Laser-induced transient grating analysis of dynamics of interaction between sensory rhodopsin II D75N and the HtrII transducer.

The interaction between sensory rhodopsin II (SRII) and its transducer HtrII was studied by the time-resolved laser-induced transient grating method using the D75N mutant of SRII, which exhibits minimal visible light absorption changes during its photocycle, but mediates normal phototaxis responses. Flash-induced transient absorption spectra of transducer-free D75N and D75N joined to 120 amino-acid residues of the N-terminal part of the SRII transducer protein HtrII (DeltaHtrII) showed only one spectrally distinct K-like intermediate in their photocycles, but the transient grating method resolved four intermediates (K(1)-K(4)) distinct in their volumes. D75N bound to HtrII exhibited one additional slower kinetic species, which persists after complete recovery of the initial state as assessed by absorption changes in the UV-visible region. The kinetics indicate a conformationally changed form of the transducer portion (designated Tr*), which persists after the photoreceptor returns to the unphotolyzed state. The largest conformational change in the DeltaHtrII portion was found to cause a DeltaHtrII-dependent increase in volume rising in 8 micros in the K(4) state and a drastic decrease in the diffusion coefficient (D) of K(4) relatively to those of the unphotolyzed state and Tr*. The magnitude of the decrease in D indicates a large structural change, presumably in the solvent-exposed HAMP domain of DeltaHtrII, where rearrangement of interacting molecules in the solvent would substantially change friction between the protein and the solvent.

Method for the determination of specific molecular markers of biomass burning in lake sediments

Fire has an influence on regional to global atmospheric chemistry and climate. Molecular markers of biomass burning archived in lake sediments are becoming increasingly important in paleoenvironmental reconstruction and may help determine the interaction between climate and fire activity. Here, we present a high performance anion exchange chromatography–mass spectrometry method to allow separation and analysis of levoglucosan, mannosan and galactosan in lake sediments, with implications for reconstructing past biomass burning events. Determining mannosan and galactosan in Lake Kirkpatrick, New Zealand (45.03°S, 168.57°E) sediment cores and comparing these isomers with the more abundant biomass burning markers levoglucosan and charcoal represents a significant advancement in our ability to analyze past fire activity. Levoglucosan, mannosan and galactosan concentrations correlated significantly with macroscopic charcoal concentration. Levoglucosan/mannosan and levoglucosan/(mannosan + galactosan) ratios may help determine not only when fires occurred, but also if changes in the primary burned vegetation occurred.

An Aquaculture-Based Method for Calibrated Bivalve Isotope Paleothermometry

To quantify species- specific relationships between bivalve carbonate isotope geochemistry ( delta O-18(c)) and water conditions ( temperature and salinity, related to water isotopic composition [delta O-18(w)]), an aquaculture-based methodology was developed and applied to Mytilus edulis ( blue mussel). The four- by- three factorial design consisted of four circulating temperature baths ( 7, 11, 15, and 19 degrees C) and three salinity ranges ( 23, 28, and 32 parts per thousand ( ppt); monitored for delta O-18(w) weekly). In mid- July of 2003, 4800 juvenile mussels were collected in Salt Bay, Damariscotta, Maine, and were placed in each configuration. The size distribution of harvested mussels, based on 105 specimens, ranged from 10.9 mm to 29.5 mm with a mean size of 19.8 mm. The mussels were grown in controlled conditions for up to 8.5 months, and a paleotemperature relationship based on juvenile M. edulis from Maine was developed from animals harvested at months 4, 5, and 8.5. This relationship [ T degrees C = 16.19 (+/- 0.14) - 4.69 (+/- 0.21) {delta O-18(c) VPBD - delta O-18(w) VSMOW} + 0.17 (+/- 0.13) {delta O-18(c) VPBD - delta O-18(w) VSMOW}(2); r(2) = 0.99; N = 105; P < 0.0001] is nearly identical to the Kim and O'Neil ( 1997) abiogenic calcite equation over the entire temperature range ( 7 - 19 degrees C), and it closely resembles the commonly used paleotemperature equations of Epstein et al. ( 1953) and Horibe and Oba ( 1972). Further, the comparison of the M. edulis paleotemperature equation with the Kim and O'Neil ( 1997) equilibrium- based equation indicates that M. edulis specimens used in this study precipitated their shell in isotopic equilibrium with ambient water within the experimental uncertainties of both studies. The aquaculture- based methodology described here allows similar species- specific isotope paleothermometer calibrations to be performed with other bivalve species and thus provides improved quantitative paleoenvironmental reconstructions.

