Quantitative NME microscopy of iron transport in methanogenic aggregates

Transport of micronutrients (iron, cobalt, nickel, etc.) within biofilms matrixes such as methanogenic granules is of high importance, because these are either essential or toxic for the microorganisms living inside the biofilm. The present study demonstrates quantitative measurements of metal transport inside these biofilms using T1 weighted 3D RARE. It is shown that iron(II)-EDTA diffusion within the granule is independent of direction or the inner structure of the granules. Assuming position dependence of the spin-lattice relaxivity, Fick’s law for diffusion in a sphere can be applied to simulate the diffusion within the methanogenic granules under investigation. A relatively low diffusion coefficient of 2.5*10-11 m2·s-1 was obtained for iron diffusion within the methanogenic granul

Monitoring herpetofauna in a managed forest landscape: effects of habitat types and census techniques

We surveyed the herpetofaunal (amphibian and reptile) communities inhabiting five types of habitat on a managed landscape. We conducted monthly surveys during 1997 in four replicate plots of each habitat type using several different methods of collection. Communities of the two wetland habitats (bottomland wetlands and isolated upland wetlands) were clearly dissimilar from the three terrestrial communities (recent clearcut, pine plantation, and mixed pine–hardwood forest). Among the three terrestrial habitats, the total herpetofaunal communities were dissimilar (P\u3c0.10), although neither faunal constituent group alone (amphibians and squamate reptiles) varied significantly with regard to habitat. Three survey techniques used in the terrestrial habitats were not equally effective in that they resulted in the collection of different subsets of the total herpetofauna. The drift fence technique revealed the presence of more species and individuals in every habitat and was the only one to detect species dissimilarity among habitats. Nonetheless, coverboards contributed to measures of abundance and revealed species not detected by other techniques. We suggest that a combination of census techniques be used when surveying and monitoring herpetofaunal communities in order to maximize the detection of species

High-Temperature Quantum Tunneling and Hydrogen Bonding Rearrangements Characterize the Solid-Solid Phase Transitions in a Phosphonium-Based Protic Ionic Liquid

We report the complex phase behavior of the glass forming protic ionic liquid (PIL) d3-octylphosphonium bis(trifluoromethylsulfonyl)imide [C8H17PD3][NTf2] by means of solid-state NMR spectroscopy. Combined line shape and spin relaxation studies of the deuterons in the PD3 group of the octylphosphonium cation allow to map and correlate the phase behavior for a broad temperature range from 71 K to 343 K. In the solid PIL at 71 K, we observed a static state, characterized by the first deuteron quadrupole coupling constant reported for PD3 deuterons. A transition enthalpy of about 12 kJmol 1 from the static to the mobile state with increasing temperature suggests the breaking of a weak, charge-enhanced hydrogen bond between cation and anion. The highly mobile phase above 100 K exhibits an almost disappearing activation barrier, strongly indicating quantum tunneling. Thus, we provide first evidence of tunneling driven mobility of the hydrogen bonded P D moieties in the glassy state of PILs, already at surprisingly high temperatures up to 200 K. Above 250 K, the mobile phase turns from anisotropic to isotropic motion, and indicates strong internal rotation of the PD3 group. The analyzed line shapes and spin relaxation times allow us to link the structural and dynamical behavior at molecular level with the phase behavior beyond the DSC traces

Challenges in integrating Escherichia coli molecular biology data

One key challenge in Systems Biology is to provide mechanisms to collect and integrate the necessary data to be able to meet multiple analysis requirements. Typically, biological contents are scattered over multiple data sources and there is no easy way of comparing heterogeneous data contents. This work discusses ongoing standardisation and interoperability efforts and exposes integration challenges for the model organism Escherichia coli K-12. The goal is to analyse the major obstacles faced by integration processes, suggest ways to systematically identify them, and whenever possible, propose solutions or means to assistmanual curation. Integration of gene, protein and compound data was evaluated by performing comparisons over EcoCyc, KEGG, BRENDA, ChEBI, Entrez Gene and UniProt contents. Cross-links, a number of standard nomenclatures and name information supported the comparisons. Except for the gene integration scenario, in no other scenario an element of integration performed well enough to support the process by itself. Indeed, both the integration of enzyme and compound records imply considerable curation. Results evidenced that, even for a well-studied model organism, source contents are still far from being as standardized as it would be desired and metadata varies considerably from source to source. Before designing any data integration pipeline, researchers should decide on the sources that best fit the purpose of analysis and be aware of existing conflicts/inconsistencies to be able to intervene in their resolution. Moreover, they should be aware of the limits of automatic integration such that they can define the extent of necessary manual curation for each application.Portuguese FCT funded MIT-Portugal Program in Bioengineering (MIT-Pt/BS-BB/0082/2008); PhD grant from FCT (ref. SFRH/BD/22863/2005) to S.

