CWRML: representing crop wild relative conservation and use data in XML

Background Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange. Results Crop Wild Relative Markup Language (CWRML) was developed to represent the data necessary for crop wild relative conservation and ensure that they can be effectively utilised for crop improvement. The schema partitions data into taxon-, site-, and population-specific elements, to allow for integration with other more general conservation biology schemata which may emerge as accepted standards in the future. These elements are composed of sub-elements, which are structured in order to facilitate the use of the schema in a variety of crop wild relative conservation and use contexts. Pre-existing standards for data representation in conservation biology were reviewed and incorporated into the schema as restrictions on element data contents, where appropriate. Conclusion CWRML provides a flexible data communication format for representing in situ and ex situ conservation status of individual taxa as well as their utilisation potential. The development of the schema highlights a number of instances where additional standards-development may be valuable, particularly with regard to the representation of population-specific data and utilisation potential. As crop wild relatives are intrinsically no different to other wild plant species there is potential for the inclusion of CWRML data elements in the emerging standards for representation of biodiversity data

Representation of Markov chains by random maps: existence and regularity conditions

We systematically investigate the problem of representing Markov chains by families of random maps, and which regularity of these maps can be achieved depending on the properties of the probability measures. Our key idea is to use techniques from optimal transport to select optimal such maps. Optimal transport theory also tells us how convexity properties of the supports of the measures translate into regularity properties of the maps via Legendre transforms. Thus, from this scheme, we cannot only deduce the representation by measurable random maps, but we can also obtain conditions for the representation by continuous random maps. Finally, we present conditions for the representation of Markov chain by random diffeomorphisms.Comment: 22 pages, several changes from the previous version including extended discussion of many detail

Long-Term Treatment with Extended-Release Carbidopa– Levodopa (IPX066) in Early and Advanced Parkinson’s Disease: A 9-Month Open-Label Extension Trial

Background and Objective IPX066 is a multiparticulate extended-release formulation of carbidopa–levodopa, designed to produce prolonged therapeutic levodopa plasma concentrations. This 9-month open-label extension study assessed its long-term safety and clinical utility in early and advanced Parkinson’s disease (PD). Methods Participants were enrolled from two phase III IPX066 studies and one open-label phase II study. Early PD patients were titrated to an appropriate dosing regimen while advanced patients started with regimens established in the antecedent studies. Adjustment was allowed throughout the extension. Clinical utility measures included the Unified Parkinson’s Disease Rating Scale (UPDRS) and Patient Global Impression (PGI) ratings. Results Among 268 early PD patients, 53.4 % reported adverse events (AEs) and 1.1 % (three patients) discontinued due to AEs; the most frequent AEs were nausea (5.6 %) and insomnia (5.6 %). Among 349 advanced patients, 60.2 % reported AEs and 3.7 % (13 patients) discontinued due to AEs; the most frequent AEs were dyskinesia (6.9 %) and fall (6.6 %). At month 9 (or early termination), 78.3 % of early patients were taking IPX066 three times daily (median: 720 mg/day) and 87.7 % of advanced patients were taking IPX066 three or four times daily (median: 1450 mg/day). Adjusting for 70 % bioavailability relative to immediate-release (IR) carbidopa–levodopa, the median dosages correspond to *500 and *1015 mg/day of IR levodopa in early and advanced PD, respectively. Based on the plasma profiles previously observed in PD patients, the IPX066 regimens in the extension can be estimated to provide a levodopa Cmax (maximum plasma drug concentration) similar to or lower than that provided by IR regimens during the antecedent trials. UPDRS and PGI findings showed sustained treatment effects throughout the extension. Conclusion During 9 months of extended use, IPX066 exhibited a safety/tolerability profile consistent with dopaminergic PD therapy

Towards understanding the myometrial physiome: approaches for the construction of a virtual physiological uterus

