Transportable setup for amplifier phase fidelity measurements

One possible laser source for the Laser Interferometer Space Antenna (LISA) consists of an Ytterbium-doped fiber amplifier originally developed for inter-satellite communication, seeded by the laser used for the technology demonstrator mission LISA Pathfinder. LISA needs to transmit clock information between its three spacecraft to correct for phase noise between the clocks on the individual spacecraft. For this purpose phase modulation sidebands at GHz frequencies will be imprinted on the laser beams between spacecraft. Differential phase noise between the carrier and a sideband introduced within the optical chain must be very low. We report on a transportable setup to measure the phase fidelity of optical amplifiers.

Lipid-Based Liquid Crystals As Carriers for Antimicrobial Peptides: Phase Behavior and Antimicrobial Effect

International audience

The use of mo and cu monochromatic radiations for quantitative phase analysis: study of the accuracy

Cement hydration is a very complex process in which crystalline phases are dissolving in water and after supersaturation hydrated crystalline and amorphous phases precipitate. Great efforts are being made to develop analytical tools to accurately quantify these processes and X-ray Powder Diffraction (XRPD) combined with Rietveld methodology is a suitable tool to quantify these complex mixtures and their time evolutions. However, some problems/drawbacks should be overcome to fully apply it to cement pastes characterization in order to get accurate phase analyses. In order to tackle this issue, a comparison of the Rietveld quantitative phase analyses (RQPA) obtained using Cu-Kα1, Mo-Kα1, and synchrotron strictly monochromatic radiations of three set of mixtures with increasing amounts of a given phase (spiking-method) is presented. The main aim is to test a simple hypothesis: high energy Mo-radiation, combined with high resolution laboratory X-ray powder diffraction optics, could yield more accurate RQPA, for challenging samples, than well-established Cu-radiation procedure(s). Firstly, a series of crystalline inorganic phase mixtures with increasing amounts of an analyte was studied in order to determine if Mo-Kα1 methodology is as robust as the well-established Cu-Kα1 one. Secondly, a series of crystalline organic phase mixtures with increasing amounts of an organic compound was analyzed. This type of mixture can result in transparency problems in reflection and inhomogeneous loading in narrow capillaries for transmission studies. Finally, a third series with variable amorphous content was studied. Limit of detection in Cu-patterns, ~0.2 wt%, are slightly lower than those derived from Mo-patterns, ~0.3 wt%, for similar recording times and limit of quantification for a well crystallized inorganic phase using laboratory powder diffraction was established ~0.10 wt%. From the obtained results it is inferred that RQPA from Mo-Kα1 radiation have slightly better accuracies than those obtained from Cu-Kα1. The results obtained in the previous comparison have been taken into account to obtain accurate RQPA, including the amorphous component with internal standard methodology, of hydrating cement pastes. The final goal of this second study was understanding the early-stage hydration mechanisms of a variety of cementing systems (Ordinary Portland Cement or Belite Alite Ye’elimite cement) as a function of water content, superplasticizer additives and type and content of sulfate source. In order to do so, X-ray powder diffraction data were taken in-situ with the humidity chamber coupled to the Mo-Kα1 powder diffractometer. Some results of this ongoing investigation will be reported and discussed.

A Collaborative IT Network for Three Adriatic Maritime Ports

Part 21: Mobility and Logistics

The joint European Research Infrastructure Network for Coastal Observatories: Achievements and Strategy for the Future