Gibbs point process approximation: Total variation bounds using Stein's method

We obtain upper bounds for the total variation distance between the distributions of two Gibbs point processes in a very general setting. Applications are provided to various well-known processes and settings from spatial statistics and statistical physics, including the comparison of two Lennard-Jones processes, hard core approximation of an area interaction process and the approximation of lattice processes by a continuous Gibbs process. Our proof of the main results is based on Stein's method. We construct an explicit coupling between two spatial birth-death processes to obtain Stein factors, and employ the Georgii-Nguyen-Zessin equation for the total bound.

A new method to measure higher visual functions in an immersive environment

BACKGROUND: Higher visual functions can be defined as cognitive processes responsible for object recognition, color and shape perception, and motion detection. People with impaired higher visual functions after unilateral brain lesion are often tested with paper pencil tests, but such tests do not assess the degree of interaction between the healthy brain hemisphere and the impaired one. Hence, visual functions are not tested separately in the contralesional and ipsilesional visual hemifields. METHODS: A new measurement setup, that involves real-time comparisons of shape and size of objects, orientation of lines, speed and direction of moving patterns, in the right or left visual hemifield, has been developed. The setup was implemented in an immersive environment like a hemisphere to take into account the effects of peripheral and central vision, and eventual visual field losses. Due to the non-flat screen of the hemisphere, a distortion algorithm was needed to adapt the projected images to the surface. Several approaches were studied and, based on a comparison between projected images and original ones, the best one was used for the implementation of the test. Fifty-seven healthy volunteers were then tested in a pilot study. A Satisfaction Questionnaire was used to assess the usability of the new measurement setup. RESULTS: The results of the distortion algorithm showed a structural similarity between the warped images and the original ones higher than 97%. The results of the pilot study showed an accuracy in comparing images in the two visual hemifields of 0.18 visual degrees and 0.19 visual degrees for size and shape discrimination, respectively, 2.56° for line orientation, 0.33 visual degrees/s for speed perception and 7.41° for recognition of motion direction. The outcome of the Satisfaction Questionnaire showed a high acceptance of the battery by the participants. CONCLUSIONS: A new method to measure higher visual functions in an immersive environment was presented. The study focused on the usability of the developed battery rather than the performance at the visual tasks. A battery of five subtasks to study the perception of size, shape, orientation, speed and motion direction was developed. The test setup is now ready to be tested in neurological patients.

New method for porewater extraction from claystone and determination of transport properties with results for Opalinus Clay (Switzerland)

A new technique to porewater extraction from claystone employs advective displacement of the in situ porewater by traced artificial porewater. Monitoring of tracer breakthrough yields species-specific transport properties. Results for Opalinus Clay from the Mont Terri Research Laboratory indicate that the chemical disturbances due to the method are minimal, and the observed significant differences in transport properties for Br– and 2H are in agreement with existing data. Sampling times are 2–4 months, and observation of tracer breakthrough takes 12–24 months at hydraulic conductivity of ∼10-13 m/s.

