SIRIS-Lab/unlabelled-sti-corpus huggingface dataset:
3D-Integrated single photon detector

Photonics, in recognition of its strategic significance and pervasiveness throughout many industrial sectors, has been identified as one of the Key Enabling Technologies for Europe. Photonics in combination with quantum information science has great potential to facilitate, transform and innovate future technologies for the better. The Proof of Concept (PoC) project intends to contribute to this by developing and testing a communication platform prototype, comprised of single photon detectors, which are efficiently coupled to single mode fibers using an innovative laser written device. This enables the integration of single photon detectors on innovative glass waveguides. These glass integrated photonic circuits offer excellent specifics for on-chip quantum optics implementations in terms of scattering losses, offering flexibility of the waveguide geometry and ensuring high coupling efficiency with optical fibers.
The device developed and tested in the PoC, directly addresses a market need for an integrated and efficient on-chip communication systems. Current available systems have limitations involving high costs, complex production, and inefficient coupling of detectors to optical fibers. The proposed platform will offer 1.) a simplified production process, 2.) high optical fiber coupling efficiency 3.) improved performance levels, 4.) high cost efficiency, and 5.) compactness. Such systems can be applied in a wide range of communication and non-communication applications, such as free-space optical communication, quantum communication, quantum cryptography, DNA sequencing, single molecule detection and material analysis. Moreover, the future commercialisation of quantum computing is expected to create a vast demand for these communication systems. 
In addition to the technology PoC, the project carries out IPR strategy considerations through patenting actions, determines the market potential, seeks market feedback, and plans for post-PoC commercialisation paths.
Mechanism of atp dependent chromatin modelling and editing by ino80 remodellers

Nucleosomes, ~147 base pairs of DNA wrapped around an histone protein octamer, package and protect nuclear DNA but also carry important biological information. The position and composition of nucleosomes along chromosomal DNA is a key element of defining the state and identity of a cell. Chromatin remodellers are ATP dependent molecular machines that position, move or edit nucleosomes in a genome wide manner. Collectively, they shape the nucleosome landscape and play central roles in the maintenance and differentiation of cells, but also in pathological transformations. INO80, a megadalton large remodeller consisting of 15 or more subunits, is involved in replication, gene expression and DNA repair. It models chromatin by positioning barrier nucleosomes around nucleosome free regions, editing nucleosomes and generating nucleosome arrays. However, structural mechanisms for INO80 and other remodelling machines are poorly understood due to their complexity. To provide a comprehensive mechanistic framework, to understand how INO80 senses nucleosome free regions to position barrier nucleosomes and how it generates arrays or senses DNA breaks, I propose a challenging but ground-breaking endeavour using a combination of cryo-EM and functional approaches. We address structures of fungal and human INO80 complexes at promoter regions, on di-nucleosomes and at DNA ends and develop quantitative positioning assays to reveal common and distinct features of shaping chromatin in different species. We also explore cryo-EM as tool towards revealing distinct steps the chemo-mechanical remodelling reactions. The proposed research will help derive fundamental molecular principles underlying the modelling of the nucleosome landscape.
Phylogenetic placement of metagenomic reads using the minimum evolution principle

A central problem of computational metagenomics is determining the correct placement into an existing phylogenetic tree of individual reads (nucleotide sequences of varying lengths, ranging from hundreds to thousands of bases) obtained using next-generation sequencing of DNA samples from a mixture of known and unknown species. Correct placement allows us to easily identify or classify the sequences in the sample as to taxonomic position or function.Here we propose a novel method (PhyClass), based on the Minimum Evolution (ME) phylogenetic inference criterion, for determining the appropriate phylogenetic position of each read. Without using heuristics, the new approach efficiently finds the optimal placement of the unknown read in a reference phylogenetic tree given a sequence alignment for the taxa in the tree. In short, the total resulting branch length for the tree is computed for every possible placement of the unknown read and the placement that gives the smallest value for this total is the best (optimal) choice. By taking advantage of computational efficiencies and mathematical formulations, we are able to find the true optimal ME placement for each read in the phylogenetic tree. Using computer simulations, we assessed the accuracy of the new approach for different read lengths over a variety of data sets and phylogenetic trees. We found the accuracy of the new method to be good and comparable to existing Maximum Likelihood (ML) approaches.In particular, we found that the consensus assignments based on ME and ML approaches are more correct than either method individually. This is true even when the statistical support for read assignments was low, which is inevitable given that individual reads are often short and come from only one gene.
Model-Driven Comparison of State-Machine-Based and Deferred-Update Replication Schemes