This document is summarizing a major part of the work performed by the FP7-JERICO consortium, including 27 partner institutions, during 4 years (2011-2015). Its objective is to propose a strategy for the European coastal observation and monitoring. To do so we give an overview of the main achievements of the FP7-JERICO project. From this overview, gaps are analysed to draw some recommendations for the future. Overview, gaps and recommendation are addressed at both Hardware and Software levels of the JERICO Research Infrastructure. The main part of the document is built upon this analysis to outcome a general strategy for the future, giving priorities to be targeted and some possible funding mechanisms, but also upon discussions held in dedicated JERICO strategy workshops. This document was initiated in 2014 by the coordination team but considering the fact that an overview of the entire project and its achievement were needed to feed this strategy deliverable it couldn’t ended before the end of FP7-JERICO, April 2015. The preparation of the JERICO-NEXT proposal in summer 2014 to answer an H2020 call for proposals pushed the consortium ahead, fed deep thoughts about this strategy but the intention was to not propose a strategy only bounded by the JERICO-NEXT answer. Authors are conscious that writing JERICO-NEXT is even drawing a bias in the thoughts and they tried to be opened. Nevertheless, comments are always welcome to go farther ahead. Structure of the document The Chapter 3 introduces the need of sustained coastal observatories, from different point of view including a short description of the FP7-JERICO project. In Chapter 4, an analysis of the JERICO coastal observatory Hardware (platforms and sensors) in terms of Status at the end of JERICO, identified gaps and recommendations for further development is provided region by region. The main challenges that remain to be overcome is also summarized. Chapter 5 is dedicated the JERICO infrastructure Software (calibration, operation, quality assessment, data management) and the progress made through JERICO on harmonization of procedures and definition of best practices. Chapter 6 provides elements of a strategy towards sustainable and integrated coastal observations for Europe, drawing a roadmap for cost-effective scientific-based consolidation of the present infrastructure while maximizing the potential arising from JERICO in terms of innovation, wealth-creation, and business development. After reading the chapter 3, for who doesn’t know JERICO, any chapter can be read independently. More details are available in the JERICO final reports and its intermediate reports; all are available on the JERICO web site (www.jerico-FP7.eu) as well as any deliverable. Each chapter will list referring JERICO documents. A small bibliographic list is available at the end of this deliverable.

Endoscopic optical coherence tomography : design and application

This thesis presents an investigation on endoscopic optical coherence tomography (OCT). As a noninvasive imaging modality, OCT emerges as an increasingly important diagnostic tool for many clinical applications. Despite of many of its merits, such as high resolution and depth resolvability, a major limitation is the relatively shallow penetration depth in tissue (about 2∼3 mm). This is mainly due to tissue scattering and absorption. To overcome this limitation, people have been developing many different endoscopic OCT systems. By utilizing a minimally invasive endoscope, the OCT probing beam can be brought to the close vicinity of the tissue of interest and bypass the scattering of intervening tissues so that it can collect the reflected light signal from desired depth and provide a clear image representing the physiological structure of the region, which can not be disclosed by traditional OCT. In this thesis, three endoscope designs have been studied. While they rely on vastly different principles, they all converge to solve this long-standing problem.

A hand-held endoscope with manual scanning is first explored. When a user is holding a hand- held endoscope to examine samples, the movement of the device provides a natural scanning. We proposed and implemented an optical tracking system to estimate and record the trajectory of the device. By registering the OCT axial scan with the spatial information obtained from the tracking system, one can use this system to simply ‘paint’ a desired volume and get any arbitrary scanning pattern by manually waving the endoscope over the region of interest. The accuracy of the tracking system was measured to be about 10 microns, which is comparable to the lateral resolution of most OCT system. Targeted phantom sample and biological samples were manually scanned and the reconstructed images verified the method.

Next, we investigated a mechanical way to steer the beam in an OCT endoscope, which is termed as Paired-angle-rotation scanning (PARS). This concept was proposed by my colleague and we further developed this technology by enhancing the longevity of the device, reducing the diameter of the probe, and shrinking down the form factor of the hand-piece. Several families of probes have been designed and fabricated with various optical performances. They have been applied to different applications, including the collector channel examination for glaucoma stent implantation, and vitreous remnant detection during live animal vitrectomy.

Lastly a novel non-moving scanning method has been devised. This approach is based on the EO effect of a KTN crystal. With Ohmic contact of the electrodes, the KTN crystal can exhibit a special mode of EO effect, termed as space-charge-controlled electro-optic effect, where the carrier electron will be injected into the material via the Ohmic contact. By applying a high voltage across the material, a linear phase profile can be built under this mode, which in turn deflects the light beam passing through. We constructed a relay telescope to adapt the KTN deflector into a bench top OCT scanning system. One of major technical challenges for this system is the strong chromatic dispersion of KTN crystal within the wavelength band of OCT system. We investigated its impact on the acquired OCT images and proposed a new approach to estimate and compensate the actual dispersion. Comparing with traditional methods, the new method is more computational efficient and accurate. Some biological samples were scanned by this KTN based system. The acquired images justified the feasibility of the usage of this system into a endoscopy setting. My research above all aims to provide solutions to implement an OCT endoscope. As technology evolves from manual, to mechanical, and to electrical approaches, different solutions are presented. Since all have their own advantages and disadvantages, one has to determine the actual requirements and select the best fit for a specific application.