Premature labour (PTL) is the single most significant factor contributing to neonatal morbidity in Europe with enormous attendant healthcare and social costs. Consequently, it remains a major challenge to alleviate the cause and impact of this condition. Our ability to improve the diagnosis and treatment of women most at risk of PTL is, however, actually hampered by an incomplete understanding of the ways in which the functions of the uterine myocyte are integrated to effect an appropriate biological response at the multicellular whole organ system. The level of organization required to co-ordinate labouring uterine contractile effort in time and space can be considered immense. There is a multitude of what might be considered mini-systems involved, each with their own regulatory feedback cycles, yet they each, in turn, will influence the behaviour of a related system. These include, but are not exclusive to, gestational-dependent regulation of transcription, translation, post-translational modifications, intracellular signaling dynamics, cell morphology, intercellular communication and tissue level morphology. We propose that in order to comprehend how these mini-systems integrate to facilitate uterine contraction during labour (preterm or term) we must, in concert with biological experimentation, construct detailed mathematical descriptions of our findings. This serves three purposes: firstly, providing a quantitative description of series of complex observations; secondly, proferring a database platform that informs further testable experimentation; thirdly, advancing towards the establishment of a virtual physiological uterus and in silico clinical diagnosis and treatment of PTL

Long-term treatment with extended-release carbidopa-levodopa (IPX066) in early and advanced Parkinson's Disease : a 9-month open-label extension trial

Background and Objective IPX066 is a multiparticulate extended-release formulation of carbidopa–levodopa, designed to produce prolonged therapeutic levodopa plasma concentrations. This 9-month open-label extension study assessed its long-term safety and clinical utility in early and advanced Parkinson’s disease (PD). Methods Participants were enrolled from two phase III IPX066 studies and one open-label phase II study. Early PD patients were titrated to an appropriate dosing regimen while advanced patients started with regimens established in the antecedent studies. Adjustment was allowed throughout the extension. Clinical utility measures included the Unified Parkinson’s Disease Rating Scale (UPDRS) and Patient Global Impression (PGI) ratings. Results Among 268 early PD patients, 53.4 % reported adverse events (AEs) and 1.1 % (three patients) discontinued due to AEs; the most frequent AEs were nausea (5.6 %) and insomnia (5.6 %). Among 349 advanced patients, 60.2 % reported AEs and 3.7 % (13 patients) discontinued due to AEs; the most frequent AEs were dyskinesia (6.9 %) and fall (6.6 %). At month 9 (or early termination), 78.3 % of early patients were taking IPX066 three times daily (median: 720 mg/day) and 87.7 % of advanced patients were taking IPX066 three or four times daily (median: 1450 mg/day). Adjusting for 70 % bioavailability relative to immediate-release (IR) carbidopa–levodopa, the median dosages correspond to *500 and *1015 mg/day of IR levodopa in early and advanced PD, respectively. Based on the plasma profiles previously observed in PD patients, the IPX066 regimens in the extension can be estimated to provide a levodopa Cmax (maximum plasma drug concentration) similar to or lower than that provided by IR regimens during the antecedent trials. UPDRS and PGI findings showed sustained treatment effects throughout the extension. Conclusion During 9 months of extended use, IPX066 exhibited a safety/tolerability profile consistent with dopaminergic PD therapy

Large-scale sequestration of atmospheric carbon via plant roots in natural and agricultural ecosystems: why and how

The soil holds twice as much carbon as does the atmosphere, and most soil carbon is derived from recent photosynthesis that takes carbon into root structures and further into below-ground storage via exudates therefrom. Nonetheless, many natural and most agricultural crops have roots that extend only to about 1 m below ground. What determines the lifetime of below-ground C in various forms is not well understood, and understanding these processes is therefore key to optimising them for enhanced C sequestration. Most soils (and especially subsoils) are very far from being saturated with organic carbon, and calculations show that the amounts of C that might further be sequestered (http://dbkgroup.org/carbonsequestration/rootsystem.html) are actually very great. Breeding crops with desirable below-ground C sequestration traits, and exploiting attendant agronomic practices optimised for individual species in their relevant environments, are therefore important goals. These bring additional benefits related to improvements in soil structure and in the usage of other nutrients and water

Multiscale modelling of ceramic nanoparticle interactions and their influence on the thermal conductivity of nanofluids

