Understanding climate data through commentary metadata: the CHARMe project

We describe the CHARMe project, which aims to link climate datasets with publications, user feedback and other items of "commentary metadata". The system will help users learn from previous community experience and select datasets that best suit their needs, as well as providing direct traceability between conclusions and the data that supported them. The project applies the principles of Linked Data and adopts the Open Annotation standard to record and publish commentary information. CHARMe contributes to the emerging landscape of "climate services", which will provide climate data and information to influence policy and decision-making. Although the project focuses on climate science, the technologies and concepts are very general and could be applied to other fields.

Cigarette smoke-induced neurogenic inflammation is mediated by α,β-unsaturated aldehydes and the TRPA1 receptor in rodents

Cigarette smoke (CS) inhalation causes an early inflammatory response in rodent airways by stimulating capsaicin-sensitive sensory neurons that express transient receptor potential cation channel, subfamily V, member 1 (TRPV1) through an unknown mechanism that does not involve TRPV1. We hypothesized that 2 alpha,beta-unsaturated aldehydes present in CS, crotonaldehyde and acrolein, induce neurogenic inflammation by stimulating TRPA1, an excitatory ion channel coexpressed with TRPV1 on capsaicin-sensitive nociceptors. We found that CS aqueous extract (CSE), crotonaldehyde, and acrolein mobilized Ca2+ in cultured guinea pig jugular ganglia neurons and promoted contraction of isolated guinea pig bronchi. These responses were abolished by a TRPA1-selective antagonist and by the aldehyde scavenger glutathione but not by the TRPV1 antagonist capsazepine or by ROS scavengers. Treatment with CSE or aldehydes increased Ca2+ influx in TRPA1-transfected cells, but not in control HEK293 cells, and promoted neuropeptide release from isolated guinea pig airway tissue. Furthermore, the effect of CSE and aldehydes on Ca2+ influx in dorsal root ganglion neurons was abolished in TRPA1-deficient mice. These data identify alpha,beta-unsaturated aldehydes as the main causative agents in CS that via TRPA1 stimulation mediate airway neurogenic inflammation and suggest a role for TRPA1 in the pathogenesis of CS-induced diseases.

Virgin olive oil phenolics extract inhibit invasion of HT115 human colon cancer cells in vitro and in vivo

The decreased cancer risk associated with consumption of olive oil may be due to the presence of phenolics which can modulate pathways including apoptosis and invasion that are relevant to carcinogenesis. We have previously shown that a virgin olive oil phenolics extract (OVP) inhibited invasion of HT115 colon cancer cells in vitro. In the current study we assessed the in vitro effects of OVP (25 μg mL(-1)) on HT115 cell migration, spreading and integrin expression. Furthermore, the anti-metastatic activity of OVP - at a dose equivalent to 25 mg per kg per day for 2, 8 or 10 weeks - was assessed in a Severe Combined ImmunoDeficiency (SCID) Balb-c mouse model. After 24 h OVP did not inhibit cell migration but significantly reduced cell spreading on fibronectin (65% of control; p < 0.05) and expression of a range of α and β integrins was modulated. In vivo, OVP by gavage significantly (p < 0.05) decreased not only tumour volume but also the number of metastases in SCID Balb-c mice. Collectively, the data suggest that - possibly through modulation of integrin expression - OVP decreases invasion in vitro and also inhibits metastasis in vivo.

Contractual restrictions on lawful use of information: sole-source databases protected by the back door?

This article is concerned with the risks associated with the monopolisation of information that is available from a single source only. Although there is a longstanding consensus that sole-source databases should not receive protection under the EU Database Directive, and there are legislative provisions to ensure that lawful users have access to a database’s contents, Ryanair v PR Aviation challenges this assumption by affirming that the use of non-protected databases can be restricted by contract. Owners of non-protected databases can contractually exclude lawful users from taking the benefit of statutorily permitted uses, because such databases are not covered from the legislation that declares this kind of contract null and void. We argue that this judgment is not consistent with the legislative history and can have a profound impact on the functioning of the digital single market, where new information services, such as meta-search engines or price-comparison websites, base their operation on the systematic extraction and re-utilisation of materials available from online sources. This is an issue that the Commission should address in a forthcoming evaluation of the Database Directive.