Effect of a Traditional Processing Method on the Chemical Composition of Local White Lupin (Lupinus albus L.) Seed in North-Western Ethiopia

The effect of a traditional Ethiopian lupin processing method on the chemical composition of lupin seed samples was studied. Two sampling districts, namely Mecha and Sekela, representing the mid- and high-altitude areas of north-western Ethiopia, respectively, were randomly selected. Different types of traditionally processed and marketed lupin seed samples (raw, roasted, and fi nished) were collected in six replications from each district. Raw samples are unprocessed, and roasted samples are roasted using fi rewood. Finished samples are those ready for human consumption as snack. Thousand seed weight for raw and roasted samples within a study district was similar (P > 0.05), but it was lower (P < 0.01) for fi nished samples compared to raw and roasted samples. The crude fi bre content of fi nished lupin seed sample from Mecha was lower (P < 0.01) than that of raw and roasted samples. However, the different lupin samples from Sekela had similar crude fi bre content (P > 0.05). The crude protein and crude fat contents of fi nished samples within a study district were higher (P < 0.01) than those of raw and roasted samples, respectively. Roasting had no effect on the crude protein content of lupin seed samples. The crude ash content of raw and roasted lupin samples within a study district was higher (P < 0.01) than that of fi nished lupin samples of the respective study districts. The content of quinolizidine alkaloids of fi nished lupin samples was lower than that of raw and roasted samples. There was also an interaction effect between location and lupin sample type. The traditional processing method of lupin seeds in Ethiopia has a positive contribution improving the crude protein and crude fat content, and lowering the alkaloid content of the fi nished product. The study showed the possibility of adopting the traditional processing method to process bitter white lupin for the use as protein supplement in livestock feed in Ethiopia, but further work has to be done on the processing method and animal evaluation.

Fluid-structure interaction of an elastic pipe immersed inside a coaxial rigid pipe: a model for the Tullio phenomenon

An axisymmetric, elastic pipe is filled with an incompressible fluid and is immersed in a second, coaxial rigid pipe which contains the same fluid. A pressure pulse in the outer fluid annulus deforms the elastic pipe which invokes a fluid motion in the fluid core. It is the aim of this study to investigate streaming phenomena in the core which may originate from such a fluid-structure interaction. This work presents a numerical solver for such a configuration. It was developed in the OpenFOAM software environment and is based on the Arbitrary Lagrangian Eulerian (ALE) approach for moving meshes. The solver features a monolithic integration of the one-dimensional, coupled system between the elastic structure and the outer fluid annulus into a dynamic boundary condition for the moving surface of the fluid core. Results indicate that our configuration may serve as a mechanical model of the Tullio Phenomenon (sound-induced vertigo).

Tumour border configuration in colorectal cancer: proposal for an alternative scoring system based on the percentage of infiltrating margin.

AIMS Information on tumour border configuration (TBC) in colorectal cancer (CRC) is currently not included in most pathology reports, owing to lack of reproducibility and/or established evaluation systems. The aim of this study was to investigate whether an alternative scoring system based on the percentage of the infiltrating component may represent a reliable method for assessing TBC. METHODS AND RESULTS Two hundred and fifteen CRCs with complete clinicopathological data were evaluated by two independent observers, both 'traditionally' by assigning the tumours into pushing/infiltrating/mixed categories, and alternatively by scoring the percentage of infiltrating margin. With the pushing/infiltrating/mixed pattern method, interobserver agreement (IOA) was moderate (κ = 0.58), whereas with the percentage of infiltrating margins method, IOA was excellent (intraclass correlation coefficient of 0.86). A higher percentage of infiltrating margin correlated with adverse features such as higher grade (P = 0.0025), higher pT (P = 0.0007), pN (P = 0.0001) and pM classification (P = 0.0063), high-grade tumour budding (P < 0.0001), lymphatic invasion (P < 0.0001), vascular invasion (P = 0.0032), and shorter survival (P = 0.0008), and was significantly associated with an increased probability of lymph node metastasis (P < 0.001). CONCLUSIONS Information on TBC gives additional prognostic value to pathology reports on CRC. The novel proposed scoring system, by using the percentage of infiltrating margin, outperforms the 'traditional' way of reporting TBC. Additionally, it is reproducible and simple to apply, and can therefore be easily integrated into daily diagnostic practice.

Identification of Novel Death-Associated Protein Kinase 2 Interaction Partners by Proteomic Screening Coupled with Bimolecular Fluorescence Complementation.

