Search

This research presents a case study exploring the potential for demand side flexibility at a cluster of university buildings. The study investigates the potential of a collection of various electrical devices, excluding heating and cooling systems. With increasing penetration of renewable electricity sources and the phasing out of dispatchable fossil sources, matching grid generation with grid demand will become difficult using traditional grid management methods alone. Additionally, grid congestion is a pressing problem. Demand side management in buildings may contribute to a solution to these problems. Currently demand response is, however, not yet exploited at scale. In part, this is because it is unclear how this flexibility can be translated into successful business models, or whether this is possible under the current market regime. This research gives insight into the potential value of energy demand flexibility in reducing energy costs and increasing the match between electricity demand and purchased renewable electricity. An inventory is made of on-site electrical devices that offer load flexibility and the magnitude and duration of load shifting is estimated for each group of devices. A demand response simulation model is then developed that represents the complete collection of flexible devices. This model, addresses demand response as a ‘distribute candy’ problem and finds the optimal time-of-use for shiftable electricity demand whilst respecting the flexibility constraints of the electrical devices. The value of demand flexibility at the building cluster is then assessed using this simulation model, measured electricity consumption, and data regarding the availability of purchased renewables and day-ahead spot prices. This research concludes that coordinated demand response of large variety of devices at the building cluster level can improve energy matching by 0.6-1.5% and reduce spot market energy cost by 0.4-3.2%.

Cua Dai inlet is a typical microtidal, mixed energy-wave dominated inlet in a tropical monsoon regime in central Vietnam. Both the river flow regime and coastal processes such as induced by waves and tides influence Cua Dai Inlet and its adjacent coasts. Cua Dai Beach, the northern adjacent coast of Cua Dai inlet, has experienced severe erosion since 1995 due to an apparent non-periodic cyclic process, a decrease of sediment supply from the river, estuary and squeeze by coastal developments (Do et al. in J Coast Res 34(1):6–25, 2018). The inlet channel has shifted from North to South which served as an important controlling mechanism for the creation of a new ebb shoal. However, the role of the ebb-tidal delta in relation to the channel shifting and seasonal varying hydrodynamic conditions (river discharge and wave climate) remains poorly understood. Most studies have only considered the impact of waves and tides on the development of the ebb tidal delta. No study has included the impact of a varying river discharge on ebb shoal development and inlet migration. This chapter investigates the seasonal varying hydrodynamics and sediment transport of the inlet and adjacent coasts due to the seasonal varying river discharge and wave climate. The 2DH process-based morphodynamic numerical model (Delft3D) is applied using schematized wave conditions and river discharge. Six simulations with varying dominant wave conditions for the winter and for the summer are executed in combination with varying river discharge classes that corresponding to the dry, wet and flood seasons. There exists an East North East monsoon with a flood season from September to December, an East North East monsoon with a wet season from January to March, and a dry bidirectional South East/East North East monsoon from April to August. We investigate the effect of the seasonal wave climate and seasonal river discharges at Cua Dai inlet by analyzing the effects on the resulting hydrodynamics, sediment transports and potential morphological changes through the inlet and at the adjacent coasts. Primary results indicate that the seasonal variation in the wave climate has a strong influence on the sediment transport patterns in the adjacent coasts. The variation in the river flow dominates the magnitude of sediment transport through the inlet. The results of the simulations show that the inlet generally imports sediment into the estuary except in the case of the flood season. During the flood season the estimated sediment export is significant. Interestingly, the wave direction that varies during summer also influences the magnitude of sediment import into the estuary. Waves coming from the ENE contributes to larger sediment import than waves coming from the SE.

We report a novel two-photon fluorescence microscope based on a fast-switching liquid crystal spatial light modulator and a pair of galvo-resonant scanners for large-scale recording of neural activity from the mammalian brain. The utilized imaging technique is capable of monitoring large populations of neurons spread across different layers of the neocortex in awake and behaving mice. During each imaging session, all visual stimulus driven somatic activity could be recorded in the same behavior state. We observed heterogeneous response to different types of visual stimuli from ~ 3,300 excitatory neurons reaching from layer II/III to V of the striate cortex.

