Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices.

Agitation conditions for the culture and detachment of hMSCs from microcarriers in multiple bioreactor platforms

In our recent work in different bioreactors up to 2.5L in scale, we have successfully cultured hMSCs using the minimum agitator speed required for complete microcarrier suspension, N JS. In addition, we also reported a scaleable protocol for the detachment from microcarriers in spinner flasks of hMSCs from two donors. The essence of the protocol is the use of a short period of intense agitation in the presence of enzymes such that the cells are detached; but once detachment is achieved, the cells are smaller than the Kolmogorov scale of turbulence and hence not damaged. Here, the same approach has been effective for culture at N JS and detachment in-situ in 15mL ambr™ bioreactors, 100mL spinner flasks and 250mL Dasgip bioreactors. In these experiments, cells from four different donors were used along with two types of microcarrier with and without surface coatings (two types), four different enzymes and three different growth media (with and without serum), a total of 22 different combinations. In all cases after detachment, the cells were shown to retain their desired quality attributes and were able to proliferate. This agitation strategy with respect to culture and harvest therefore offers a sound basis for a wide range of scales of operation.

Interaction of Kelvin waves and nonlocality of energy transfer in superfluids

We argue that the physics of interacting Kelvin Waves (KWs) is highly nontrivial and cannot be understood on the basis of pure dimensional reasoning. A consistent theory of KW turbulence in superfluids should be based upon explicit knowledge of their interactions. To achieve this, we present a detailed calculation and comprehensive analysis of the interaction coefficients for KW turbuelence, thereby, resolving previous mistakes stemming from unaccounted contributions. As a first application of this analysis, we derive a local nonlinear (partial differential) equation. This equation is much simpler for analysis and numerical simulations of KWs than the Biot-Savart equation, and in contrast to the completely integrable local induction approximation (in which the energy exchange between KWs is absent), describes the nonlinear dynamics of KWs. Second, we show that the previously suggested Kozik-Svistunov energy spectrum for KWs, which has often been used in the analysis of experimental and numerical data in superfluid turbulence, is irrelevant, because it is based upon an erroneous assumption of the locality of the energy transfer through scales. Moreover, we demonstrate the weak nonlocality of the inverse cascade spectrum with a constant particle-number flux and find resulting logarithmic corrections to this spectrum.

Fiscal adjustment and economic growth in the European Union

The current world economic crisis induced countries to launch wide-scale spending programmes all over the world. Member states of the European Union have not been an exception to this trend. While deficit spending may increase the aggregate demand, it can also accelerate indebtedness and make the required spending cuts politically risky later on. However, deficit financing is not a new phenomenon in the EU; it has been widely practiced in the last couple of decades. As the crisis seems to come to an end, countries with huge deficits should adopt exit strategies now, thereby reducing deficit and debt and reintroducing fiscal discipline, a requirement laid down in the Stability and Growth Pact. Nevertheless, former adjustment processes can provide ample evidence for successful and politically viable fiscal consolidations. In certain cases, even economic activity started to accelerate as a response to the welldesigned adjustment measures. Based on the previous experiences of EU states, the aim of this paper is, therefore, to identify the conditions that may determine a fiscal consolidation to be successful in terms of a reduced debt ratio and a positive economic growth.

A tranzakciós költségek és a szabványosítás kapcsolata (Relationship between transaction costs and standardization)

Az elmúlt néhány évtizedben a szabványosítás terén igen komoly változások mentek végbe. Ugrásszerűen megnőtt a szabványok száma, és jelentősen átalakult a szabványosítás folyamata is. Ezzel párhuzamosan a téma gazdasági hatásaival foglalkozó kutatások száma is megsokszorozódott, ami elsősorban a hálózati externáliák irodalmának robbanásszerű gyarapodásának köszönhető. Jelen tanulmány – az elméletek fősodrától eltérően – a tranzakciós költségek elméletében (TKE) helyezi el a szabványosítást. A szabványok és a tranzakciós költségek kapcsolatáról már születtek korábban is tanulmányok, de ezek a szabványoknak a tranzakciós költségekre gyakorolt hatásaira fókuszáltak. A tanulmány ezzel szemben arra helyezi a hangsúlyt, hogy azonosítsa a tranzakciós költségeknek a szabványosításra gyakorolt hatásait. A kutatás célja, hogy olyan elméleti alapot adjon, amelyben a témakör átfogóan elemezhető. A fő kutatási kérdés az, hogy mitől függ az, hogy melyik mechanizmus kereteiben érdemes a szabványosítást lebonyolítani. ________ Significant changes have characterized the last few decades of standardization. The number of standards has dramatically increased and processes of standardization have also changed a lot. At the same time the amount of researches that are concerned with the economic impact of standardization has also multiplied due to the boom in the literature of network externalities. Unlike the mainstream, this paper places standardization in the theory of transaction cost economics. Although there are earlier papers that are concerned with the relationship between standards and transaction costs, these studies focus on the impact of standards on transaction costs. In contrast, this paper lays emphasis on the identification of the impact of transaction costs on standardization. This study aims to provide a theoretical basis for the comprehensive analyses. The main research question: What determines which coordination mechanism is used to evolve a standard?