In this paper, we analyze and experimentally compare state-machine-based and deferred-update (or transactional) replication, both relying on atomic broadcast. We define a model that describes the upper and lower bounds on the execution of concurrent requests by a service replicated using either scheme. The model is parametrized by the degree of parallelism in either scheme, the number of processor cores, and the type of requests. We analytically compared both schemes and a non-replicated service, considering a bcast- and request-execution-dominant workloads. To evaluate transactional replication experimentally, we developed Paxos STM---a novel fault-tolerant distributed software transactional memory with programming constructs for transaction creation, abort, and retry. For state-machine-based replication, we used JPaxos. Both systems share the same implementat ion of atomic broadcast based on the Paxos algorithm. We present the results of performance evaluation of both replication schemes, and a non-replicated (thus prone to failures) service, considering various workloads. The key result of our theoretical and experimental work is that neither system is superior in all cases. We discuss these results in the paper.
Understanding the birefringence effects in an all-fiber device based on photonic crystal fibers with integrated electrodes

In this work, we study a special kind of photonic crystal fibers with two integrated electrodes. The device operation is based on induced birefringence caused by mechanical stress when electrical current heats the internal electrodes. Due to the complex structure of the a finite element model was carried out to determine the strain distributions generated at the center region of the fiber core, and hence taking the induced change in the refractive index as a change in the effective refractive index due to the transferred heat. Here, we explain the interesting result that fiber birefringence axes rotated asymptotically with temperature. The analysis shows that this rotation of the birefringence axes is the cause of a nonlinear variation of the effective refractive index of the fundamental mode. Full text: PDF References: P.St.J. Russell, Photonic-Crystal Fibers, J. Lightwave Technol. 24, 4729 (2006). [CrossRef] B.J. Eggleton, C. Kerbage, P.S. Westbrook, R.S. Windeler, A. Hale, Microstructured optical fiber devices, Opt. Exp. 9, 698 (2001), [CrossRef] T.T. Larsen, A. Bjarklev, D.S. Hermann, J. Broeng, devices based on liquid crystal photonic bandgap fibres, Opt. Exp. 11, 2589 (2003), [CrossRef] F. Du, Y.-Q. Lu, and S.-T. Wu, Electrically tunable liquid-crystal photonic crystal fiber, Appl. Phys. Lett. 85, 2181 (2004). [CrossRef] G. Chesini et al., All-fiber devices based on photonic crystal fibers with integrated electrodes, Opt. Exp. 17, 1660 (2009), [CrossRef] E. Reyes-Vera et al. in Latin America Optics and Photonics Conference (LAOP) (Washington, Optical Society of America 2010), ThF2. S.P. Timoshenko, J.N. Goodier, Theory of Elasticity, 3rd ed. (New York, McGraw-Hill 1970). J.F. Botero-Cadavid, J.D. Causado-Buelvas, P. Torres, Spectral Properties of Locally Pressed Fiber Bragg Gratings Written in Polarization Maintaining Fibers, J. Lightwave Technol. 28, 1291 (2010). [CrossRef] Z. Yu, O. Tarasenko, W. Margulis, and P. -Y. Fonjallaz, Birefringence switching of Bragg gratings in fibers with internal electrodes, Opt. Exp. 16, 8229 (2008), [CrossRef] S.H. Lee, B.H. Kim, W.-T. Han, Effect of filler metals on the temperature sensitivity of side-hole fiber, Opt. Exp. 17, 9712-9717 (2009), [CrossRef]
Carrier-Selective contacts for silicon photovoltaics based on broadband-transparent oxides