There is currently a lack of a reliable theory capable of making accurate predictions of the thermal enhancement in nanofluids (with relatively low solid volume fractions). The work described therefore assesses the thermal conductivity of nanoparticle suspensions in fluids using a Lagrangian particle tracking-based computational modelling technique. A 3D, multiphase fluid-solid model is developed which predicts the motion of suspended nanoparticles. The nanofluid is predicted using an Eulerian-Lagrangian hybrid approach with a constant timestep. This technique takes various multiscale forces into consideration in the calculations, whose characteristic scales are quite different, providing for the first time an analysis of all factors affecting the stability and thermal conductivity of nanofluids. The system considered consists of 71 nm diameter Al2O3 ceramic nanoparticles suspended in water, with homogeneous temperature distributions ranging from 25 °C to 85 °C, at various volume fractions between 1% and 5%. The results of the simulations demonstrate the effectiveness of the presented technique, with predictions elucidating the role of Brownian motion, fluid viscous drag, inter-particle collisions and DLVO attraction and repulsion forces on nanofluid stability. Results indicate that aggregated nanoparticles formed in the suspensions, at various particle concentrations, play an important role in the thermal behaviour of the nanofluids. Predictions are in agreement with theoretical and experimental results obtained in related studies. The thermal characteristics of nanofluids are also considered as a function of temperature, system chemistry and time (measured from an initially homogeneously dispersed state). The proven enhancement in the conductivity of fluids affected by the addition of nanoparticles has great potential to assist the development of commercial nanofluid technology aimed at energy efficient and sustainable processes

Hemispheric asymmetry of endogenous neural oscillations in young children: implications for hearing speech in noise

Speech signals contain information in hierarchical time scales, ranging from short-duration (e.g., phonemes) to long-duration cues (e.g., syllables, prosody). A theoretical framework to understand how the brain processes this hierarchy suggests that hemispheric lateralization enables specialized tracking of acoustic cues at different time scales, with the left and right hemispheres sampling at short (25 ms; 40 Hz) and long (200 ms; 5 Hz) periods, respectively. In adults, both speech-evoked and endogenous cortical rhythms are asymmetrical: low-frequency rhythms predominate in right auditory cortex, and high-frequency rhythms in left auditory cortex. It is unknown, however, whether endogenous resting state oscillations are similarly lateralized in children. We investigated cortical oscillations in children (3–5 years; N = 65) at rest and tested our hypotheses that this temporal asymmetry is evident early in life and facilitates recognition of speech in noise. We found a systematic pattern of increasing leftward asymmetry for higher frequency oscillations; this pattern was more pronounced in children who better perceived words in noise. The observed connection between left-biased cortical oscillations in phoneme-relevant frequencies and speech-in-noise perception suggests hemispheric specialization of endogenous oscillatory activity may support speech processing in challenging listening environments, and that this infrastructure is present during early childhood

Analysis of landrace cultivation in Europe: A means to support in situ conservation of crop diversity

During the last century, the progressive substitution of landraces with modern, high yielding varieties, led to a dramatic reduction of in situ conserved crop diversity in Europe. Nowadays there is limited and scattered information on where landraces are cultivated. To fill this gap and lay the groundwork for a regional landrace in situ conservation strategy, information on more than 19,335 geo-referenced landrace cultivation sites were collated from 14 European countries. According to collected data, landraces of 141 herbaceous and 48 tree species are cultivated across Europe: Italy (107 species), Greece (93), Portugal (45) and Spain (44) hold the highest numbers. Common bean, onion, tomato, potato and apple are the species of main interest in the covered countries. As from collected data, about 19.8% of landrace cultivation sites are in protected areas of the Natura 2000 network. We also got evidence that 16.7% and 19.3% of conservation varieties of agricultural species and vegetables are currently cultivated, respectively. Results of the GIS analysis allowed the identification of 1261 cells (25 km × 25 km) including all the cultivation sites, distributed across all European biogeographical regions. Data of this study constitute the largest ever produced database of in situ-maintained landraces and the first attempt to create an inventory for the entire Europe. The availability of such resource will serve for better planning of actions and development of policies to protect landraces and foster their use