Model estimation of cerebral hemodynamics between blood flow and volume changes: A data-based modeling approach

It is well known that there is a dynamic relationship between cerebral blood flow (CBF) and cerebral blood volume (CBV). With increasing applications of functional MRI, where the blood oxygen-level-dependent signals are recorded, the understanding and accurate modeling of the hemodynamic relationship between CBF and CBV becomes increasingly important. This study presents an empirical and data-based modeling framework for model identification from CBF and CBV experimental data. It is shown that the relationship between the changes in CBF and CBV can be described using a parsimonious autoregressive with exogenous input model structure. It is observed that neither the ordinary least-squares (LS) method nor the classical total least-squares (TLS) method can produce accurate estimates from the original noisy CBF and CBV data. A regularized total least-squares (RTLS) method is thus introduced and extended to solve such an error-in-the-variables problem. Quantitative results show that the RTLS method works very well on the noisy CBF and CBV data. Finally, a combination of RTLS with a filtering method can lead to a parsimonious but very effective model that can characterize the relationship between the changes in CBF and CBV.

A model of the dynamic relationship between blood flow and volume changes during brain activation

The temporal relationship between changes in cerebral blood flow (CBF) and cerebral blood volume (CBV) is important in the biophysical modeling and interpretation of the hemodynamic response to activation, particularly in the context of magnetic resonance imaging and the blood oxygen level-dependent signal. Grubb et al. (1974) measured the steady state relationship between changes in CBV and CBF after hypercapnic challenge. The relationship CBV proportional to CBFPhi has been used extensively in the literature. Two similar models, the Balloon (Buxton et al., 1998) and the Windkessel (Mandeville et al., 1999), have been proposed to describe the temporal dynamics of changes in CBV with respect to changes in CBF. In this study, a dynamic model extending the Windkessel model by incorporating delayed compliance is presented. The extended model is better able to capture the dynamics of CBV changes after changes in CBF, particularly in the return-to-baseline stages of the response.

Estimating the volume of tephra deposits: a new simple strategy

Volume determination of tephra deposits is necessary for the assessment of the dynamics and hazards of explosive volcanoes. Several methods have been proposed during the past 40 years that include the analysis of crystal concentration of large pumices, integrations of various thinning relationships, and the inversion of field observations using analytical and computational models. Regardless of their strong dependence on tephra-deposit exposure and distribution of isomass/isopach contours, empirical integrations of deposit thinning trends still represent the most widely adopted strategy due to their practical and fast application. The most recent methods involve the best fitting of thinning data using various exponential seg- ments or a power-law curve on semilog plots of thickness (or mass/area) versus square root of isopach area. The exponential method is mainly sensitive to the number and the choice of straight segments, whereas the power-law method can better reproduce the natural thinning of tephra deposits but is strongly sensitive to the proximal or distal extreme of integration. We analyze a large data set of tephra deposits and propose a new empirical method for the deter- mination of tephra-deposit volumes that is based on the integration of the Weibull function. The new method shows a better agreement with observed data, reconciling the debate on the use of the exponential versus power-law method. In fact, the Weibull best fitting only depends on three free parameters, can well reproduce the gradual thinning of tephra deposits, and does not depend on the choice of arbitrary segments or of arbitrary extremes of integration.

Changes in light intensity can influence age at sexual maturity in domestic pullets

1. Shaver White and ISA Brown pullets were reared to 140 d in groups of 8 in cages on a 10-h photoperiod of incandescent light and maintained at an illuminance of 3 or 25 lux, or transferred from 3 to 25 lux or from 25 to 3 lux at 63 or 112 d of age. 2. There was no significant difference in sexual maturity, measured as eggs per 100 bird.d at 139 and 140 d, for ISA Brown maintained on 3 or 25 lux, but Shaver White pullets exposed to constant 3 lux matured significantly later than those maintained on 25 lux. 3. In Shaver Whites, sexual maturity was significantly delayed by an increase from 3 to 25 lux at 63 and 112 d, and advanced by a decrease from 25 to 3 lux at 112 d. Sexual maturity of ISA Browns was not significantly affected by a change in illuminance at 63 or 112 d, though responses were in the same direction as for Shaver Whites. 4. In both breeds, total feed consumed to 112 d was higher for birds on 3 lux than 25 lux, but lower between 112 d and 140 d when birds on 25 lux underwent rapid sexual development. In both breeds, body weight at 63 d was higher for birds exposed to 3 lux than 25 lux, but body weight gain thereafter was similar for the two light intensities. 5. In both breeds, plasma luteinising hormone (LH) concentration at 63 and 112 d was lower in birds maintained on 3 lux than 25 lux. At 63 and 112 d, transfers from 25 to 3 lux depressed, whereas transfers from 3 to 25 lux at 63 d, but not at 112 d, increased plasma LH. 6. Advances or delays in sexual maturity induced by changes in illuminance were not correlated with differences in feed intake, body weight gain, or with changes in plasma LH. 7. One possible explanation for the inverse relationship between the direction of change in illuminance at 63 and 112 d in pullets exposed to a 10-h photoperiod and the age at which they became sexually mature is that changes in light intensity and/or spectral composition affect the entrainment of the circadian rhythm of photoinducibility, to effect a phase shift in the photoinducible phase and/or the responsiveness of phototransduction pathways.