Death-associated protein kinase 2 (DAPK2) is a Ca(2+)/calmodulin-dependent Ser/Thr kinase that possesses tumor-suppressive functions and regulates programmed cell death, autophagy, oxidative stress, hematopoiesis, and motility. As only few binding partners of DAPK2 have been determined, the molecular mechanisms governing these biological functions are largely unknown. We report the identification of 180 potential DAPK2 interaction partners by affinity purification-coupled mass spectrometry, 12 of which are known DAPK binding proteins. A small subset of established and potential binding proteins detected in this screen was further investigated by bimolecular fluorescence complementation (BiFC) assays, a method to visualize protein interactions in living cells. These experiments revealed that α-actinin-1 and 14-3-3-β are novel DAPK2 binding partners. The interaction of DAPK2 with α-actinin-1 was localized at the plasma membrane, resulting in massive membrane blebbing and reduced cellular motility, whereas the interaction of DAPK2 with 14-3-3-β was localized to the cytoplasm, with no impact on blebbing, motility, or viability. Our results therefore suggest that DAPK2 effector functions are influenced by the protein's subcellular localization and highlight the utility of combining mass spectrometry screening with bimolecular fluorescence complementation to identify and characterize novel protein-protein interactions.

Gene by smoking interaction in blood pressure

Hypertension (HT) is mediated by the interaction of many genetic and environmental factors. Previous genome-wide linkage analysis studies have found many loci that show linkage to HT or blood pressure (BP) regulation, but the results were generally inconsistent. Gene by environment interaction is among the reasons that potentially explain these inconsistencies between studies. Here we investigate influences of gene by smoking (GxS) interaction on HT and BP in European American (EA), African American (AA) and Mexican American (MA) families from the GENOA study. A variance component-based method was utilized to perform genome-wide linkage analysis of systolic blood pressure (SBP), diastolic blood pressure (DBP), and HT status, as well as bivariate analysis for SBP and DBP for smokers, non-smokers, and combined groups. The most significant results were found for SBP in MA. The strongest signal was for chromosome 17q24 (LOD = 4.2), increased to (LOD = 4.7) in bivariate analysis but there was no evidence of GxS interaction at this locus (p = 0.48). Two signals were identified only in one group: on chromosome 15q26.2 (LOD = 3.37) in non-smokers and chromosome 7q21.11 (LOD = 1.4) in smokers, both of which had strong evidence for GxS interaction (p = 0.00039 and 0.009 respectively). There were also two other signals, one on chromosome 20q12 (LOD = 2.45) in smokers, which became much higher in the combined sample (LOD = 3.53), and one on chromosome 6p22.2 (LOD = 2.06) in non-smokers. Neither peak had very strong evidence for GxS interaction (p = 0.08 and 0.06 respectively). A fine mapping association study was performed using 200 SNPs in 30 genes located under the linkage signals on chromosomes 15 and 17. Under the chromosome 15 peak, the association analysis identified 6 SNPs accounting for a 7 mmHg increase in SBP in MA non-smokers. For the chromosome 17 linkage peak, the association analysis identified 3 SNPs accounting for a 6 mmHg increase in SBP in MA. However, none of these SNPs was significant after correcting for multiple testing, and accounting for them in the linkage analysis produced very small reductions in the linkage signal. ^ The linkage analysis of BP traits considering the smoking status produced very interesting signals for SBP in the MA population. The fine mapping association analysis gave some insight into the contribution of some SNPs to two of the identified signals, but since these SNPs did not remain significant after multiple testing correction and did not explain the linkage peaks, more work is needed to confirm these exploratory results and identify the culprit variations under these linkage peaks. ^

The identification and regulation of a novel interaction occurring between $\beta$-catenin and the actin -bundling protein fascin