Climate variability of the last 1000 years in the NW Pacific: high resolution, multi-biomarker records from Lake Toyoni

The East Asian Monsoon (EAM) is an active component of the global climate system and has a profound social and economic impact in East Asia and its surrounding countries. Its impact on regional hydrological processes may influence society through industrial water supplies, food productivity and energy use. In order to predict future rates of climate change, reliable and accurate reconstructions of regional temperature and rainfall are required from all over the world to test climate models and better predict future climate variability. Hokkaido is a region which has limited palaeo-climate data and is sensitive to climate change. Instrumental data show that the climate in Hokkaido is influenced by the East Asian Monsoon (EAM), however, instrumental data is limited to the past ~150 years. Therefore down-core climate reconstructions, prior to instrumental records, are required to provide a better understanding of the long-term behaviour of the climate drivers (e.g. the EAM, Westerlies, and teleconnections) in this region. The present study develops multi-proxy reconstructions to determine past climatic and hydrologic variability in Japan over the past 1000 years and aid in understanding the effects of the EAM and the Westerlies independently and interactively. A 250-cm long sediment core from Lake Toyoni, Hokkaido was retrieved to investigate terrestrial and aquatic input, lake temperature and hydrological changes over the past 1000-years within Lake Toyoni and its catchment using X-Ray Fluorescence (XRF) data, alkenone palaeothermometry, the molecular and hydrogen isotopic composition of higher plant waxes (δD(HPW)). Here, we conducted the first survey for alkenone biomarkers in eight lakes in the Hokkaido, Japan. We detected the occurrence of alkenones within the sediments of Lake Toyoni. We present the first lacustrine alkenone record from Japan, including genetic analysis of the alkenone producer. C37 alkenone concentrations in surface sediments are 18µg C37 g−1 of dry sediment and the dominant alkenone is C37:4. 18S rDNA analysis revealed the presence of a single alkenone producer in Lake Toyoni and thus a single calibration is used for reconstructing lake temperature based on alkenone unsaturation patterns. Temperature reconstructions over the past 1000 years suggest that lake water temperatures varies between 8 and 19°C which is in line with water temperature changes observed in the modern Lake Toyoni. The alkenone-based temperature reconstruction provides evidence for the variability of the EAM over the past 1000 years. The δD(HPW) suggest that the large fluctuations (∼40‰) represent changes in temperature and source precipitation in this region, which is ultimately controlled by the EAM system and therefore a proxy for the EAM system. In order to complement the biomarker reconstructions, the XRF data strengthen the lake temperature and hydrological reconstructions by providing information on past productivity, which is controlled by the East Asian Summer monsoon (EASM) and wind input into Lake Toyoni, which is controlled by the East Asian Winter Monsoon (EAWM) and the Westerlies. By combining the data generated from XRF, alkenone palaeothermometry and the δD(HPW) reconstructions, we provide valuable information on the EAM and the Westerlies, including; the timing of intensification and weakening, the teleconnections influencing them and the relationship between them. During the Medieval Warm Period (MWP), we find that the EASM dominated and the EAWM was suppressed, whereas, during the Little Ice Age (LIA), the influence of the EAWM dominated with time periods of increased EASM and Westerlies intensification. The El Niño Southern Oscillation (ENSO) significantly influenced the EAM; a strong EASM occurred during El Niño conditions and a strong EAWM occurred during La Niña. The North Atlantic Oscillation, on the other hand, was a key driver of the Westerlies intensification; strengthening of the Westerlies during a positive NAO phase and weakening of the Westerlies during a negative NAO phase. A key finding from this study is that our data support an anti-phase relationship between the EASM and the EAWM (e.g. the intensification of the EASM and weakening of the EAWM and vice versa) and that the EAWM and the Westerlies vary independently from each other, rather than coincide as previously suggested in other studies.

The'cave' mineral oxammite: a high resolution thermogravimetry and Raman spectroscopic study

The thermal decomposition of natural ammonium oxalate known as oxammite has been studied using a combination of high resolution thermogravimetry coupled to an evolved gas mass spectrometer and Raman spectroscopy coupled to a thermal stage. Three mass loss steps were found at 57, 175 and 188°C attributed to dehydration, ammonia evolution and carbon dioxide evolution respectively. Raman spectroscopy shows two bands at 3235 and 3030 cm-1 attributed to the OH stretching vibrations and three bands at 2995, 2900 and 2879 cm-1, attributed to the NH vibrational modes. The thermal degradation of oxammite may be followed by the loss of intensity of these bands. No intensity remains in the OH stretching bands at 100°C and the NH stretching bands show no intensity at 200°C. Multiple CO symmetric stretching bands are observed at 1473, 1454, 1447 and 1431cm-1, suggesting that the mineral oxammite is composed of a mixture of chemicals including ammonium oxalate dihydrate, ammonium oxalate monohydrate and anhydrous ammonium oxalate.

