bluuebunny/crossref_metadata_2025 huggingface dataset:
On the computability of affordances as relations
Authors: Maier Jonathan R.A.
Published: July 2015

One of the principal advantages of affordance-based design is that Gibson's theory of affordances is a relational theory, akin to other relational approaches such as relational biology and relational computer science. The relationships between artifacts and their designers and users are of such primary importance that only a theory that is able to deal with those relationships directly appears to be sufficient for describing the wide breadth of problems in engineering design. However, there is no precise definition for what qualifies as a relational theory. In mathematics, we do find something approaching a theory of relations, dating back at least to Charles Peirce'sLogic of Relativesaround 1870. While rather general, Peirce's ideas on the subject laid the foundation for advances in the 20th century, including the relational model of databases. This paper is a first attempt at applying the mathematics of relations to affordances, with the aim of more precisely characterizing affordances, which heretofore have been difficult to define and, lacking appropriate mathematics, nearly impossible to subject to computation. Meanwhile, the implicit computability of affordances as relations is demonstrated by examples drawn from engineering, physics, computer science, biology, and architecture.
Three methods for identifying novel affordances
Authors: Shu L.H. , Srivastava J. , Chou A. , Lai S.
Published: July 2015

We describe three approaches to identify novel product affordances: affordance of absence; insights from lead users, specifically do-it-yourselfers (DIYers); and natural-language searches. While these approaches were separately pursued, we show their connection to each other in this paper. We begin by describing the affordance of absence, inspired by insights on affordances arising from a lack of resources. For example, in the absence of specialized tools, more general tools are used to accomplish similar tasks. Such absence clarifies how other tools could be modified to add relevant features and identifies critical features of the absent tool. In addition, the temporary removal of physical features and objects enables user interaction in ways that may not emerge in their presence. Affordance of absence has the potential to more fully specify affordances for a given object and to help overcome functional fixedness. For the second approach, we describe insights from DIYers obtained from the “IKEA hackers” online community. We consider DIYers lead users for seeking out and exploiting product affordances, often transforming product functions dramatically. We also discuss their projects through the lens of affordance of absence. For the third approach, we outline our natural-language approach to affordance extraction, beginning with consumer product reviews provided for Canadian Tire, a major Canadian retailer. We describe efforts toward automatically identifying less common affordances, and the use of cue phrases to highlight insightful DIY transformations from the IKEA hackers community. Finally, we comment on the potential value of this work for product design in general.
Toward automating affordance-based design
Authors: Mata Ivan , Fadel Georges , Mocko Gregory
Published: July 2015

The objective of this research is to develop a computational representation of knowledge associated with affordance-based design (ABD). The ABD ontology formalizes the entities, properties, and relationships within the domains of ABD. The ontology enables designers to describe the affordances of existing products and specify the intended affordances of future products in line with ABD. The ontology consists of 14 concepts and 5 relationships. The ontology is developed using Protégé 4.3 and DL-query to query and reason with the ontology. The ontology is demonstrated using a consumer vacuum cleaner. The formal ontology serves as the basis for developing computer support for ABD applications. When implemented, these design tools will help designers manage the affordances of artifacts being designed, specifying the interacting entities of every affordance when a three-dimensional model of the artifact is available. Further, these software tools could be used to support ABD methods.
Affordances and use plans: An analysis of two alternatives to function-based design
Authors: Pols Auke J.K.
Published: July 2015

Function-based design approaches have been criticized for being too narrow to properly guide design. Specifically, they are said to be unable to cope with nonfunctional considerations, such as cost or maintenance issues without invoking other concepts, such as constraints. This paper investigates two alternative conceptualizations of the design process: the practical affordance-based design approach, as elaborated by Maier and Fadel, and the more theoretical use plan approach by Houkes and Vermaas. This paper compares function-, affordance-, and use plan-based design approaches. It highlights strengths and weaknesses of each approach and proposes a definition of the function of an artifact in terms of its affordances.
An affordance-based approach for generating user-specific design specifications
Authors: Cormier Phillip , Lewis Kemper
Published: July 2015