This project aims at a cost-effective efficiency enhancement of Si solar cells towards their theoretical maximum of about 29% by moving away from the diffused-junction paradigm. This will reduce the energy fabrication costs on the €/kWh level and thereby increase the competiveness and profitability of photovoltaic systems. Crystalline Si (c-Si) solar cells are since decades the most established photovoltaic technology. Their main advantages are long lifetime (>25 years), non-toxicity and the high abundance of Si. However, for full competitiveness with traditional sources of electricity, important new steps need to be taken to increase their performance. 
An innovative contacting scheme will be developed that eliminates the main loss mechanisms in c-Si solar cells arising from doped pn-junctions and the direct contact of metal with Si. The novel contacts will be broadband optically transparent, generate a highly passivating and carrier-selective interface to Si and will enable solar cells without doped pn-junctions. No cost-intensive patterning technique is required for the device fabrication and parasitic optical absorption, as present in Si heterojunction solar cells, will be minimized. The novel contacts consist of three layers: a 1-2 nm thick tunnelling SiO2 layer for chemical passivation of the Si surface, a wide-bandgap conductive metal oxide layer providing a specific energy band alignment, and a highly conductive transparent oxide (TCO) for carrier transport to external metal contacts and optimum light coupling into the solar cell device. The contacts will be used for the fabrication of Si solar cells which are devoid of doped pn-junctions and achieve both high open-circuit voltages and photo currents. The structure of the photovoltaic device will be optimized for the application in regular 1-sun modules and for both III-V/Si and perovskite/Si tandem cell applications with potential for flat-plate efficiencies well above 30%.
Gendered nostalgia: neo-ottomanism in islamist women’s media in turkey

Neo-Ottomanism (NO), the aim to revitalize the Ottoman imperial past in contemporary Turkish society, constitutes the ideological basis of the populist authoritarianism of the AKP, the ruling Islamist party in Turkey, since 2007. Thanks to its spread in the cultural field, chiefly in TV series, it has been gaining increasing popularity in Turkey and its diaspora. Considering its nationalist and Islamist roots, claims of authenticity and uses of history and nostalgia, which work to legitimize gender inequalities, and also the gender-blind scholarly approaches to it, this project aims to elucidate the gendered nature of NO and how Islamist women, who mostly support the AKP, become creative agents in its reproduction. The project will examine gendered aspects of neo-Ottomanist nostalgia and their sophisticated transmission in Islamist women’s periodicals in Turkey. Its novel insights will fill the critical lacuna of a gender study of NO and provide a more complex image of “Islamist women”. Its research methodology includes content analysis of articles containing Ottomanist nostalgia for discursive, visual, and paratextual reproductions; and interviews with their authors to reveal their perceptions of and nostalgia with Ottoman past and the process of their active involvement in NO’s popularization. The findings will link with Turkish studies, South-East European studies, and studies of gender, media, and cultural heritage; and reach to feminist groups, journalists, policy makers, teachers of religion and fashion lovers. As a researcher who has worked on the subjects of power and discourse, women and Islam in Turkey, and NO and nostalgia, I have essential knowledge, experience and enthusiasm for the project. It will be a unique career opportunity as it will equip me to take part in collaborative research projects and apply for tenured posts in EU. The supervisor and the hosting research centre offer the best possible interdisciplinary expertise and academic networks.
Ultrafast molecular structural dynamics

Chemical reactions in solution are strongly influenced by femtosecond solvent-solute dynamics. Likewise, proteins provide specific environments to control the outcome of substrate reactions. The molecular understanding of these effect are currently poorly developed. 

I propose to fill this knowledge gap by ‘filming’ elementary chemical reactions in solution and in proteins. I will pioneer new time-resolved scattering and diffraction experiments using X-ray Free Electron Lasers (XFELs).