A model study of factors influencing projected changes in regional sea level over the 21st century

In addition to projected increases in global mean sea level over the 21st century, model simulations suggest there will also be changes in the regional distribution of sea level relative to the global mean. There is a considerable spread in the projected patterns of these changes by current models, as shown by the recent Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment (AR4). This spread has not reduced from that given by the Third Assessment models. Comparison with projections by ensembles of models based on a single structure supports an earlier suggestion that models of similar formulation give more similar patterns of sea level change. Analysing an AR4 ensemble of model projections under a business-as-usual scenario shows that steric changes (associated with subsurface ocean density changes) largely dominate the sea level pattern changes. The relative importance of subsurface temperature or salinity changes in contributing to this differs from region to region and, to an extent, from model-to-model. In general, thermosteric changes give the spatial variations in the Southern Ocean, halosteric changes dominate in the Arctic and strong compensation between thermosteric and halosteric changes characterises the Atlantic. The magnitude of sea level and component changes in the Atlantic appear to be linked to the amount of Atlantic meridional overturning circulation (MOC) weakening. When the MOC weakening is substantial, the Atlantic thermosteric patterns of change arise from a dominant role of ocean advective heat flux changes.

Detecting regular sound changes in linguistics as events of concerted evolution

Background: Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family. Results: Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular sound change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations. Conclusions: We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.

Perturbation growth at the convective scale for CSIP IOP18

The Met Office Unified Model is run for a case observed during Intensive Observation Period 18 (IOP18) of the Convective Storms Initiation Project (CSIP). The aims are to identify the physical processes that lead to perturbation growth at the convective scale in response to model-state perturbations and to determine their sensitivity to the character of the perturbations. The case is strongly upper-level forced but with detailed mesoscale/convective-scale evolution that is dependent on smaller-scale processes. Potential temperature is perturbed within the boundary layer. The effects on perturbation growth of both the amplitude and typical scalelength of the perturbations are investigated and perturbations are applied either sequentially (every 30 min throughout the simulation) or at specific times. The direct effects (within one timestep) of the perturbations are to generate propagating Lamb and acoustic waves and produce generally small changes in cloud parameters and convective instability. In exceptional cases a perturbation at a specific gridpoint leads to switching of the diagnosed boundary-layer type or discontinuous changes in convective instability, through the generation or removal of a lid. The indirect effects (during the entire simulation) are changes in the intensity and location of precipitation and in the cloud size distribution. Qualitatively different behaviour is found for strong (1K amplitude) and weak (0.01K amplitude) perturbations, with faster growth after sunrise found only for the weaker perturbations. However, the overall perturbation growth (as measured by the root-mean-square error of accumulated precipitation) reaches similar values at saturation, regardless of the perturbation characterisation.

Analysis and application of ichnofabrics

Bioturbation at all scales, which tends to replace the primary fabric of a sediment by the ichnofabric (the overall fabric of a sediment that has been bioturbated), is now recognised as playing a major role in facies interpretation. The manner in which the substrate may be colonized, and the physical, chemical and ecological controls (grainsize, sedimentation rate, oxygenation, nutrition, salinity, ethology, community structure and succession), together with the several ways in which the substrate is tiered by bioturbators, are the factors and processes that determine the nature of the ichnofabric. Eleven main styles of substrate tiering are described, ranging from single, pioneer colonization to complex tiering under equilibria, their modification under environmental deterioration and amelioration, and diagenetic enhancement or obscuration. Ichnofabrics may be assessed by four attributes: primary sedimentary factors, Bioturbation Index (BI), burrow size and frequency, and ichnological diversity. Construction of tier and ichnofabric constituent diagrams aid visualization and comparison. The breaks or changes in colonization and style of tiering at key stratal surfaces accentuate the surfaces, and many reflect a major environmental shift of the trace-forming biota. due to change in hydrodynamic regime (leading to non-deposition and/or erosion and/or lithification), change in salinity regime, or subaerial exposure. The succession of gradational or abrupt changes in ichnofabric through genetically related successions, together with changes in colonization and tiering across event beds, may also be interpreted in terms of changes in environmental parameters. It is not the ichnotaxa per se that are important in discriminating between ichnofabrics, but rather the environmental conditions that determine the overall style of colonization. Fabrics composed of different ichnotaxa (and different taphonomies) but similar tier structure and ichnoguild may form in similar environments of different age or different latitude. Appreciation of colonization and tiering styles places ancient ichnofabrics on a sound processrelated basis for environmental interpretation. (C) 2002 Elsevier Science B.V. All rights reserved.