PHI-base update: additions to the pathogen–host interaction database

The pathogen–host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/

Inovação urbana e recursos humanos para gestão de cidades sustentáveis

Este ensaio teórico, com base em literatura, reflexões, e práticas, tem como objetivo apresentar e discorrer sobre as principais contribuições resultantes do segundo seminário do Ciclo UrbanSus – Inovação, Sustentabilidade e Ação Sistêmica nas Cidades, em particular nos painéis sobre inovação urbana e capacitação de recursos humanos. O texto reforça a importância das abordagens multissetoriais, multiprofissionais e interdisciplinares para potencializar o uso de novas ideias, novas formas de gestão e novas tecnologias na direção da sustentabilidade urbana. Entre os principais desafios são destacados: a transferência de tecnologia e a educação computacional; a superação dos interesses econômicos de curto prazo, novos modelos para financiamento de soluções inteligentes; e para governança; métodos diagnósticos que aproveitem as massas de dados; e o fortalecimento das estratégias para difusão do conhecimento, incluindo o papel das universidades e dos cursos de pós-graduação.This theoretical essay, based on literature, reflections and practices, aims to present and discuss the main contributions from the second seminar of the UrbanSus Cycle – Innovation, Sustainability and Systemic Action in Cities, particularly in the panels on urban innovation and human resources enablement. The text stresses the importance of multisector, multiprofessional and interdisciplinary approaches to promote the use of new ideas, new forms of management and new technologies towards urban sustainability. Among the main challenges, the following are highlighted: technology transfer and computer education; overcoming short-term economic interests; new models to fund smart solutions and for governance; diagnostic methods that leverage large quantities of data; and the strengthening of strategies for knowledge sharing, including the role of universities and postgraduate courses

Data-driven campaigning and democratic disruption : evidence from six advanced democracies

Data-driven campaigning has become one of the key foci for academic and non-academic audiences interested in political communication. Widely seen to have transformed political practice, it is often argued that data-driven campaigning is a force of significant democratic disruption because it contributes to a fragmentation of political discourse, undermines prevailing systems of electoral accountability and subverts ‘free’ and ‘fair’ elections. In this article, we present one of the very first cross-national analyses of data-driven campaigning by political parties. Drawing on empirical research conducted by experts in six advanced democracies, we show that the data-driven campaign practices seen to threaten democracy are often not manifest in party campaigns. Instead, we see a set of practices that build on pre-existing techniques and which are far less sophisticated than is often assumed. Indeed, we present evidence that most political parties lack the capacity to execute the hyper-intensive practices often associated with data-driven campaigning. Hence, while there is reason to remain alert to the challenges data-driven campaigning produces for democratic norms, we argue that this practice is not inherently disruptive, but rather exemplifies the evolving nature of political campaigning in the 21st century

Grey and white matter correlates of recent and remote autobiographical memory retrieval:Insights from the dementias

The capacity to remember self-referential past events relies on the integrity of a distributed neural network. Controversy exists, however, regarding the involvement of specific brain structures for the retrieval of recently experienced versus more distant events. Here, we explored how characteristic patterns of atrophy in neurodegenerative disorders differentially disrupt remote versus recent autobiographical memory. Eleven behavioural-variant frontotemporal dementia, 10 semantic dementia, 15 Alzheimer's disease patients and 14 healthy older Controls completed the Autobiographical Interview. All patient groups displayed significant remote memory impairments relative to Controls. Similarly, recent period retrieval was significantly compromised in behavioural-variant frontotemporal dementia and Alzheimer's disease, yet semantic dementia patients scored in line with Controls. Voxel-based morphometry and diffusion tensor imaging analyses, for all participants combined, were conducted to investigate grey and white matter correlates of remote and recent autobiographical memory retrieval. Neural correlates common to both recent and remote time periods were identified, including the hippocampus, medial prefrontal, and frontopolar cortices, and the forceps minor and left hippocampal portion of the cingulum bundle. Regions exclusively implicated in each time period were also identified. The integrity of the anterior temporal cortices was related to the retrieval of remote memories, whereas the posterior cingulate cortex emerged as a structure significantly associated with recent autobiographical memory retrieval. This study represents the first investigation of the grey and white matter correlates of remote and recent autobiographical memory retrieval in neurodegenerative disorders. Our findings demonstrate the importance of core brain structures, including the medial prefrontal cortex and hippocampus, irrespective of time period, and point towards the contribution of discrete regions in mediating successful retrieval of distant versus recently experienced events

Contrasting prefrontal cortex contributions to episodic memory dysfunction in behavioural variant frontotemporal dementia and alzheimer's disease

Recent evidence has questioned the integrity of episodic memory in behavioural variant frontotemporal dementia (bvFTD), where recall performance is impaired to the same extent as in Alzheimer's disease (AD). While these deficits appear to be mediated by divergent patterns of brain atrophy, there is evidence to suggest that certain prefrontal regions are implicated across both patient groups. In this study we sought to further elucidate the dorsolateral (DLPFC) and ventromedial (VMPFC) prefrontal contributions to episodic memory impairment in bvFTD and AD. Performance on episodic memory tasks and neuropsychological measures typically tapping into either DLPFC or VMPFC functions was assessed in 22 bvFTD, 32 AD patients and 35 age- and education-matched controls. Behaviourally, patient groups did not differ on measures of episodic memory recall or DLPFC-mediated executive functions. BvFTD patients were significantly more impaired on measures of VMPFC-mediated executive functions. Composite measures of the recall, DLPFC and VMPFC task scores were covaried against the T1 MRI scans of all participants to identify regions of atrophy correlating with performance on these tasks. Imaging analysis showed that impaired recall performance is associated with divergent patterns of PFC atrophy in bvFTD and AD. Whereas in bvFTD, PFC atrophy covariates for recall encompassed both DLPFC and VMPFC regions, only the DLPFC was implicated in AD. Our results suggest that episodic memory deficits in bvFTD and AD are underpinned by divergent prefrontal mechanisms. Moreover, we argue that these differences are not adequately captured by existing neuropsychological measures