Using femtosecond time-resolved X-ray scattering, I plan to decipher the structural dynamics of bond breaking and bond formation in iodine containing compounds in solution. I will pioneer time-resolved fluctuation correlation X-ray scattering to recover full electron density maps of the reaction trajectories at an atomic resolution. I will visualize the as yet unknown structures of reaction intermediates and the solvent response. 

Furthermore, I propose to investigate the molecular photoresponse of phytochrome photoconversion with femtosecond time-resolved serial microcrystallography. Phytochromes are ubiquitous photosensory proteins in plants and are essential to all vegetation on earth. I will resolve how the chromophore and the protein react collectively to photoexcitation and how this leads to conformational changes.

Combined, this interdisciplinary project will yield microscopic understanding on how the surrounding of reactants guides the outcome of elementary (bio)chemical reactions. 

This program builds on my strengths in structural biology of phytochromes (Takala et al., Nature, 2014), time-resolved X-ray scattering (Westenhoff et al., Nature Methods 2010), and femtosecond spectroscopy (21 papers in PRL, JACS, Nature Methods 2006-2012 & 2016).

The new XFEL-based methods will have wide-ranging applications in chemistry and biology. My work will open new horizons in physical chemistry and structural biology.
Feather sampling provides an unreliable source of DNA that may well have significant long-term impacts: a reply to Katzner et al.

We were pleased to see that our recent point-of-view article (McDonald and Griffi th 2011) has lead to further discussion on this important issue (Katzner et al. 2012). One of our primary goals was to encourage researchers to consider both the potential impacts of their sampling methodologies upon subjects, and also the level of information that particular methods are likely to provide. Whilst we are therefore pleased that Katzner et al. (2012) have continued the discussion and helped to raise the profi le of important issues surrounding the biological sampling of avian tissues, we are disappointed that they have misrepresented our original message. Th e primary critique raised by Katzner et al. (2012) centres on our reputed suggestion that blood sampling was a ‘ one-size-fi ts-all approach ’ to ornithology. Th is main criticism of our article is somewhat weakened by the fact that nowhere in our article did we either state or imply this to be the case. In fact, the opposite is true, in several places in our article we explicitly suggested that feather sampling may well be the best practise in some situations. Th e clearest statement to this eff ect is on the very fi rst page of our article: ‘ Note that we support the obtainment of feather material, after applying an appropriate degree of ethical rigour, when no other means exists for obtaining these data ’ . At present, there is a lack of data that has specifi cally tested for impacts of feather sampling, be it feather plucking or clipping, which makes it very diffi cult to judge the longterm impacts of these techniques. Again, we implore ornithologists to publish data on any potential impacts (or lack thereof ) of feather sampling at their earliest opportunity. Th e main thrust of our article was two-fold. First, to highlight the relatively poor DNA extraction rates associated with feather versus blood sources. Second, to identify some studies that determined signifi cant negative impacts of feather sampling. Th e latter are typically swept under the carpet as ‘ insignifi cant ’ – perusal of the literature suggests that this is not the case for a range of species (Chai and Dudley 1999, Th ompson et al. 2010). Katzner et al. (2012) raise four points in their article that they claim contradict our views, we address each below. 1. Science methodology should be driven by research questions
Development of the Community Active Sensor Module (CASM): Forward Simulation

Abstract. Modern data assimilation frameworks require sophisticated physical and radiative models to guide assimilation and interpretation of satellite-based observations. To date, satellite-based infrared and passive microwave radiances, in various scenarios, are being assimilated operationally at multiple centers around the world (e.g., ECMWF, NOAA), however precipitating/cloudy radiances assimilation is still under development for most observation streams. Additionally, with the advent of space-based precipitation radars (e.g., TRMM, GPM, CloudSat), active microwave scatterometers (e.g., RapidScat), and radar altimeters (e.g., JASON), interest in directly assimilating satellite-based active microwave observations is increasing. This paper describes the development of the Community Active Sensor Module (CASM), which is designed to simulate active microwave sensor observations, consistent with current and future sensors. This paper presents the forward modeling component of CASM, providing a model description, key physical elements, and sensitivity to the various inputs and implicit / explicit assumptions. CASM is also evaluated against the the Global Precipitation Measurement Mission Dual-Frequency Precipitation Radar (GPM DPR) observations in both a targeted case study and a global, year-long analysis.
YUKAWA CORRECTIONS TO THE NEWTONIAN GRAVITATIONAL POTENTIAL: FINITE SIZE EFFECTS IN A RECENT EXPERIMENT