When developing an artifact, designers must first understand the problem. This includes the benefits that the artifact must deliver and the user variation that is present. Each user has a unique set of human factors, preferences, personal knowledge, and solution constraints that could potentially influence the characteristics of the artifact. Currently, there is little work supporting the process of how to formally generate user-specific design specifications, resulting inad hocora prioridecisions when generating design specifications. Further, because most design processes generate design specifications manually, the number of design specifications is not typically addressed at the user level. This research presents an affordance-based approach for use in the early stages of design to help designers establish user-specific design specifications. This information can then be used in the creation of a system or set of systems that meets the demands of both the user(s) and the organization that is developing the artifact. An affordance-based approach is leveraged because it maintains the relational field of view among the user, existing artifacts, and the artifact(s) being designed. Once individual design specifications are generated, designers can use this information in later stages of the design process.
A methodology of design for affordances using affordance feature repositories
Authors: Kim Yong Se
Published: July 2015

People 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

The 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.
The approximation theorem for the Λμ-calculus
Authors: DE'LIGUORO UGO
Published: July 2015

We consider a notion of approximation for terms of de Groote–Saurin Λμ-calculus. Then, we introduce an intersection type assignment system for that calculus which is invariant under subject conversion. The type assignment system also induces a filter model, which is an extensional Λμ-model in the sense of Nakazawa and Katsumata. We then establish the approximation theorem, stating that a type can be assigned to a term in the system if and only if it can be assigned to same of its approximations.
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

The 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.
Sea slugs (Gastropoda: Heterobranchia) from a poorly known area in North-east Brazil: filling gaps in Atlantic distributions
Authors: Galvão Filho Hilton C. , Araújo Ana K. , Silva Felipe V. , Azevedo Victor M.D. , Meirelles Carlos A.O. , Matthews-Cascon Helena
Published: July 2015

Qualitative samples of ‘opisthobranchs’ were collected from different beaches and estuaries in Ceará State, North-east Brazil. Further species distributions from the literature were used to infer patterns of distribution and to analyse faunal similarity among Atlantic biogeographic areas, Brazilian zones and the Ceará State. A total of 35 new records are reported for the Ceará State, including 19 new records from the North-east Brazilian Shelf (NBS), 12 new from the Brazilian Province and two new records from the South Atlantic. More than half of the species in this area are common between the Caribbean and Brazilian provinces, which demonstrates their capacity for crossing the Amazon–Orinoco barrier. The high percentage of occurrence in the NBS and the South Brazilian Bight, when compared to neighbouring zones, may be attributed to the poor knowledge of the Brazilian ‘opisthobranch’ fauna.
Dynamic party unity: the US Congress in comparative perspective
Authors: Weber Till , Parsons Craig
Published: July 2015

Moises Ostrogorski once denounced political parties for burying diverse concerns of pluralistic societies under monolithic electoral options. E.E. Schattschneider celebrated them for the same reason: organizing choice and ‘responsible party government’ amid pluralistic complexity. Comparativists have found both dynamics in European legislatures: most European parties exhibit the high average levels of voting unity that Schattschneider’s theory implies, but also display rather Ostrogorskian cycles of discipline, stifling dissent on divisive issues at election time. We use comparativists’ tools to explore the dynamics and normative quality of party unity in the different terrain of the US Congress. We find similar cycles of unity in roll-call voting, but in the American context – with more loosely organized parties, especially historically but still today – Ostrogorskian stifling of dissent operates against a less Schattschneiderian background. In comparative perspective, Congressional parties muffle divisive issues more effectively than they deliver governance, with tenuous implications for representation.
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.
Individual Differences in Personality Traits
Authors: Karimizadeh A. , Mahnam Amin , Yazdchi M. R. , Besharat M. A.
Published: July 2015