Intentions of UK farmers toward biofuel crop production: Implications for policy targets and land use change

The United States and the European Union have set targets for biofuel production to decrease reliance on fossil fuels and to reduce fossil carbon emissions. Attainment of biofuel targets d6pends upon policy and infrastructure development but also on production of suitable raw materials. Production of relevant crops relies on the decisions that farmers make in their economic and political environment. We need to identify any farmer-related barriers to biofuel production and to determine whether novel policy and technology are required to meet targets. These aspects of the emerging biofuel industry are relevant across international barriers and have notyet been addressed quantitatively. We describe a case study from the UK of farmers' intentions toward producing two biofuel crops for which refining capacity either exists or is under construction. Given farmers' intentions, current land use, and conversion efficiency, we estimate potential biofuel production. These estimates indicate that EU targets are not achievable using domestically grown raw materials without policy intervention, use of alternative feedstocks, and either significant improvements in processing efficiency or largescale changes in land use.

Nitrogen processes in aquatic ecosystems

Executive summary Nature of the problem (science/management/policy) • Freshwater ecosystems play a key role in the European nitrogen (N) cycle, both as a reactive agent that transfers, stores and processes N loadings from the atmosphere and terrestrial ecosystems, and as a natural environment severely impacted by the increase of these loadings. Approaches • This chapter is a review of major processes and factors controlling N transport and transformations for running waters, standing waters, groundwaters and riparian wetlands. Key findings/state of knowledge • The major factor controlling N processes in freshwater ecosystems is the residence time of water, which varies widely both in space and in time, and which is sensitive to changes in climate, land use and management. • The effects of increased N loadings to European freshwaters include acidification in semi-natural environments, and eutrophication in more disturbed ecosystems, with associated loss of biodiversity in both cases. • An important part of the nitrogen transferred by surface waters is in the form of organic N, as dissolved organic N (DON) and particulate organic N (PON). This part is dominant in semi-natural catchments throughout Europe and remains a significant component of the total N load even in nitrate enriched rivers. • In eutrophicated standing freshwaters N can be a factor limiting or co-limiting biological production, and control of both N and phosphorus (P) loading is oft en needed in impacted areas, if ecological quality is to be restored. Major uncertainties/challenges • The importance of storage and denitrifi cation in aquifers is a major uncertainty in the global N cycle, and controls in part the response of catchments to land use or management changes. In some aquifers, the increase of N concentrations will continue for decades even if efficient mitigation measures are implemented now. • Nitrate retention by riparian wetlands has oft en been highlighted. However, their use for mitigation must be treated with caution, since their effectiveness is difficult to predict, and side effects include increased DON emissions to adjacent open waters, N2O emissions to the atmosphere, and loss of biodiversity. • In fact, the character and specific spatial origins of DON are not fully understood, and similarly the quantitative importance of indirect N2O emissions from freshwater ecosystems as a result of N leaching losses from agricultural soils is still poorly known at the regional scale. • These major uncertainties remain due to the lack of adequate monitoring (all forms of N at a relevant frequency), especially – but not only – in the southern and eastern EU countries. Recommendations (research/policy) • The great variability of transfer pathways, buffering capacity and sensitivity of the catchments and of the freshwater ecosystems calls for site specific mitigation measures rather than standard ones applied at regional to national scale. • The spatial and temporal variations of the N forms, the processes controlling the transport and transformation of N within freshwaters, require further investigation if the role of N in influencing freshwater ecosystem health is to be better understood, underpinning the implementation of the EU Water Framework Directive for European freshwaters.

A novel study of the polymerisation process involved in the formation of the network component of polymer-stabilised liquid crystals within electro-optic cells using high performance liquid chromatography

Polymer-stabilised liquid crystals are systems in which a small amount of monomer is dissolved within a liquid crystalline host, and then polymerised in situ to produce a network. The progress of the polymerisation, performed within electro-optic cells, was studied by establishing an analytical method novel to these systems. Samples were prepared by photopolymerisation of the monomer under well-defined reaction conditions; subsequent immersion in acetone caused the host and any unreacted monomer to dissolve. High performance liquid chromatography was used to separate and detect the various solutes in the resulting solutions, enabling the amount of unreacted monomer for a given set of conditions to be quantified. Longer irradiations cause a decrease in the proportion of unreacted monomer since more network is formed, while a more uniform LC director alignment (achieved by decreasing the sample thickness) or a higher level of order (achieved by decreasing the polymerisation temperature) promotes faster reactions.