Thermal treatment of weddellite—a Raman and infrared emission spectroscopic study

Thermal transformations of natural calcium oxalate dihydrate known in mineralogy as weddellite have been undertaken using a combination of Raman microscopy and infrared emission spectroscopy. The vibrational spectroscopic data was complimented with high resolution thermogravimetric analysis combined with evolved gas mass spectrometry. TG–MS identified three mass loss steps at 114, 422 and 592 °C. In the first mass loss step water is evolved only, in the second and third steps carbon dioxide is evolved. The combination of Raman microscopy and a thermal stage clearly identifies the changes in the molecular structure with thermal treatment. Weddellite is the phase in the temperature range up to the pre-dehydration temperature of 97 °C. At this temperature, the phase formed is whewellite (calcium oxalate monohydrate) and above 114 °C the phase is the anhydrous calcium oxalate. Above 422 °C, calcium carbonate is formed. Infrared emission spectroscopy shows that this mineral decomposes at around 650 °C. Changes in the position and intensity of the C=O and C---C stretching vibrations in the Raman spectra indicate the temperature range at which these phase changes occur.

Primary alkaline battery cathodes a three-scale model

A mathematical model for the galvanostatic discharge and recovery of porous, electrolytic manganese dioxide cathodes, similar to those found within primary alkaline batteries is presented. The phenomena associated with discharge are modeled over three distinct size scales, a cathodic (or macroscopic) scale, a porous manganese oxide particle (or microscopic) scale, and a manganese oxide crystal (or submicroscopic) scale. The physical and chemical coupling between these size scales is included in the model. In addition, the model explicitly accounts for the graphite phase within the cathode. The effects that manganese oxide particle size and proton diffusion have on cathodic discharge and the effects of intraparticle voids and microporous electrode structure are predicted using the model.

Membrane associated transporter protein gene (SLC45A2) and the genetic basis of normal human pigmentation variation