Patterns and Drivers of the Agri-Food Intra-Industry Trade of European Union Countries

This paper investigates the drivers of agri-food intra-industry trade (IIT) indices in the European Union (EU-27) member states during the period from 2000–2011. The increased proportion of IIT in matched two-way agri-food trade of the EU-27 member states is consistent with economic integration and economic growth. When export prices were at least 15% higher than the import prices, high-vertical IIT, increased for most member states. This finding suggests that quality improvements occurred when comparing agri-food exports to similar imports of agri-food products. The IIT indices for both horizontal and vertical IIT are positively associated with higher economic development levels, new EU membership and EU enlargement. Additionally, as higher levels of economic development decreases, the size of the economy and marginal IIT increases the effects of agri-food trade liberalization on the costs of the labor market adjustment. Understanding how improvements in agri-food trade quality impact agribusiness and managerial competitiveness reveal significant policy implications.

Structural adjustment and labor in Jamaica and the Dominican Republic

Statement of the problem. It seeks to examine whether structural adjustment in Jamaica produced the desired developmental effects for labor--both organized and non-unionized--and if there is any significant difference in the Dominican Republic, which did not undergo that economic transformation. The research hypothesis is; "Structural Adjustment leads to Marginalization of labor."^ Methodology used. The methodology is mostly a straight cross-sectional analysis using data sets and publications from the UN, ILO, World Bank and IDB, as well as local statistical sources. The dissertation is primarily an historical to contemporary analysis of the Jamaican experience under structural adjustment, as it related to labor. To a greater extent it involves a straight cross-national comparison on the historical experiences of each country and a discussion of the relative similarities and differences between them, and the impact these features had on labor.^ Summary of findings. In the end, the question is asked as to whether internal factors are important in the relative success or failure of development strategies. From the data there is some indication that under structural adjustment there has been limited economic benefits for labor in Jamaica while labor standards have not improved. In the Dominican Republic the economic performance has been similar but the labor standards have improved significantly. This thus leads to the conclusion that structural adjustment may have been a factor in the resistance to labor's empowerment.^ Nevertheless, the study also shows that there may have been a causal role which local power relations had. The suggestion from the study is that in analyzing the phenomenon, attention must be paid to internal as well as external dynamics and variables. ^

The acceptability and utility of voir dire questionnaires in Florida Circuit Civil Court

This study examined the acceptability and utility of the content of an extensive automobile tort voir dire questionnaire in Florida Circuit Civil Court. The ultimate purpose was to find questionnaire items from established measures that have demonstrated utility in uncovering biases that were at the same time not objectionable to the courts. The survey instrument included a venireperson questionnaire that used case-specific attitudinal and personality measures as well as typical information asked about personal history. The venireperson questionnaire incorporated measures that have proven reliable in other personal injury studies (Hans, & Lofquist, 1994). In order to examine judges' ratings, the questionnaire items were grouped into eight categories. Claims Consciousness scale measures general attitudes towards making claims based on one's legal rights. Belief in a Just World measures how sympathetic the juror would be to people who have suffered injuries. Political Efficacy is another general attitude scale that identifies attitudes towards the government. Litigation Crisis scales elicits attitudes about civil litigation. Case Specific Beliefs about Automobile Accidents and Litigation were taken from questionnaires developed and used in auto torts and other personal injury cases. Juror's personal history was divided into Demographics and Trial Relevant Attitudes. Ninety-seven circuit civil judges critiqued the questionnaire for acceptability, relevance to the type of case presented, and usefulness to attorneys for determining peremptories. ^ The majority of judges' responses confirmed that the central dimension in judicial thinking is juror qualification rather than juror partiality. Only three of the eight voir dire categories were considered relevant by more than 50 percent of the judges: Trial Relevant Experiences, Juror Demographics, and Tort Reform. Additionally, several acceptable items from generally disapproved categories were identified among the responses. These were general and case specific attitudinal items that are related to tort reform. We discuss the utility of voir dire items for discerning juror partiality. ^