Catenins were first characterized as linking the cytoplasmic domains of cadherin cell-cell adhesion molecules to the cortical actin cytoskeleton. In addition to their essential role in modulating cadherin adhesion, catenins have more recently been indicated to participate in cell and developmental signaling pathways. $\beta$-catenin, for example, associates directly with receptor tyrosine kinases and transcription factors such as LEF-1/TCF, and tranduces developmental signals within the Wnt pathway. $\beta$-catenin also appear to a role in regulating cell proliferation via its interaction with the tumor supressor protein APC. I have employed the yeast two-hybrid method to reveal that fascin, a bundler of actin filaments, binds to $\beta$-catenin's central Armadillo-repeat domain. The $\beta$-catenin-fascin interaction exists in cell lines as well as in animal brain tissues as revealed by immunoprecipitation analysis, and substantiated in vitro with purified proteins. Fascin additionally binds to plakoglobin, which contains a more divergent Armadillo-repeat domain. Fascin and E-cadherin utilize a similar binding-site within $\beta$-catenin, such that they form mutually exclusive complexes with $\beta$-catenin. Fascin and $\beta$-catenin co-localize at cell-cell borders and dynamic cell leading edges of epithelial and endothelial cells. Total immunoprecipitable b-catein has several isoforms, only the hyperphosphorylated isoform 1 associated with fascin. An increased $\beta$-catenin-fascin interaction was observed in HGF stimulated cells, and in Xenopus embryos injected with src kinase RNAs. The increased $\beta$-catenin association with fascin is correlated with increased levels of $\beta$-catenin phosphorylation. $\beta$-catenin, but not fascin, can be readily phosphorylated on tyrosine in vivo following src injection of embryos, or in vitro following v-src addition to purified protein components. These observations suggest a role of $\beta$-catenin phosphorylation in regulating its interaction with fascin, and src kinase may be an important regulator of the $\beta$-catenin-fascin association in vivo. The $\beta$-catenin-fascin interaction represents a novel catenin complex, that may conceivably regulate actin cytoskeletal structures, cell adhesion, and cellular motility, perhaps in a coordinate manner with its functions in cadherin and APC complexes. ^

Measurement of the electron neutrino charged-current interaction rate on water with the T2K ND280 π0 detector

This paper presents a measurement of the charged current interaction rate of the electron neutrino beam component of the beam above 1.5 GeV using the large fiducial mass of the T2K π0 detector. The predominant portion of the νe flux (∼85%) at these energies comes from kaon decays. The measured ratio of the observed beam interaction rate to the predicted rate in the detector with water targets filled is 0.89 ± 0.08 (stat.) ± 0.11 (sys.), and with the water targets emptied is 0.90 ± 0.09 (stat.) ± 0.13 (sys.). The ratio obtained for the interactions on water only from an event subtraction method is 0.87 ± 0.33 (stat.) ± 0.21 (sys.). This is the first measurement of the interaction rate of electron neutrinos on water, which is particularly of interest to experiments with water Cherenkov detectors.

Development of Efficient Techniques for the Analysis and Design of Antennas in Dual-Reflectarray Configuration