This work is concerned with the genetic basis of normal human pigmentation variation. Specifically, the role of polymorphisms within the solute carrier family 45 member 2 (SLC45A2 or membrane associated transporter protein; MATP) gene were investigated with respect to variation in hair, skin and eye colour ― both between and within populations. SLC45A2 is an important regulator of melanin production and mutations in the gene underly the most recently identified form of oculocutaneous albinism. There is evidence to suggest that non-synonymous polymorphisms in SLC45A2 are associated with normal pigmentation variation between populations. Therefore, the underlying hypothesis of this thesis is that polymorphisms in SLC45A2 will alter the function or regulation of the protein, thereby altering the important role it plays in melanogenesis and providing a mechanism for normal pigmentation variation. In order to investigate the role that SLC45A2 polymorphisms play in human pigmentation variation, a DNA database was established which collected pigmentation phenotypic information and blood samples of more than 700 individuals. This database was used as the foundation for two association studies outlined in this thesis, the first of which involved genotyping two previously-described non-synonymous polymorphisms, p.Glu272Lys and p.Phe374Leu, in four different population groups. For both polymorphisms, allele frequencies were significantly different between population groups and the 272Lys and 374Leu alleles were strongly associated with black hair, brown eyes and olive skin colour in Caucasians. This was the first report to show that SLC45A2 polymorphisms were associated with normal human intra-population pigmentation variation. The second association study involved genotyping several SLC45A2 promoter polymorphisms to determine if they also played a role in pigmentation variation. Firstly, the transcription start site (TSS), and hence putative proximal promoter region, was identified using 5' RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE). Two alternate TSSs were identified and the putative promoter region was screened for novel polymorphisms using denaturing high performance liquid chromatography (dHPLC). A novel duplication (c.–1176_–1174dupAAT) was identified along with other previously described single nucleotide polymorphisms (c.–1721C>G and c.–1169G>A). Strong linkage disequilibrium ensured that all three polymorphisms were associated with skin colour such that the –1721G, +dup and –1169A alleles were associated with olive skin in Caucasians. No linkage disequilibrium was observed between the promoter and coding region polymorphisms, suggesting independent effects. The association analyses were complemented with functional data, showing that the –1721G, +dup and –1169A alleles significantly decreased SLC45A2 transcriptional activity. Based on in silico bioinformatic analysis that showed these alleles remove a microphthalmia-associated transcription factor (MITF) binding site, and that MITF is a known regulator of SLC45A2 (Baxter and Pavan, 2002; Du and Fisher, 2002), it was postulated that SLC45A2 promoter polymorphisms could contribute to the regulation of pigmentation by altering MITF binding affinity. Further characterisation of the SLC45A2 promoter was carried out using luciferase reporter assays to determine the transcriptional activity of different regions of the promoter. Five constructs were designed of increasing length and their promoter activity evaluated. Constitutive promoter activity was observed within the first ~200 bp and promoter activity increased as the construct size increased. The functional impact of the –1721G, +dup and –1169A alleles, which removed a MITF consensus binding site, were assessed using electrophoretic mobility shift assays (EMSA) and expression analysis of genotyped melanoblast and melanocyte cell lines. EMSA results confirmed that the promoter polymorphisms affected DNA-protein binding. Interestingly, however, the protein/s involved were not MITF, or at least MITF was not the protein directly binding to the DNA. In an effort to more thoroughly characterise the functional consequences of SLC45A2 promoter polymorphisms, the mRNA expression levels of SLC45A2 and MITF were determined in melanocyte/melanoblast cell lines. Based on SLC45A2’s role in processing and trafficking TYRP1 from the trans-Golgi network to stage 2 melanosmes, the mRNA expression of TYRP1 was also investigated. Expression results suggested a coordinated expression of pigmentation genes. This thesis has substantially contributed to the field of pigmentation by showing that SLC45A2 polymorphisms not only show allele frequency differences between population groups, but also contribute to normal pigmentation variation within a Caucasian population. In addition, promoter polymorphisms have been shown to have functional consequences for SLC45A2 transcription and the expression of other pigmentation genes. Combined, the data presented in this work supports the notion that SLC45A2 is an important contributor to normal pigmentation variation and should be the target of further research to elucidate its role in determining pigmentation phenotypes. Understanding SLC45A2’s function may lead to the development of therapeutic interventions for oculocutaneous albinism and other disorders of pigmentation. It may also help in our understanding of skin cancer susceptibility and evolutionary adaptation to different UV environments, and contribute to the forensic application of pigmentation phenotype prediction.

The way forward : report on the preparatory phase of prefabricated building design and construction methodology: identifying critical issues and recommending the way forward

This is an initial report of the PolyU SD part of the team to study Pre-fabricated Building Design and Construction Methodology and marks the completion of Phase 1. It follows our first notes prepared for the meeting on 2 February that identified some critical issues including future lifestyles, life expectancy of buildings, sustainability, size, flexibility and planning considerations. It is also an expansion of our presentation in Dongguan on 23 February. It is not a comprehensive survey of existing approaches or possible ways forward, but it has homed in on certain specific issues and does give specific examples to make the suggestions concrete. It is recommended that more comprehensive research be done to establish previous work and experience internationally. It is also recommended that more research be done on lifestyles as a preliminary to developing at least three concepts for evaluation before proceeding to the detailed design of one concept for full prototyping and market testing. The goal at this point is not to define a single direction but to suggest several future trajectories for further consideration. By the same token, this report is not intended as an exhaustive description of the considerable base of knowledge and ideas brought by the PolyU team to this exciting task. Before taking on an issue of this magnitude and importance in the definition of Hong Kong's future, one must carry out a thoughtful analysis of the issues at hand and an informed definition of paradigms, directions, goals and methods whereby our energies can be best used in the next steps. This report is the result of this analysis

Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

What value do users derive from social network applications?

Research on social networking sites like Facebook is emerging but sparse. This exploratory study investigates the value users derive from self-described ‘cool’ Facebook applications, and explores the features that either encourage or discourage users to recommend applications to their friends. The concepts of value and cool are explored in a social networking context. Our qualitative data reveals consumers derive a combination of functional value along with either social or emotional value from the applications. Female Facebook users indicate self-expression as important motivators, while males tend to use Facebook applications to socially compete. Three broad categories emerged for application features; symmetrical features can both encourage or discourage recommendation, polar features where different levels of the same feature encourage or discourage, and uni-directional features only encourage or discourage but not both. Recommending or not recommending an application tends to be the result of a combination of features and context, rather than one feature in isolation.