Abstract. During the last decade, an increasing number of studies have used neuroscientific methods to examine the relationships between different personality traits and brain structures. This includes the Magnetic Resonance Imaging (MRI)-based analysis of correlations between individual differences in personality traits and the structural variance of specific brain regions. Perfectionism is a personality trait that remains relatively stable over time, and it is influenced by heredity. In this study, the possible brain regions that structurally correlated with both positive and negative perfectionism were investigated. Voxel-based morphometry was used to analyze the whole brain MRI images of 49 participants, and their levels of perfectionism were also evaluated using a standard scale. The statistical analysis revealed significant correlations between negative perfectionism and the gray matter volume of the thalamus and left posterior parietal cortex (precuneus) structures. This finding suggests that differences in perfectionism between individuals may reflect structural variances in these regions of the brain.
Oral Immune Activation by Disgust and Disease-Related	Pictures
Authors: Stevenson Richard J. , Hodgson Deborah , Oaten Megan J. , Sominsky Luba , Mahmut Mehmet , Case Trevor I.
Published: July 2015

Abstract. Both disgust and disease-related images appear able to induce an innate immune response but it is unclear whether these effects are independent or rely upon a common shared factor (e.g., disgust or disease-related cognitions). In this study we directly compared these two inductions using specifically generated sets of images. One set was disease-related but evoked little disgust, while the other set was disgust evoking but with less disease-relatedness. These two image sets were then compared to a third set, a negative control condition. Using a wholly within-subject design, participants viewed one image set per week, and provided saliva samples, before and after each viewing occasion, which were later analyzed for innate immune markers. We found that both the disease related and disgust images, relative to the negative control images, were not able to generate an innate immune response. However, secondary analyses revealed innate immune responses in participants with greater propensity to feel disgust following exposure to disease-related and disgusting images. These findings suggest that disgust images relatively free of disease-related themes, and disease-related images relatively free of disgust may be suboptimal cues for generating an innate immune response. Not only may this explain why disgust propensity mediates these effects, it may also imply a common pathway.
Simulating a Warmer, Drier Arctic
Authors: Wheeling Kate
Published: July 2015

Field experiments examine the effect of rising temperatures and drying soils on carbon dynamics in the Arctic.
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

AF9 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.
Controversies concerning thymus‐derived regulatory T cells: fundamental issues and a new perspective
Authors: Ono Masahiro , Tanaka Reiko J
Published: July 2015

Thymus‐derived regulatory T cells (Tregs) are considered to be a distinct T‐cell lineage that is genetically programmed and specialised for immunosuppression. This perspective is based on the key evidence that CD25+ Tregs emigrate to neonatal spleen a few days later than other T cells and that thymectomy of 3‐day‐old mice depletes Tregs only, causing autoimmune diseases. Although widely believed, the evidence has never been reproduced as originally reported, and some studies indicate that Tregs exist in neonates. Thus we examine the consequences of the controversial evidence, revisit the fundamental issues of Tregs and thereby reveal the overlooked relationship of T‐cell activation and Foxp3‐mediated control of the T‐cell system. Here we provide a new model of Tregs and Foxp3, a feedback control perspective, which views Tregs as a component of the system that controls T‐cell activation, rather than as a distinct genetically programmed lineage. This perspective provides new insights into the roles of self‐reactivity, T cell–antigen‐presenting cell interaction and T‐cell activation in Foxp3‐mediated immune regulation.
The danger model: questioning an unconvincing theory
Authors: Józefowski Szczepan
Published: July 2015

Janeway's pattern recognition theory holds that the immune system detects infection through a limited number of the so‐called pattern recognition receptors (PRRs). These receptors bind specific chemical compounds expressed by entire groups of related pathogens, but not by host cells (pathogen‐associated molecular patterns (PAMPs). In contrast, Matzinger's danger hypothesis postulates that products released from stressed or damaged cells have a more important role in the activation of immune system than the recognition of nonself. These products, named by analogy to PAMPs as danger‐associated molecular patterns (DAMPs), are proposed to act through the same receptors (PRRs) as PAMPs and, consequently, to stimulate largely similar responses. Herein, I review direct and indirect evidence that contradict the widely accepted danger theory, and suggest that it may be false.
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