We provide a formalism to calculate the effect of the finite size of the sample on hypothetical Yukawa-like corrections to the Newtonian gravitational potential. It is explicitly shown that finite size effect contributions are negligible when the extent of the sample is larger than the range of the Yukawa term. In particular we show that these contributions are small in the configuration of a recent experiment. In the experiment a gold coated sphere was moved across the interface between two materials with different mass densities. In view of these new experimental results, we analyze the situation when the error on the hypothetical correction could result to be significant.
Optical imaging of molecular and signalling activity in real-time: application to flatfish metamorphosis

Aquaculture is a sustainable means of generating high-quality fish to satisfy the growing global fish consumption. Flatfish are attractive species for aquaculture due to their high market value and consumer demand. However, abnormal development during metamorphosis is often a problem and has hampered the development of successful flatfish aquaculture. Hence, it is critical to understand the specific molecular signalling pathways associated with abnormal metamorphosis.  
Larval metamorphosis has been studied using histological sections and gene expression profiling. However, the first requires sacrificing fish and the latter uses pool of larvae. Hence, there is an increasing demand for 3D imaging tools to directly visualise the mechanisms of metamorphosis in whole live flatfish. This offers a unique opportunity for optical imaging (OI) modalities, which are becoming popular for imaging targeted biological processes in model organisms (e.g. zebrafish). However, their full potential for biology and non-model organisms is being overlooked.  
The vision for this fellowship is to develop a non-invasive OI tool for real-time 3D in vivo imaging, for studying the molecular mechanisms regulating flatfish metamorphosis. The project combines recent advances in the mathematics of forward and inverse problems, marine molecular biology and modern OI technologies, including selective plane illumination microscopy and optical projection tomography. The developed OI tools will provide clear high-resolution pictures from the inside of live flatfish. Accurate light propagation models and image reconstruction methods will be developed to obtain high-quality images of biological significance. Moreover, novel acquisition schemes will be implemented to enable real-time 3D imaging. Finally, the OI tools will be used for in vivo flatfish imaging to obtain markers of normal and abnormal metamorphosis. This is essential to establish a sustainable and profitable flatfish aquaculture industry.
SALONE DEL MOBILE 2022

THE INTERNATIONAL FURNITURE EXHIBITION IS THE MOST IMPORTANT FAIR AND MEETING POINT, WORLDWIDE, FOR OPERATORS IN THE HOME-FURNISHING SECTOR. RODA HAS PARTICIPATED ASSIDUOUSLY FOR YEARS, AND WILL ALSO PARTICIPATE IN THE 2022 EDITION.
Factor Augmented Artificial Neural Network Model

This paper brings together two important developments in forecasting literature; the artificial neural networks and factor models. The paper introduces the factor augmented artificial neural network (FAANN) hybrid model in order to produce a more accurate forecasting. Theoretical and empirical findings have indicated that integration of various models can be an effective way of improving on their predictive performance, especially when the models in the ensemble are quite different. The proposed model is used to forecast three time series variables using large South African monthly panel, namely, deposit rate, gold mining share prices and Long term interest rate, using monthly data over the in-sample period (training set) 1992:1---2006:12. The variables are used to compute out-of-sample (testing set) results for 3, 6 and 12 month-ahead forecasts for the period of 2007:1---2011:12. The out-of-sample root mean square error findings show that the FAANN model yields substantial improvements over the autoregressive AR benchmark model and standard dynamic factor model (DFM). The Diebold---Mariano test results also further confirm the superiority of the FAANN model forecast performance over the AR benchmark model and the DFM model forecasts. The superiority of the FAANN model is due to the ANN flexibility to account for potentially complex nonlinear relationships that are not easily captured by linear models.