single 4H gold nanoribbons is observed. Furthermore, the 4H hexagonal phases of silver, palladium and platinum can be readily stabilized through direct epitaxial growth of these metals on the 4H gold nanoribbon surface. Our findings may open up new strategies for the crystal phase-controlled synthesis of advanced noble metal nanomaterials.
Ant groups optimally amplify the effect of transiently informed individuals
Authors: Gelblum Aviram , Pinkoviezky Itai , Fonio Ehud , Ghosh Abhijit , Gov Nir , Feinerman Ofer 
Published: July 2015

AbstractTo cooperatively transport a large load, it is important that carriers conform in their efforts and align their forces. A downside of behavioural conformism is that it may decrease the group’s responsiveness to external information. Combining experiment and theory, we show how ants optimize collective transport. On the single-ant scale, optimization stems from decision rules that balance individuality and compliance. Macroscopically, these rules poise the system at the transition between random walk and ballistic motion where the collective response to the steering of a single informed ant is maximized. We relate this peak in response to the divergence of susceptibility at a phase transition. Our theoretical models predict that the ant-load system can be transitioned through the critical point of this mesoscopic system by varying its size; we present experiments supporting these predictions. Our findings show that efficient group-level processes can arise from transient amplification of individual-based knowledge.
Quantum Monte Carlo study of the phase diagram of solid molecular hydrogen at extreme pressures
Authors: Drummond N. D. , Monserrat Bartomeu , Lloyd-Williams Jonathan H. , Ríos P. López , Pickard Chris J. , Needs R. J. 
Published: July 2015

AbstractEstablishing the phase diagram of hydrogen is a major challenge for experimental and theoretical physics. Experiment alone cannot establish the atomic structure of solid hydrogen at high pressure, because hydrogen scatters X-rays only weakly. Instead, our understanding of the atomic structure is largely based on density functional theory (DFT). By comparing Raman spectra for low-energy structures found in DFT searches with experimental spectra, candidate atomic structures have been identified for each experimentally observed phase. Unfortunately, DFT predicts a metallic structure to be energetically favoured at a broad range of pressures up to 400 GPa, where it is known experimentally that hydrogen is non-metallic. Here we show that more advanced theoretical methods (diffusion quantum Monte Carlo calculations) find the metallic structure to be uncompetitive, and predict a phase diagram in reasonable agreement with experiment. This greatly strengthens the claim that the candidate atomic structures accurately model the experimentally observed phases.
A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae
Authors: Atack John M. , Srikhanta Yogitha N. , Fox Kate L. , Jurcisek Joseph A. , Brockman Kenneth L. , Clark Tyson A. , Boitano Matthew , Power Peter M. , Jen Freda E.-C. , McEwan Alastair G. , Grimmond Sean M. , Smith Arnold L. , Barenkamp Stephen J. , Korlach Jonas , Bakaletz Lauren O. , Jennings Michael P. 
Published: July 2015

AbstractNon-typeable Haemophilus influenzae contains an N6-adenine DNA-methyltransferase (ModA) that is subject to phase-variable expression (random ON/OFF switching). Five modA alleles, modA2, modA4, modA5, modA9 and modA10, account for over two-thirds of clinical otitis media isolates surveyed. Here, we use single molecule, real-time (SMRT) methylome analysis to identify the DNA-recognition motifs for all five of these modA alleles. Phase variation of these alleles regulates multiple proteins including vaccine candidates, and key virulence phenotypes such as antibiotic resistance (modA2, modA5, modA10), biofilm formation (modA2) and immunoevasion (modA4). Analyses of a modA2 strain in the chinchilla model of otitis media show a clear selection for ON switching of modA2 in the middle ear. Our results indicate that a biphasic epigenetic switch can control bacterial virulence, immunoevasion and niche adaptation in an animal model system.
Phytochrome diversity in green plants and the origin of canonical plant phytochromes
Authors: Li Fay-Wei , Melkonian Michael , Rothfels Carl J. , Villarreal Juan Carlos , Stevenson Dennis W. , Graham Sean W. , Wong Gane Ka-Shu , Pryer Kathleen M. , Mathews Sarah 
Published: July 2015

AbstractPhytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades. Surprisingly, the phytochrome portions of algal and land plant neochromes, a chimera of phytochrome and phototropin, appear to share a common origin. Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives.
A molecular propeller effect for chiral separation and analysis
Authors: Clemens Jonathon B. , Kibar Osman , Chachisvilis Mirianas 
Published: July 2015