Respiratory complex I converts the free energy of ubiquinone reduction by NADH into a proton motive force, a redox reaction catalyzed by flavin mononucleotide(FMN) and a chain of seven iron–sulfur centers. Electron transfer rates between the centers were determined by ultrafast freezequenching and analysis by EPR and UV/Vis spectroscopy. The complex rapidly oxidizes three NADH molecules. The electron-tunneling rate between the most distant centers in the middle of the chain depends on the redox state of center N2 at the end of the chain, and is sixfold slower when N2 is reduced. The conformational changes that accompany reduction of N2 decrease the electronic coupling of the longest electro ntunneling step. The chain of iron–sulfur centers is not just a simple electron-conducting wire; it regulates the electrontunneling rate synchronizing it with conformation-mediated proton pumping, enabling efficient energy conversion. Synchronization of rates is a principle means of enhancing the specificity of enzymatic reactions.

Information-driven docking is currently one of the most successful approaches to obtain structural models of protein interactions as demonstrated in the latest round of CAPRI. While various experimental and computational techniques can be used to retrieve information about the binding mode, the availability of three-dimensional structures of the interacting partners remains a limiting factor. Fortunately, the wealth of structural information gathered by large-scale initiatives allows for homology-based modeling of a significant fraction of the protein universe. Defining the limits of information-driven docking based on such homology models is therefore highly relevant. Here we show, using previous CAPRI targets, that out of a variety of measures, the global sequence identity between template and target is a simple but reliable predictor of the achievable quality of the docking models. This indicates that a well-defined overall fold is critical for the interaction. Furthermore, the quality of the data at our disposal to characterize the interaction plays a determinant role in the success of the docking. Given reliable interface information we can obtain acceptable predictions even at low global sequence identity. These results, which define the boundaries between trustworthy and unreliable predictions, should guide both experts and nonexperts in defining the limits of what is achievable by docking. This is highly relevant considering that the fraction of the interactome amenable for docking is only bound to grow as the number of experimentally solved structures increases. Proteins 2013; 81:2119-2128. (c) 2013 Wiley Periodicals, Inc.

The development of dunes is characterized by the alternating effects of erosion during storm events and growth during milder conditions. The quantification of dune growth due to aeolian processes has received some attention but uncertainty remains on where the dune sand, which accommodates growing dunes, originates from in the coastal profile. In this paper we hypothesize that sediment eroded from the upper beach is the main sediment supply for aeolian sediment transport governing dune growth. To test this hypothesis we have analyzed morphological profiles collected monthly at three different field sites (Noordwijk, Vlugtenburg and Narrabeen) during several years. No significant erosive trend due to aeolian processes was found at the upper beach at this temporal resolution. We conclude that it is highly unlikely that the main supply for aeolian sediment transport governing dune growth was located at the upper beach. The intertidal zone might be a relevant alternative source of sediment in the cross shore profile.

In this study a novel hydroxylamine oxidoreductase (HAO) was purified and characterized from an anaerobic ammonium-oxidizing (Anammox) enrichment culture. The enzyme, which constituted about 9% of the protein mass in the soluble fraction of the cell extract, was able to oxidize hydroxylamine and hydrazine. When phenazine methosulfate and methylthiazolyltetrazolium bromide were used as electron acceptors, a V(max) [21 and 1.1 micromol min(-)(1) (mg of protein)(-)(1)] and K(m) (26 and 18 microM) for hydroxylamine and hydrazine were determined, respectively. The hydroxylamine oxidoreductase is a trimer and contains about 26 hemes per 183 kDa. As deduced from UV/vis spectra, hydroxylamine reduced more and different cytochromes than hydrazine. The dithionite-reduced spectrum showed an unusual 468 nm peak. Inhibition experiments with H(2)O(2) showed that hydroxylamine bound to this P-468 cytochrome, which is assumed to be the putative substrate binding site. Cyanide and hydrazine inhibited the oxidation of hydroxylamine. The amino acid sequences of several peptide fragments of HAO from Anammox showed a clear difference with the deduced amino acid sequence of HAO from the aerobic ammonia-oxidizing bacterium Nitrosomonas europaea. In EPR spectra of the Anammox HAO, two g-values (g(z)() = 2.37 and 2.42) were observed, which were not present in HAO of N. europaea.