Teacher-student relationships and the link to academic adjustment and emotional well-being in early adolescence

The role of support from teachers on the academic and emotional adjustment of a ethnically and economically diverse sample of adolescents was examined. Analyses were conducted on data from a larger study examining social networks across the transition to junior high school. Participants in the current study included 694 African-American, Hispanic-American and European-American students in grades 6 and 8 from public elementary schools in South Florida. Some of these schools are located in economically distressed areas and some are in middle income areas. Children were interviewed, and information on teacher social support resources, school stressors, risk and academic and emotional adjustment was obtained. Several significant findings emerged from the analyses. First, overall teacher support was a significant predictor of a wide range of academic and emotional adjustment outcomes. Second, teacher support compensated for low peer support on teacher rated behavior problems. Third, teacher support interacted with school stress to predict depressed affect and self esteem. Fourth, teacher support interacted with low ecological risk conditions to predict feelings of loneliness. ^

Distribution and ecology of amphibians and reptiles in a fragmented landscape, northeastern Bolivia

Habitat loss and fragmentation have been implicated as driving forces behind recent waves of extinction. The regional landscape where this study occurred is a mosaic of forest and grassland, and therefore provides an ideal system with which to investigate the implications of habitat patchiness for the distribution and ecology of organisms. Here I describe patterns of amphibian and reptile distribution among and within habitats at the study site, investigate associations between habitat and community structure, describe nested subset patterns on forest islands, and quantify the relationship between body size and density across ecological scales and taxonomic groups. ^ Species richness did not vary across habitats, between forest island isolation classes or between island edges and cores. In contrast, species composition varied at all three ecological scales, reflecting differences in the distribution of both forest and open-habitat affiliated species. Species composition was associated with multivariate habitat profiles, with differences occurring along the isolation gradient of forest islands rather than the area gradient. The relationship between species composition and habitat was stronger for amphibians than for reptiles, a pattern that may be ascribed to physiological differences between the two groups. Analysis of nested subset pattern of community structure indicated that species composition of islands is nested as a function of isolation. Four species whose distribution on forest islands seems to be dispersal-limited drive the relationship between nestedness and isolation. Although there were several examples of shifts in body size across spatial scales and taxonomic groups, body size was not associated with density as predicted by theory, which may reflect differences between real and habitat islands, or differential responses of poikilothermic vertebrates to changes in density relative to homeotherms. ^ Taken together, the strongest result to emerge from this research is the importance of isolation, rather than area, on community structure in this system. Much evidence suggested that different ecological groups of species show distinct patterns of distribution both within and among habitat types. This suggests that species distributions at this site are not the result of 'neutral' processes at the community level, but rather reflect fundamental differences in the ecology of component species. ^

Characterization, sources, and transformations of dissolved organic matter (DOM) in Florida coastal Everglades (FCE)

Dissolved organic matter (DOM) is one of the largest carbon reservoirs on this planet and is present in aquatic environments as a highly complex mixture of organic compounds. The Florida coastal Everglades (FCE) is one of the largest wetlands in the world. DOM in this system is an important biogeochemical component as most of the nitrogen (N) and phosphorous (P) are in organic forms. Achieving a better understanding of DOM dynamics in large coastal wetlands is critical, and a particularly important issue in the context of Everglades restoration. In this work, the environmental dynamics of surface water DOM on spatial and temporal scales was investigated. In addition, photo- and bio-reactivity of this DOM was determined, surface-to-groundwater exchange of DOM was investigated, and the size distribution of freshwater DOM in Everglades was assessed. The data show that DOM dynamics in this ecosystem are controlled by both hydrological and ecological drivers and are clearly different on spatial scales and variable seasonally. The DOM reactivity data, modeled with a multi-pool first order degradation kinetics model, found that fluorescent DOM in FCE is generally photo-reactive and bio-refractory. Yet the sequential degradation proved a “priming effect” of sunlight on the bacterial uptake and reworking of this subtropical wetland DOM. Interestingly, specific PARAFAC components were found to have different photo- and bio-degradation rates, suggesting a highly heterogeneous nature of fluorophores associated with the DOM. Surface-to-groundwater exchange of DOM was observed in different regions of the system, and compositional differences were associated with source and photo-reactivity. Lastly, the high degree of heterogeneity of DOM associated fluorophores suggested based on the degradation studies was confirmed through the EEM-PARAFAC analysis of DOM along a molecular size continuum, suggesting that the fluorescence characteristics of DOM are highly controlled by different size fractions and as such can exhibit significant differences in reactivity.