This thesis contributes to the analysis and design of printed reflectarray antennas. The main part of the work is focused on the analysis of dual offset antennas comprising two reflectarray surfaces, one of them acts as sub-reflector and the second one acts as mainreflector. These configurations introduce additional complexity in several aspects respect to conventional dual offset reflectors, however they present a lot of degrees of freedom that can be used to improve the electrical performance of the antenna. The thesis is organized in four parts: the development of an analysis technique for dualreflectarray antennas, a preliminary validation of such methodology using equivalent reflector systems as reference antennas, a more rigorous validation of the software tool by manufacturing and testing a dual-reflectarray antenna demonstrator and the practical design of dual-reflectarray systems for some applications that show the potential of these kind of configurations to scan the beam and to generate contoured beams. In the first part, a general tool has been implemented to analyze high gain antennas which are constructed of two flat reflectarray structures. The classic reflectarray analysis based on MoM under local periodicity assumption is used for both sub and main reflectarrays, taking into account the incident angle on each reflectarray element. The incident field on the main reflectarray is computed taking into account the field radiated by all the elements on the sub-reflectarray.. Two approaches have been developed, one which employs a simple approximation to reduce the computer run time, and the other which does not, but offers in many cases, improved accuracy. The approximation is based on computing the reflected field on each element on the main reflectarray only once for all the fields radiated by the sub-reflectarray elements, assuming that the response will be the same because the only difference is a small variation on the angle of incidence. This approximation is very accurate when the reflectarray elements on the main reflectarray show a relatively small sensitivity to the angle of incidence. An extension of the analysis technique has been implemented to study dual-reflectarray antennas comprising a main reflectarray printed on a parabolic surface, or in general in a curved surface. In many applications of dual-reflectarray configurations, the reflectarray elements are in the near field of the feed-horn. To consider the near field radiated by the horn, the incident field on each reflectarray element is computed using a spherical mode expansion. In this region, the angles of incidence are moderately wide, and they are considered in the analysis of the reflectarray to better calculate the actual incident field on the sub-reflectarray elements. This technique increases the accuracy for the prediction of co- and cross-polar patterns and antenna gain respect to the case of using ideal feed models. In the second part, as a preliminary validation, the proposed analysis method has been used to design a dual-reflectarray antenna that emulates previous dual-reflector antennas in Ku and W-bands including a reflectarray as subreflector. The results for the dualreflectarray antenna compare very well with those of the parabolic reflector and reflectarray subreflector; radiation patterns, antenna gain and efficiency are practically the same when the main parabolic reflector is substituted by a flat reflectarray. The results show that the gain is only reduced by a few tenths of a dB as a result of the ohmic losses in the reflectarray. The phase adjustment on two surfaces provided by the dual-reflectarray configuration can be used to improve the antenna performance in some applications requiring multiple beams, beam scanning or shaped beams. Third, a very challenging dual-reflectarray antenna demonstrator has been designed, manufactured and tested for a more rigorous validation of the analysis technique presented. The proposed antenna configuration has the feed, the sub-reflectarray and the main-reflectarray in the near field one to each other, so that the conventional far field approximations are not suitable for the analysis of such antenna. This geometry is used as benchmarking for the proposed analysis tool in very stringent conditions. Some aspects of the proposed analysis technique that allow improving the accuracy of the analysis are also discussed. These improvements include a novel method to reduce the inherent cross polarization which is introduced mainly from grounded patch arrays. It has been checked that cross polarization in offset reflectarrays can be significantly reduced by properly adjusting the patch dimensions in the reflectarray in order to produce an overall cancellation of the cross-polarization. The dimensions of the patches are adjusted in order not only to provide the required phase-distribution to shape the beam, but also to exploit the crosses by zero of the cross-polarization components. The last part of the thesis deals with direct applications of the technique described. The technique presented is directly applicable to the design of contoured beam antennas for DBS applications, where the requirements of cross-polarisation are very stringent. The beam shaping is achieved by synthesithing the phase distribution on the main reflectarray while the sub-reflectarray emulates an equivalent hyperbolic subreflector. Dual-reflectarray antennas present also the ability to scan the beam over small angles about boresight. Two possible architectures for a Ku-band antenna are also described based on a dual planar reflectarray configuration that provides electronic beam scanning in a limited angular range. In the first architecture, the beam scanning is achieved by introducing a phase-control in the elements of the sub-reflectarray and the mainreflectarray is passive. A second alternative is also studied, in which the beam scanning is produced using 1-bit control on the main reflectarray, while a passive subreflectarray is designed to provide a large focal distance within a compact configuration. The system aims to develop a solution for bi-directional satellite links for emergency communications. In both proposed architectures, the objective is to provide a compact optics and simplicity to be folded and deployed.

A method for Kinematic Calibration of a Parallel Robot by using one camera in hand and a spherical object

The main purpose of robot calibration is the correction of the possible errors in the robot parameters. This paper presents a method for a kinematic calibration of a parallel robot that is equipped with one camera in hand. In order to preserve the mechanical configuration of the robot, the camera is utilized to acquire incremental positions of the end effector from a spherical object that is fixed in the word reference frame. The positions of the end effector are related to incremental positions of resolvers of the motors of the robot, and a kinematic model of the robot is used to find a new group of parameters which minimizes errors in the kinematic equations. Additionally, properties of the spherical object and intrinsic camera parameters are utilized to model the projection of the object in the image and improving spatial measurements. Finally, the robotic system is designed to carry out tracking tasks and the calibration of the robot is validated by means of integrating the errors of the visual controller.