Several studies have shown a positive relationship between local greenspace availability and residents' health, which may offer opportunities for health improvement. This study focuses on three mechanisms through which greenery might exert its positive effect on health: stress reduction, stimulating physical activity and facilitating social cohesion. Knowledge on mechanisms helps to identify which type of greenspace is most effective in generating health benefits. In eighty neighbourhoods in four Dutch cities data on quantity and quality of streetscape greenery were collected by observations. Data on self-reported health and proposed mediators were obtained for adults by mail questionnaires (N = 1641). Multilevel regression analyses, controlling for socio-demographic characteristics, revealed that both quantity and quality of streetscape greenery were related to perceived general health, acute health-related complaints, and mental health. Relationships were generally stronger for quality than for quantity. Stress and social cohesion were the strongest mediators. Total physical activity was not a mediator. Physical activity that could be undertaken in the public space (green activity) was, but less so than stress and social cohesion. With all three mediators included in the analysis, complete mediation could statistically be proven in five out of six cases. In these analyses the contribution of green activity was often not significant. The possibility that the effect of green activity is mediated by stress and social cohesion, rather than that it has a direct health effect, is discussed.

In the past couple of years, new coastal-dune research has sprung up in the Netherlands. In this paper, we give an overview of ongoing projects at Wageningen UR, Deltares, TU Delft and UTwente: how these are connected and what type of questions are addressed. There is an increasing demand for the understanding and prediction of coastal dune dynamics, both on the short (year) and long (100 years) term. We approach this from a variety of angles: scientific and applied, short-term and long-term, data-driven and model-based, biotic and abiotic, process-based and rule-based, and focused on components and integrated. We give examples of results and end with a discussion of the benefits of this integrated approach.

We conducted a cytogenetic study of sexual lines of Boechera stricta and Boechera holboellii (2n = 14) and seven diploid apomictic accessions of their interspecific hybrid Boechera divaricarpa and B. holboellii (2n = 14 or 15). By studying chromosome morphology, rDNA repeats, genome painting, male meiosis, pollen morphology, and flow-cytometry seed screens, we revealed an unexpected plethora of chromosome forms, pairing behavior, and hybrid composition in all apomictic lines. Genome painting demonstrated that the apomicts are alloploid with variable numbers of B. stricta and B. holboellii-like chromosomes. We assume that large-scale homeologous chromosome substitutions took place in the apomictic hybrids that resulted from recurrent diploid-polyploid transitions through restitutional meiosis and polyploidy-diploid transitions through reductional meiosis. A second peculiarity was the presence of a largely heterochromatic chromosome (Het) in all apomictic accessions (2n = 14 and 15) and an additional smaller chromosome (Del) in the aneuploids (2n = 15). Both chromosomes share repetitive pericentromere repeats with those from the sexual B. stricta, suggesting that they originated from this species. Pairing and behavior at meiosis I of the Het share features with both Y and B chromosomes and suggest that the Del arose from a translocation event or homeologous recombination between a B. holboellii (or related taxon) and a B. stricta chromosome. Based on its presence exclusively in apomictic accessions, we propose that the Het chromosome plays a role in the genetic control of apomixis.

Whole-cell suspensions of T. ferrireducens reduced Fe(III) citrate, Fe(III)-EDTA, and ferrihydrite with glycerol as an electron donor. After cell disruption, the highest activity was registered with Fe(III)-EDTA as the electron acceptor and NADH or NAD(P)H as electron donors. About 80% of the NAD(P)H-dependent Fe(III)-EDTA reductase activities were associated with the membrane fraction of the cells. Treatment of the membranes with lauryl maltoside led to complete solubilization of the NADH-dependent and 70% solubilization of the NADPH-dependent Fe(III)-EDTA reductase activities. After purification by ion-exchange chromatography, the NADH-dependent activity was concentrated 8-fold, and the NADPH-dependent activity was concentrated 11-fold, with a yield of about 10% for both activities. The Fe(III)-EDTA-reducing enzyme complex included c-type cytochromes and a protein with a molecular mass of ca. 115 k Da, consisting of two polypeptides. This is the first description of membrane-bound Fe(III)-reducing oxidoreductase activities from a gram-positive dissimilatory Fe(III)-reducing bacterium.