Local biomass control on the composition and reactivity of particulate organic matter in aquatic environments

Freshwater ecosystems have been recognized as important components of the global carbon cycle, and the flux of organic matter (OM) from freshwater to marine environments can significantly affect estuarine and coastal productivity. The focus of this study was the assessment of carbon dynamics in two aquatic environments, namely the Florida Everglades and small prairie streams in Kansas, with the aim of characterizing the biogeochemistry of OM. In the Everglades, particulate OM (POM) is mostly found as a layer of flocculent material (floc). While floc is believed to be the main energy source driving trophic dynamics in this oligotrophic wetland, not much is known about its biogeochemistry. The objective of this study was to determine the origin/sources of OM in floc using biomarkers and pigment-based chemotaxonomy to assess specific biomass contributions to this material, on a spatial (freshwater marshes vs. mangrove fringe) and seasonal (wet vs. dry) scales. It was found that floc OM is derived from the local vegetation (mainly algal components and macrophyte litter) and its composition is controlled by seasonal drivers of hydrology and local biomass productivity. Photo-reactivity experiments showed that light exposure on floc resulted in photo-dissolution of POC with the generation of significant amounts of both dissolved OM (DOM) and nutrients (N & P), potentially influencing nutrient dynamics in this ecosystem. The bio-reactivity experiments determined as the amount and rate of CO2 evolution during incubation were found to vary on seasonal and spatial scales and were highly influenced by phosphorus limitation. Not much is known on OM dynamics in small headwater streams. The objective of this study was to determine carbon dynamics in sediments from intermittent prairie streams, characterized by different vegetation cover for their watershed (C4 grasses) vs. riparian zone (C3 plants). In this study sedimentary OM was characterized using a biomarker and compound specific carbon stable isotope approach. It was found that the biomarker composition of these sediments is dominated by higher plant inputs from the riparian zone, although inputs from adjacent prairie grasses were also apparent. Conflicting to some extent with the River Continuum Concept, sediments of the upper reaches contained more degraded OM, while the lower reaches were enriched in fresh material deriving from higher plants and plankton sources as a result of hydrological regimes and particle sorting.

Hurricane disturbance and recovery of energy balance, CO2 fluxes and canopy structure in a mangrove forest of the Florida Everglades

Eddy covariance (EC) estimates of carbon dioxide (CO2) fluxes and energy balance are examined to investigate the functional responses of a mature mangrove forest to a disturbance generated by Hurricane Wilma on October 24, 2005 in the Florida Everglades. At the EC site, high winds from the hurricane caused nearly 100% defoliation in the upper canopy and widespread tree mortality. Soil temperatures down to -50 cm increased, and air temperature lapse rates within the forest canopy switched from statically stable to statically unstable conditions following the disturbance. Unstable conditions allowed more efficient transport of water vapor and CO2 from the surface up to the upper canopy layer. Significant increases in latent heat fluxes (LE) and nighttime net ecosystem exchange (NEE) were also observed and sensible heat fluxes (H) as a proportion of net radiation decreased significantly in response to the disturbance. Many of these impacts persisted through much of the study period through 2009. However, local albedo and MODIS (Moderate Resolution Imaging Spectro-radiometer) data (the Enhanced Vegetation Index) indicated a substantial proportion of active leaf area recovered before the EC measurements began 1 year after the storm. Observed changes in the vertical distribution and the degree of clumping in newly emerged leaves may have affected the energy balance. Direct comparisons of daytime NEE values from before the storm and after our measurements resumed did not show substantial or consistent differences that could be attributed to the disturbance. Regression analyses on seasonal time scales were required to differentiate the storm's impact on monthly average daytime NEE from the changes caused by interannual variability in other environmental drivers. The effects of the storm were apparent on annual time scales, and CO2 uptake remained approximately 250 g C m-2 yr-1 lower in 2009 compared to the average annual values measured in 2004-2005. Dry season CO2 uptake was relatively more affected by the disturbance than wet season values. Complex leaf regeneration dynamics on damaged trees during ecosystem recovery are hypothesized to lead to the variable dry versus wet season impacts on daytime NEE. In contrast, nighttime CO2 release (i.e., nighttime respiration) was consistently and significantly greater, possibly as a result of the enhanced decomposition of litter and coarse woody debris generated by the storm, and this effect was most apparent in the wet seasons compared to the dry seasons. The largest pre- and post-storm differences in NEE coincided roughly with the delayed peak in cumulative mortality of stems in 2007-2008. Across the hurricane-impacted region, cumulative tree mortality rates were also closely correlated with declines in peat surface elevation. Mangrove forest-atmosphere interactions are interpreted with respect to the damage and recovery of stand dynamics and soil accretion processes following the hurricane.