Search engine liability for autocomplete suggestions: personality, privacy and the power of the algorithm

This article is concerned with the liability of search engines for algorithmically produced search suggestions, such as through Google’s ‘autocomplete’ function. Liability in this context may arise when automatically generated associations have an offensive or defamatory meaning, or may even induce infringement of intellectual property rights. The increasing number of cases that have been brought before courts all over the world puts forward questions on the conflict of fundamental freedoms of speech and access to information on the one hand, and personality rights of individuals— under a broader right of informational self-determination—on the other. In the light of the recent judgment of the Court of Justice of the European Union (EU) in Google Spain v AEPD, this article concludes that many requests for removal of suggestions including private individuals’ information will be successful on the basis of EU data protection law, even absent prejudice to the person concerned.

Sparta and the English Republic

In 1659-60, James Harrington and Henry Stubbe, two republican authors, engaged in a bad-tempered pamphlet debate about the constitution of classical Sparta. This took place in the context of political collapse after the fall of the Cromwellian Protectorate, as republicans desperately attempted to devise safeguards which could prevent the return of monarchy. Questions of constitutional form were not always at the forefront of 1650s English republicanism, but Harrington’s ideal constitution of ‘Oceana’ brought these questions to the fore in 1659’s discussions. Sparta formed a key plank of the ‘ancient prudence’ which supported Harrington’s theory, and like Stubbe he drew on Nicolaus Cragius’ De Republica Lacedaemoniorum (1593) for evidence, and was attracted to some of the more apparently ‘aristocratic’ elements of the Spartan constitution. However, classical texts and modern scholarly authority, such as Cragius’, were not the only ingredients in the English version of the ‘classical republican’ tradition; sixteenth- and seventeenth-century political thinkers and current exigencies also shaped Harrington and Stubbe’s arguments. Both Harrington and Stubbe ended up challenging the scholarly and ancient consensus that Sparta was an aristocracy or mixed polity, Harrington reinterpreting it to assimilate it to ‘democracy’, and Stubbe attempting to rehabilitate a model of benign ‘oligarchy’.

Varieties of parliamentarianism

From the start of the English civil war, the parliamentarians were a fragmented coalition, held together by distrust of the king and a belief that Parliament was entitled to lead action to remedy his government’s deficiencies. The driving motivations of parliamentarians were various, including the religious commitments of puritanism, legalistic thought about the ancient constitution, and more radical notions of republicanism or natural rights. Historians have disputed whether parliamentarianism had an inherent strand of radicalism – or radical potential – from the early 1640s, but radicalization certainly took place as the civil wars went on, alongside more ‘conservative’ reactions against the propaganda and wartime measures employed by parliament. Parliamentarian radicalism itself was varied in character, embracing the Levellers’ populism, parliamentary absolutism, and millenarian and providentialist ideas.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

Upper limit on the cosmic-ray photon flux above 10(19) eV using the surface detector of the Pierre Auger Observatory

A method is developed to search for air showers initiated by photons using data recorded by the surface detector of the Auger Observatory. The approach is based on observables sensitive to the longitudinal shower development, the signal risetime and the curvature of the shower front. Applying this method to the data, tipper limits on the flux of photons of 3.8 x 10(-3), 2.5 x 10(-3), and 2.2 x 10(-3) km(-2) sr(-1) yr(-1) above 10(19) eV, 2 x 10(19) eV, and 4 x 10(19) eV are derived, with corresponding limits on the fraction of photons being 2.0%, 5.1%, and 31% (all limits at 95% c.l.). These photon limits disfavor certain exotic models of sources of cosmic rays. The results also show that the approach adopted by the Auger Observatory to calibrate the shower energy is not strongly biased by a contamination from photons. (C) 2008 Elsevier B.V. All rights reserved.

Correlation of the highest-energy cosmic rays with the positions of nearby active galactic nuclei

Data collected by the Pierre Auger Observatory provide evidence for anisotropy in the arrival directions of the cosmic rays with the highest-energies, which are correlated with the positions of relatively nearby active galactic nuclei (AGN) [Pierre Auger Collaboration, Science 318 (2007) 938]. The correlation has maximum significance for cosmic rays with energy greater than similar to 6 x 10(19) eV and AGN at a distance less than similar to 75 Mpc. We have confirmed the anisotropy at a confidence level of more than 99% through a test with parameters specified a priori, using an independent data set. The observed correlation is compatible with the hypothesis that cosmic rays with the highest-energies originate from extra-galactic sources close enough so that their flux is not significantly attenuated by interaction with the cosmic background radiation (the Greisen-Zatsepin-Kuz`min effect). The angular scale of the correlation observed is a few degrees, which suggests a predominantly light composition unless the magnetic fields are very weak outside the thin disk of our galaxy. Our present data do not identify AGN as the sources of cosmic rays unambiguously, and other candidate sources which are distributed as nearby AGN are not ruled out. We discuss the prospect of unequivocal identification of individual sources of the highest-energy cosmic rays within a few years of continued operation of the Pierre Auger Observatory. (C) 2008 Elsevier B.V. All rights reserved.