During intervertebral disc (IVD) maturation, notochordal cells (NCs) are replaced by chondrocyte-like cells (CLCs) in the nucleus pulposus, suggesting that NCs play a role in maintaining tissue health. Affirmatively, NC-conditioned medium (NCCM) exerts regenerative effects on CLC proliferation and extracellular matrix (ECM) production. The aim of this study was to identify NC-secreted substances that stimulate IVD regeneration. By mass spectrometry of porcine, canine and human NCCM, 149, 170 and 217 proteins were identified, respectively, with 66 proteins in common. Mainly ECM-related proteins were identified, but also organelle-derived and membrane-bound vesicle proteins. To determine whether the effect of NCCM was mediated by soluble and/or pelletable factors, porcine and canine NCCM were separated into a soluble (NCCM-S; peptides and proteins) and pelletable (NCCM-P; protein aggregates and extracellular vesicles) fraction by ultracentrifugation, and tested on bovine and canine CLCs in vitro, respectively. In each model, NCCM-S exerted a more pronounced anabolic effect than NCCM-P. However, glycosaminoglycan (GAG) uptake from the medium into the carrier gel prevented more definite conclusions. While the effect of porcine NCCM-P on bovine CLCs was negligible, canine NCCM-P appeared to enhance GAG and collagen type II deposition by canine CLCs. In conclusion, porcine and canine NCCM exerted their anabolic effects mainly through soluble factors, but also the pelletable NCCM factors showed moderate regenerative potential. Although the regenerative potential of NCCM-P should not be overlooked, future studies should focus on unraveling the protein-based regenerative mechanism from NCCM produced from isolated NCs, e.g. by NCCM fractionation and pathway blocking studies.

Coastal dune systems provide valuable functions that are threatened by human activity and climate change. Preserving and strengthening coastal dunes through coastal management and the implementation of interventions require accurate predictions of coastal dune development. The development of coastal dunes is driven by complex interactions between aeolian and marine processes. The aim of this thesis is to determine how marine and aeolian processes influence coastal dune development on yearly to decadal scale. Specifically, the effect of sea level rise and aeolian processes related to grain size were investigated.

This thesis explores the nature of aeolian sediment availability and its influence on aeolian sediment transport. The aim is to improve large scale and long term aeolian sediment transport estimates in (nourished) coastal environments. The generally poor performance of aeolian sediment transport models with respect to measurements in coastal environments is often accredited to limitations in sediment availability. Sediment availability can be limited by particular properties of the bed surface. For example, if the beach is moist or covered with non-erodible elements, like shells. If sediment availability is limited, the aeolian sediment transport rate is governed by the sediment availability rather than the wind transport capacity. Aeolian sediment availability is rather intangible as sediment availability is not only affected by aeolian processes, but also by marine and meteorological processes that act on a variety of spatial and temporal scales. The Sand Motor 21 Mm3 mega nourishment is used to quantify the spatiotemporal variations in aeolian sediment availability and its effect on aeolian sediment transport. The Sand Motor was constructed in 2011 along the Dutch coast. Aeolian sediment accumulation in the Sand Motor region is low compared to the wind transport capacity, while the Sand Motor itself is virtually permanently exposed to wind and accommodates large fetches. Aeolian sediment availability is therefore likely to dominate aeolian sediment accumulation. Multi-annual bi-monthly measurements of the Sand Motor's topography are used for a large scale aeolian sediment budget analysis. The analysis revealed that aeolian sediment supply from the dry beach area, that is almost permanently exposed to wind, diminished a half year after construction of the Sand Motor. The reduction in aeolian sediment supply is likely due to the development of a beach armor layer. In the subsequent years, two-third of the aeolian sediment deposits originate from the low-lying beaches that are frequently flooded and therefore often moist. The importance of the low-lying beaches in the Sand Motor region is tested during a six-week field campaign. Gradients in aeolian sediment transport are measured during the field campaign as to localize aeolian sediment source and sink areas. A consistent supply from the intertidal beach area was measured that was temporarily deposited at the higher dry beach. The temporary deposits were transported further during high water, when sediment supply from the intertidal beach ceased, resulting in a continuous sediment supply to the dunes. The temporary deposition of sediment at the dry beach was likely promoted by the presence of a berm that affects the local wind shear. Moreover, the berm edge coincided with the onset of the beach armor layer that might have further promoted deposition of sediment. The measurements on spatiotemporal variations in aeolian sediment availability and supply inspired an attempt to capture the characteristics of aeolian sediment availability in coastal environments in a comprehensive model approach. The resulting model simulates spatiotemporal variations in bed surface properties and their combined influence on aeolian sediment availability and transport. The implementation of multi-fraction aeolian sediment transport in the model introduces the recurrence relation between aeolian sediment availability and transport through self-grading of sediment. The model was applied in a four-year hindcast of the Sand Motor mega nourishment as first field validation. The model reproduces the multi-annual aeolian sediment erosion and deposition volumes, and the relative importance of the intertidal beach area as source of aeolian sediment well. Seasonal variations in aeolian sediment transport are incidentally missed by the model. The model accuracy is reflected in a R2 value of 0.93 when comparing time series of measured and modeled total aeolian sediment transport volumes in the four years since construction of the Sand Motor. The results suggest that indeed significant limitations in sediment availability, due to soil moisture content and beach armoring, govern aeolian sediment transport in the Sand Motor region. A comparison with a simulation without limitation in sediment availability suggests that aeolian sediment availability in the Sand Motor region is limited to about 25% of the wind transport capacity. Moreover, both spatial and temporal variations in aeolian sediment availability as well as the recurrence relation between aeolian sediment availability and transport are essential to accurate long term and large scale aeolian sediment transport estimates.