The civic achievement gap: A study on the civic knowledge, skills, and attitudes of Hispanic students in Miami-Dade County Public Schools

This study assessed the civic knowledge, skills, and attitudes of Hispanic eighth grade students in Miami-Dade County Public Schools (M-DCPS), Florida. Three hundred sixty one Hispanic students of Cuban (253), Colombian (57), and Nicaraguan (51) ancestry from 10 middle schools participated in the study. Two hundred twenty eight students were from low socio-economic status (SES) background, and 133 were of middle SES background. There were 136 boys and 225 girls. The International Association for the Evaluation of Educational Achievement Civic Education Student Questionnaire was used to collect data. The instrument assessed the students’ civic knowledge, skills, and attitudes. Multivariate analysis of variance was used to test for differences in the civic knowledge, skills, and attitudes of participants based on ancestry, SES, and gender. ^ The findings indicated that there was no significant difference in the civic knowledge, skills, and attitudes of Hispanic eighth grade students that were of Cuban, Colombian, and Nicaraguan ancestry. There was no significant difference in the civic skills and in five of the civic attitude scales for students from low SES families compared to those from middle SES families. However, there was a significant difference in the civic knowledge and in the civic attitude concerning classroom discussions and participation based on SES. The civic knowledge of middle SES students was higher than that of low SES students. Furthermore, middle SES Hispanic students displayed a higher mean score for the civic attitude of classroom discussions and participation than low SES students. There was no significant difference in the civic knowledge and in five of the civic attitude scales between boys and girls. However, there was a significant difference in the civic skills and the civic attitude of support for women’s rights between boys and girls. Hispanic girls displayed a higher mean score in civic skills than Hispanic boys. Furthermore, the mean score of civic attitude of support for women’s rights for Hispanic girls was higher than that of Hispanic boys. ^ It was concluded that Cuban, Colombian, or Nicaraguan participants did not demonstrate differences in civic attitudes and levels of civic knowledge and skills that eighth grade students possessed. In addition, when compared to boys, girls demonstrated a higher level of civic skills and a greater support for women’s rights and participation in politics and their roles in politics. Moreover, SES was demonstrated to be a key factor in the acquisition of civic knowledge, regardless of ancestry.^

Influence of teleost abundance on the distribution and abundance of sharks in Florida Bay, USA

Understanding the factors that influence the distribution and abundance of predators, including sharks, is important for predicting the impacts of human changes to the environment. Such studies are particularly important in Florida Bay, USA where there are planned large-scale changes to patterns of freshwater input from the Everglades ecosystem. Studies of many marine predators suggest that links between predator and prey habitat use may vary with spatial scale, but there have been few studies of the role of prey distribution in shaping habitat use and abundance of sharks. We used longline catches of sharks and trawls for potential teleost prey to determine the influence of teleost abundance on shark abundance at the scale of regions and habitats in Florida Bay. We found that shark catch per unit effort (CPUE) was not linked to CPUE ofteleosts at the scale of sampling sites, but shark CPUE was positively correlated with the mean CPUE for teleosts within a region. Although there does not appear to be a strong match between the abundance of teleosts and sharks at small spatial scales, regional shark abundance is likely driven, at least partially, by the availability of prey. Management strategies that influence teleost abundance will have cascading effects to higher trophic levels in Florida Bay.