Pedosedimentary, cultural and environmental significance of palaeosols within Pre-Hispanic agricultural terraces in the southern Peruvian Andes

Paleosols were exposed in sections through four abandoned pre-Hispanic agricultural terraces surrounding an infilled mire basin in the southern Peruvian Andes. The two paleosols beneath the Tocotoccasa terrace represent the original ‘natural’ solum and a later soil formed after construction of the agricultural terrace, probably during the early Middle Horizon cultural period (615–695 AD). The soil at the current surface developed subsequent to the building up and reconstruction of the terrace, possibly during the late Late Intermediate period (1200–1400 AD). Micromorphology revealed an unexpected abundance of clay coatings within the upper terrace paleosol and surface terrace soil, a phenonemon attributed to the migration and/or accumulation of neoformed clay produced from the weathering of very unstable volcanic clasts, perhaps fuelled by arid/humid climatic oscillations and/or seasonal input of irrigation waters. The paleosols at Tocotoccasa could not be correlated with any degree of confidence with those beneath the other three terraces due to differences in pedosedimentary properties and uncertainties over chronological controls. Thus, it seems likely that either the terraces were (re)constructed and utilised over different cultural periods or that there is significant variation in the extent of weathering of material used for reconstruction of the terraces. Unfortunately, it cannot be ascertained from the data available whether the terraces were abandoned for any significant period of time prior to reconstruction and, if so, whether this was a regional phenomenon related to climate, social, or economic changes.

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

Whole-genome sequencing offers new insights into the evolution of bacterial pathogens and the etiology of bacterial disease. Staph- ylococcus aureus is a major cause of bacteria-associated mortality and invasive disease and is carried asymptomatically by 27% of adults. Eighty percent of bacteremias match the carried strain. How- ever, the role of evolutionary change in the pathogen during the progression from carriage to disease is incompletely understood. Here we use high-throughput genome sequencing to discover the genetic changes that accompany the transition from nasal carriage to fatal bloodstream infection in an individual colonized with meth- icillin-sensitive S. aureus. We found a single, cohesive population exhibiting a repertoire of 30 single-nucleotide polymorphisms and four insertion/deletion variants. Mutations accumulated at a steady rate over a 13-mo period, except for a cluster of mutations preceding the transition to disease. Although bloodstream bacteria differed by just eight mutations from the original nasally carried bacteria, half of those mutations caused truncation of proteins, including a prema- ture stop codon in an AraC-family transcriptional regulator that has been implicated in pathogenicity. Comparison with evolution in two asymptomatic carriers supported the conclusion that clusters of pro- tein-truncating mutations are highly unusual. Our results demon- strate that bacterial diversity in vivo is limited but nonetheless detectable by whole-genome sequencing, enabling the study of evolutionary dynamics within the host. Regulatory or structural changes that occur during carriage may be functionally important for pathogenesis; therefore identifying those changes is a crucial step in understanding the biological causes of invasive bacterial disease.

Physically consistent responses of the global atmospheric hydrological cycle in models and observations

Robust and physically understandable responses of the global atmospheric water cycle to a warming climate are presented. By considering interannual responses to changes in surface temperature (T), observations and AMIP5 simulations agree on an increase in column integrated water vapor at the rate 7 %/K (in line with the Clausius­Clapeyron equation) and of precipitation at the rate 2-­3 %/K (in line with energetic constraints). Using simple and complex climate models, we demonstrate that radiative forcing by greenhouse gases is currently suppressing global precipitation (P) at ~ -0.15 %/decade. Along with natural variability, this can explain why observed trends in global P over the period 1988-2008 are close to zero. Regional responses in the global water cycle are strongly constrained by changes in moisture fluxes. Model simulations show an increased moisture flux into the tropical wet region at 900 hPa and an enhanced outflow (of smaller magnitude) at around 600 hPa with warming. Moisture transport explains an increase in P in the wet tropical regions and small or negative changes in the dry regions of the subtropics in CMIP5 simulations of a warming climate. For AMIP5 simulations and satellite observations, the heaviest 5-day rainfall totals increase in intensity at ~15 %/K over the ocean with reductions at all percentiles over land. The climate change response in CMIP5 simulations shows consistent increases in P over ocean and land for the highest intensities, close to the Clausius-Clapeyron scaling of 7 %/K, while P declines for the lowest percentiles, indicating that interannual variability over land may not be a good proxy for climate change. The local changes in precipitation and its extremes are highly dependent upon small shifts in the large-scale atmospheric circulation and regional feedbacks.