Biological membranes form a binding platform for a variety of proteins vital to the cell. The respiratory chain consists mostly of membrane-bound enzymes. These enzymes form a functional chain in which electrons derived from nutrition successively flow from low potential to high potential redox couples. During this process, the chemical energy is transformed to potential energy in the form of a transmembrane electrochemical gradient, which is subsequently stored in the form of ATP. The operation of this electron transfer chain and the mechanisms whereby a transmembrane electrochemical gradient is formed and utilized for ATP production are reviewed (Chapter 2). Cytochrome bd is a terminal oxidase of the aerobic respiratory pathway that catalyzes the electrogenic reduction of oxygen to water using ubiquinol as electron donor. Reports have shown that disruption of cytochrome bd in bacteria leads to increased sensitivity to hydrogen peroxide (H2O2), accumulation of H2O2 and decreased virulence. Here we show that besides its oxidase activity, cytochrome bd from Escherichia coli is a genuine quinol peroxidase that reduces hydrogen peroxide to water (Chapter 3). The observation that cytochrome bd is a quinol peroxidase, provides a biochemical basis for its role in detoxification of exogenous peroxide such as encountered in phagosomes or generated by competing bacteria in the natural environment. Another respiratory enzyme, nitric oxide reductase (Nor), an enzyme of the denitrification pathway, reduces nitric oxide (NO) to nitrous oxide (N2O). The cytochrome-c-dependent cNor was shown to be non-electrogenic, i.e. unable to conserve energy. Based on its structure, the quinol-dependent qNor, was suggested to be an electrogenic enzyme and is implicated in virulence, as it can detoxify the NO produced in phagocytes. A third type of Nor is the copper-A-Nor (CuANor) from Bacillus azotoformans (Chapters 4 and 5). This enzyme is highly homologous to the proton-pumping cytochrome ba3 oxidase. Homology modeling indicated that CuANor contains the proton entry and proton exit pathways implicated in proton pumping by the cytochrome ba3 oxidase. Using proteoliposomes, we show here that CuANor is electrogenic and thus couples NO reduction directly to the formation of a proton-dependent electochemical gradient. By employing CuANor bacilli generate more ATP than organisms that employ cNOR. More insight into the interplay between respiration for bioenergetic ends and “respiration” with detoxification as a goal can aid in the design of bacteriocidal drugs to combat human pathogens.

Array comparative genomic hybridization was used to identify copy number alterations in clear cell renal cell carcinoma (ccRCC) patient tumors to identify associations with patient/clinical characteristics. Of 763 ccRCC patients, 412 (54%) provided frozen biopsies. Clones were analyzed for significant copy number differences, adjusting for multiple comparisons and covariates in multivariate analyses. Frequent alterations included losses on: 3p (92.2%), 14q (46.8%), 8p (38.1%), 4q (35.4%), 9p (32.3%), 9q (31.8%), 6q (30.8%), 3q (29.4%), 10q (25.7%), 13q (24.5%), 1p (23.5%) and gains on 5q (60.2%), 7q (39.6%), 7p (30.6%), 5p (26.5%), 20q (25.5%), 12q (24.8%), 12p (22.8%). Stage and grade were associated with 1p, 9p, 9q, 13q and 14q loss and 12q gain. Males had more alterations compared with females, independent of stage and grade. Significant differences in the number/types of alterations were observed by family cancer history, age at diagnosis and smoking status. Von Hippel-Lindau (VHL) gene inactivation was associated with 3p loss (PE-05), and these cases had fewer alterations than wild-type cases. The fragile site flanking the FHIT locus (3p14.2) represented a unique breakpoint among VHL hypermethylated cases, compared with wild-type cases and those with sequence changes. This is the first study of its size to investigate copy number alterations among cases with extensive patient, clinical/risk factor information. Patients characterized by VHL wild-type gene status (vs sequence alterations) and male (vs female) cases had more copy number alterations regardless of diagnostic stage and grade, which could relate to poor prognosis. © 2012 Macmillan Publishers Limited. All rights reserved.