AbstractEnantiomers share nearly identical physical properties but have different chiral geometries, making their identification and separation difficult. Here we show that when exposed to a rotating electric field, the left- and right-handed chiral molecules rotate with the field and act as microscopic propellers; moreover, owing to their opposite handedness, they propel along the axis of field rotation in opposite directions. We introduce a new molecular parameter called hydrodynamic chirality to characterize the coupling of rotational motion of a chiral molecule into its translational motion and quantify the direction and velocity of such motion. We demonstrate >80% enrichment level of counterpart enantiomers in solution without using chiral selectors or circularly polarized light. We expect our results to have an impact on multiple applications in drug discovery, analytical and chiral chemistry, including determination of absolute configuration, as well as in influencing the understanding of artificial and natural molecular systems where rotational motion of the molecules is involved.
Robust interface between flying and topological qubits
Authors: Xue Zheng-Yuan , Gong Ming , Liu Jia , Hu Yong , Zhu Shi-Liang , Wang Z. D. 
Published: July 2015

AbstractHybrid architectures, consisting of conventional and topological qubits, have recently attracted much attention due to their capability in consolidating robustness of topological qubits and universality of conventional qubits. However, these two kinds of qubits are normally constructed in significantly different energy scales and thus the energy mismatch is a major obstacle for their coupling, which can support the exchange of quantum information between them. Here we propose a microwave photonic quantum bus for a strong direct coupling between the topological and conventional qubits, where the energy mismatch is compensated by an external driving field. In the framework of tight-binding simulation and perturbation approach, we show that the energy splitting of Majorana fermions in a finite length nanowire, which we use to define topological qubits, is still robust against local perturbations due to the topology of the system. Therefore, the present scheme realizes a rather robust interface between the flying and topological qubits. Finally, we demonstrate that this quantum bus can also be used to generate multipartitie entangled states with the topological qubits.
Double strand break repair by capture of retrotransposon sequences and reverse-transcribed spliced mRNA sequences in mouse zygotes
Authors: Ono Ryuichi , Ishii Masayuki , Fujihara Yoshitaka , Kitazawa Moe , Usami Takako , Kaneko-Ishino Tomoko , Kanno Jun , Ikawa Masahito , Ishino Fumitoshi 
Published: July 2015

AbstractThe CRISPR/Cas system efficiently introduces double strand breaks (DSBs) at a genomic locus specified by a single guide RNA (sgRNA). The DSBs are subsequently repaired through non-homologous end joining (NHEJ) or homologous recombination (HR). Here, we demonstrate that DSBs introduced into mouse zygotes by the CRISPR/Cas system are repaired by the capture of DNA sequences deriving from retrotransposons, genomic DNA, mRNA and sgRNA. Among 93 mice analysed, 57 carried mutant alleles and 22 of them had long de novo insertion(s) at DSB-introduced sites; two were spliced mRNAs of Pcnt and Inadl without introns, indicating the involvement of reverse transcription (RT). Fifteen alleles included retrotransposons, mRNAs and other sequences without evidence of RT. Two others were sgRNAs with one containing T7 promoter-derived sequence suggestive of a PCR product as its origin. In conclusion, RT-product-mediated DSB repair (RMDR) and non-RMDR repair were identified in the mouse zygote. We also confirmed that both RMDR and non-RMDR take place in CRISPR/Cas transfected NIH-3T3 cells. Finally, as two de novo MuERV-L insertions in C57BL/6 mice were shown to have characteristic features of RMDR in natural conditions, we hypothesize that RMDR contributes to the emergence of novel DNA sequences in the course of evolution.
Haloarchaea Endowed with Phosphorus Solubilization Attribute Implicated in Phosphorus Cycle
Authors: Yadav Ajar Nath , Sharma Divya , Gulati Sneha , Singh Surender , Dey Rinku , Pal Kamal Krishna , Kaushik Rajeev , Saxena Anil Kumar 
Published: July 2015

AbstractArchaea are unique microorganisms that are present in ecological niches of high temperature, pH and salinity. A total of 157 archaea were obtained from thirteen sediment, water and rhizospheric soil samples collected from Rann of Kutch, Gujarat, India. With an aim to screen phosphate solubilizing archaea, a new medium was designed as Haloarchaea P Solubilization (HPS) medium. The medium supported the growth and P solubilization activity of archaea. Employing the HPS medium, twenty isolates showed the P-solubilization. Phosphate solubilizing archaea were identified as seventeen distinct species of eleven genera namelyHaloarcula, Halobacterium, Halococcus, Haloferax, Halolamina, Halosarcina, Halostagnicola, Haloterrigena, Natrialba,NatrinemaandNatronoarchaeum.Natrinemasp. strain IARI-WRAB2 was identified as the most efficient P-solubilizer (134.61 mg/L) followed byHalococcus hamelinensisstrain IARI-SNS2 (112.56 mg/L). HPLC analysis detected seven different kinds of organic acids, namely: gluconic acid, citric acid, formic acid, fumaric acid succinic acid, propionic acid and tartaric acid from the cultures of these isolates. These phosphate solubilizing halophilic archaea may play a role in P nutrition to vegetation growing in these hypersaline soils. This is the first report for these haloarchaea to solubilize considerable amount of P by production of organic acids and lowering of pH.