Advanced functionality for radio analysis in the Offline software framework of the Pierre Auger Observatory

The advent of the Auger Engineering Radio Array (AERA) necessitates the development of a powerful framework for the analysis of radio measurements of cosmic ray air showers. As AERA performs ""radio-hybrid"" measurements of air shower radio emission in coincidence with the surface particle detectors and fluorescence telescopes of the Pierre Auger Observatory, the radio analysis functionality had to be incorporated in the existing hybrid analysis solutions for fluorescence and surface detector data. This goal has been achieved in a natural way by extending the existing Auger Offline software framework with radio functionality. In this article, we lay out the design, highlights and features of the radio extension implemented in the Auger Offline framework. Its functionality has achieved a high degree of sophistication and offers advanced features such as vectorial reconstruction of the electric field, advanced signal processing algorithms, a transparent and efficient handling of FFTs, a very detailed simulation of detector effects, and the read-in of multiple data formats including data from various radio simulation codes. The source code of this radio functionality can be made available to interested parties on request. (C) 2011 Elsevier B.V. All rights reserved.

Trigger and aperture of the surface detector array of the Pierre Auger Observatory

The surface detector array of the Pierre Auger Observatory consists of 1600 water-Cherenkov detectors, for the study of extensive air showers (EAS) generated by ultra-high-energy cosmic rays. We describe the trigger hierarchy, from the identification of candidate showers at the level of a single detector, amongst a large background (mainly random single cosmic ray muons), up to the selection of real events and the rejection of random coincidences. Such trigger makes the surface detector array fully efficient for the detection of EAS with energy above 3 x 10(18) eV, for all zenith angles between 0 degrees and 60 degrees, independently of the position of the impact point and of the mass of the primary particle. In these range of energies and angles, the exposure of the surface array can be determined purely on the basis of the geometrical acceptance. (C) 2009 Elsevier B.V. All rights reserved.

Atmospheric effects on extensive air showers observed with the surface detector of the Pierre Auger observatory

Atmospheric parameters, Such as pressure (P), temperature (T) and density (rho proportional to P/T), affect the development of extensive air showers initiated by energetic cosmic rays. We have Studied the impact of atmospheric variations on extensive air showers by means of the surface detector of the Pierre Auger Observatory. The rate of events shows a similar to 10% seasonal modulation and similar to 2% diurnal one. We find that the observed behaviour is explained by a model including the effects associated with the variations of P and rho. The former affects the longitudinal development of air showers while the latter influences the Moliere radius and hence the lateral distribution of the shower particles. The model is validated with full simulations of extensive air showers using atmospheric profiles measured at the site of the Pierre Auger Observatory. (C) 2009 Elsevier B.V. All rights reserved.

Upper limit on the cosmic-ray photon fraction at EeV energies from the Pierre Auger Observatory

From direct observations of the longitudinal development of ultra-high energy air showers performed with the Pierre Auger Observatory, upper limits of 3.8%, 2.4%, 3.5% and 11.7% (at 95% c.l.) are obtained on the fraction of cosmic-ray photons above 2, 3, 5 and 10 EeV (1 EeV equivalent to 10(18) eV), respectively. These are the first experimental limits on ultra-high energy photons at energies below 10 EeV. The results complement previous constraints on top-down models from array data and they reduce systematic uncertainties in the interpretation of shower data in terms of primary flux, nuclear composition and proton-air cross-section. (C) 2009 Elsevier B.V. All rights reserved.

Anisotropy and chemical composition of ultra-high energy cosmic rays using arrival directions measured by the Pierre Auger Observatory

The Pierre Auger Collaboration has reported. evidence for anisotropy in the distribution of arrival directions of the cosmic rays with energies E > E(th) = 5.5 x 10(19) eV. These show a correlation with the distribution of nearby extragalactic objects, including an apparent excess around the direction of Centaurus A. If the particles responsible for these excesses at E > E(th) are heavy nuclei with charge Z, the proton component of the sources should lead to excesses in the same regions at energies E/Z. We here report the lack of anisotropies in these directions at energies above E(th)/Z (for illustrative values of Z = 6, 13, 26). If the anisotropies above E(th) are due to nuclei with charge Z, and under reasonable assumptions about the acceleration process, these observations imply stringent constraints on the allowed proton fraction at the lower energies.