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

All 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

Gold, 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

To 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

Establishing 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

Non-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

Phytochromes 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

Enantiomers 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

Hybrid 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

The 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

Archaea 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.
Developmental and evolutionary novelty in the serrated teeth of theropod dinosaurs
Authors: Brink K. S. , Reisz R. R. , LeBlanc A. R. H. , Chang R. S. , Lee Y. C. , Chiang C. C. , Huang T. , Evans D. C.
Published: July 2015

Tooth morphology and development can provide valuable insights into the feeding behaviour and evolution of extinct organisms. The teeth of Theropoda, the only clade of predominantly predatory dinosaurs, are characterized by ziphodonty, the presence of serrations (denticles) on their cutting edges. Known today only in varanid lizards, ziphodonty is much more pervasive in the fossil record. Here we present the first model for the development of ziphodont teeth in theropods through histological, SEM and SR-FTIR analyses, revealing that structures previously hypothesized to prevent tooth breakage instead first evolved to shape and maintain the characteristic denticles through the life of the tooth. We show that this novel complex of dental morphology and tissues characterizes Theropoda, with the exception of species with modified feeding behaviours, suggesting that these characters are important for facilitating the hypercarnivorous diet of most theropods. This adaptation may have played an important role in the initial radiation and subsequent success of theropods as terrestrial apex predators.
Rapid parallel measurements of macroautophagy and mitophagy in mammalian cells using a single fluorescent biosensor
Authors: Sargsyan A. , Cai J. , Fandino L. B. , Labasky M. E. , Forostyan T. , Colosimo L. K. , Thompson S. J. , Graham T. E.
Published: July 2015

Mitochondrial dysfunction is implicated in many human diseases and occurs in normal aging. Mitochondrial health is maintained through organelle biogenesis and repair or turnover of existing mitochondria. Mitochondrial turnover is principally mediated by mitophagy, the trafficking of damaged mitochondria to lysosomes via macroautophagy (autophagy). Mitophagy requires autophagy, but is itself a selective process that relies on specific autophagy-targeting mechanisms and thus can be dissociated from autophagy under certain circumstances. Therefore, it is important to assess autophagy and mitophagy together and separately. We sought to develop a robust, high-throughput, quantitative method for monitoring both processes in parallel. Here we report a flow cytometry-based assay capable of rapid parallel measurements of mitophagy and autophagy in mammalian cells using a single fluorescent protein biosensor. We demonstrate the ability of the assay to quantify Parkin-dependent selective mitophagy in CCCP-treated HeLa cells. In addition, we show the utility of the assay for measuring mitophagy in other cell lines, as well as for Parkin-independent mitophagy stimulated by deferiprone. The assay makes rapid measurements (10,000 cells per 6 seconds) and can be combined with other fluorescent indicators to monitor distinct cell populations, enabling design of high-throughput screening experiments to identify novel regulators of mitophagy in mammalian cells.
Mitochondrial CB1 receptor is involved in ACEA-induced protective effects on neurons and mitochondrial functions
Authors: Ma Lei , Jia Ji , Niu Wen , Jiang Tao , Zhai Qian , Yang Lei , Bai Fuhai , Wang Qiang , Xiong Lize
Published: July 2015

Mitochondrial dysfunction contributes to cell death after cerebral ischemia/reperfusion (I/R) injury. Cannabinoid CB1 receptor is expressed in neuronal mitochondrial membranes (mtCB1R) and involved in regulating mitochondrial functions under physiological conditions. However, whether mtCB1R affords neuroprotection against I/R injury remains unknown. We used mouse models of cerebral I/R, primary cultured hippocampal neurons exposed to oxygen-glucose deprivation/reoxygenation (OGD/R) and Ca2+-induced injury in purified neuronal mitochondria to investigate the role of mtCB1R in neuroprotection. Our results showed selective cell-permeant CB1 receptor agonist, arachidonyl-2-chloroethylamide (ACEA), significantly up-regulated the expression of mtCB1R protein in hippocampal neurons and tissue.In vitro, ACEA restored cell viability, inhibited generation of reactive oxygen species (ROS), decreased lactate dehydrogenase (LDH) release and reduced apoptosis, improved mitochondrial function.In vivo, ACEA ameliorated neurological scores, diminished the number of TUNEL-positive neurons and decreased the expression of cleaved caspase-3. However, ACEA-induced benefits were blocked by the selective cell-permeant CB1 receptor antagonist AM251, but just partially by the selective cell-impermeant CB1 receptor antagonist hemopressin. In purified neuronal mitochondria, mtCB1R activation attenuated Ca2+-induced mitochondrial injury. In conclusion, mtCB1R is involved in ACEA-induced protective effects on neurons and mitochondrial functions, suggesting mtCB1R may be a potential novel target for the treatment of brain ischemic injury.
The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens”
Authors: Zou Geng , Bello-Orti Bernardo , Aragon Virginia , Tucker Alexander W. , Luo Rui , Ren Pinxing , Bi Dingren , Zhou Rui , Jin Hui
Published: July 2015

Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like “vampire pathogens” (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3 and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation.
Mieap suppresses murine intestinal tumor via its mitochondrial quality control
Authors: Tsuneki Masayuki , Nakamura Yasuyuki , Kinjo Takao , Nakanishi Ruri , Arakawa Hirofumi
Published: July 2015

Mieap, a novel p53-inducible protein, plays a key role in maintaining healthy mitochondria in various pathophysiological states. Here, we show that Mieap deficiency in ApcMin/+ mice is strikingly associated with the malignant progression of murine intestinal tumors. To understand the role that Mieap plays in in vivo tumorigenesis, we generated Mieap heterozygous (ApcMin/+ Mieap+/−) and homozygous (ApcMin/+ Mieap−/−) ApcMin/+ mice. Interestingly, the ApcMin/+ mice with the Mieap+/− and Mieap−/− genetic background revealed remarkable shortening of the lifetime compared to ApcMin/+ mice because of severe anemia. A substantial increase in the number and size of intestinal polyps was associated with Mieap gene deficiency. Histopathologically, intestinal tumors in the Mieap-deficient ApcMin/+ mice clearly demonstrated advanced grades of adenomas and adenocarcinomas. We demonstrated that the significant increase in morphologically unhealthy mitochondria and trace accumulations of reactive oxygen species may be mechanisms underlying the increased malignant progression of the intestinal tumors of Mieap-deficient ApcMin/+ mice. These findings suggest that the Mieap-regulated mitochondrial quality control plays a critical role in preventing mouse intestinal tumorigenesis.
Environmentally Driven Migration in a Social Network Game
Authors: Takano Masanori , Wada Kazuya , Fukuda Ichiro
Published: July 2015

Cooperative behaviors are common in humans and they are the fundamental basis of our society. Theoretical and experimental studies have modeled environments where the behaviors of humans, or agents, have been restricted to analyze their social behavior. However, it is important that such studies can be generalized to a less restrictive environment in order to understand human society. Social network games (SNGs) provide a powerful tool for the quantitative study of human behavior using a less restrictive environment than in previous studies. We focused on multilevel selection, one of the theoretical frameworks used to study the evolution of cooperation. The evolution of cooperation by multilevel selection requires that the continual assortment between cooperators and noncooperators is generated; thus, humans may have acquired mechanisms that ensure assortment (e.g., migration between groups). This study aims to investigate this mechanism in a less restrictive environment. For this purpose, we researched the effect of migration based on data analysis in an SNG where the players could behave more freely than was possible in the environments used in the previous studies. We showed that players maintained assortment between cooperators and defectors in this SNG, where it appears that environmentally driven migration generated the assortment.