Secret key exchange in ultra-long lasers by radio-frequency spectrum coding

We propose a new approach to the generation of an alphabet for secret key exchange relying on small variations in the cavity length of an ultra-long fiber laser. This new concept is supported by experimental results showing how the radio-frequency spectrum of the laser can be exploited as a carrier to exchange information. The test bench for our proof of principle is a 50 km-long fiber laser linking two users, Alice and Bob, where each user can randomly add an extra 1 km-long segment of fiber. The choice of laser length is driven by two independent random binary values, which makes such length become itself a random variable. The security of key exchange is ensured whenever the two independent random choices lead to the same laser length and, hence, to the same free spectral range.

Editorial overview:new protein production tools for structural biology

Full text: The idea of producing proteins from recombinant DNA hatched almost half a century ago. In his PhD thesis, Peter Lobban foresaw the prospect of inserting foreign DNA (from any source, including mammalian cells) into the genome of a λ phage in order to detect and recover protein products from Escherichia coli [ 1 and 2]. Only a few years later, in 1977, Herbert Boyer and his colleagues succeeded in the first ever expression of a peptide-coding gene in E. coli — they produced recombinant somatostatin [ 3] followed shortly after by human insulin. The field has advanced enormously since those early days and today recombinant proteins have become indispensable in advancing research and development in all fields of the life sciences. Structural biology, in particular, has benefitted tremendously from recombinant protein biotechnology, and an overwhelming proportion of the entries in the Protein Data Bank (PDB) are based on heterologously expressed proteins. Nonetheless, synthesizing, purifying and stabilizing recombinant proteins can still be thoroughly challenging. For example, the soluble proteome is organized to a large part into multicomponent complexes (in humans often comprising ten or more subunits), posing critical challenges for recombinant production. A third of all proteins in cells are located in the membrane, and pose special challenges that require a more bespoke approach. Recent advances may now mean that even these most recalcitrant of proteins could become tenable structural biology targets on a more routine basis. In this special issue, we examine progress in key areas that suggests this is indeed the case. Our first contribution examines the importance of understanding quality control in the host cell during recombinant protein production, and pays particular attention to the synthesis of recombinant membrane proteins. A major challenge faced by any host cell factory is the balance it must strike between its own requirements for growth and the fact that its cellular machinery has essentially been hijacked by an expression construct. In this context, Bill and von der Haar examine emerging insights into the role of the dependent pathways of translation and protein folding in defining high-yielding recombinant membrane protein production experiments for the common prokaryotic and eukaryotic expression hosts. Rather than acting as isolated entities, many membrane proteins form complexes to carry out their functions. To understand their biological mechanisms, it is essential to study the molecular structure of the intact membrane protein assemblies. Recombinant production of membrane protein complexes is still a formidable, at times insurmountable, challenge. In these cases, extraction from natural sources is the only option to prepare samples for structural and functional studies. Zorman and co-workers, in our second contribution, provide an overview of recent advances in the production of multi-subunit membrane protein complexes and highlight recent achievements in membrane protein structural research brought about by state-of-the-art near-atomic resolution cryo-electron microscopy techniques. E. coli has been the dominant host cell for recombinant protein production. Nonetheless, eukaryotic expression systems, including yeasts, insect cells and mammalian cells, are increasingly gaining prominence in the field. The yeast species Pichia pastoris, is a well-established recombinant expression system for a number of applications, including the production of a range of different membrane proteins. Byrne reviews high-resolution structures that have been determined using this methylotroph as an expression host. Although it is not yet clear why P. pastoris is suited to producing such a wide range of membrane proteins, its ease of use and the availability of diverse tools that can be readily implemented in standard bioscience laboratories mean that it is likely to become an increasingly popular option in structural biology pipelines. The contribution by Columbus concludes the membrane protein section of this volume. In her overview of post-expression strategies, Columbus surveys the four most common biochemical approaches for the structural investigation of membrane proteins. Limited proteolysis has successfully aided structure determination of membrane proteins in many cases. Deglycosylation of membrane proteins following production and purification analysis has also facilitated membrane protein structure analysis. Moreover, chemical modifications, such as lysine methylation and cysteine alkylation, have proven their worth to facilitate crystallization of membrane proteins, as well as NMR investigations of membrane protein conformational sampling. Together these approaches have greatly facilitated the structure determination of more than 40 membrane proteins to date. It may be an advantage to produce a target protein in mammalian cells, especially if authentic post-translational modifications such as glycosylation are required for proper activity. Chinese Hamster Ovary (CHO) cells and Human Embryonic Kidney (HEK) 293 cell lines have emerged as excellent hosts for heterologous production. The generation of stable cell-lines is often an aspiration for synthesizing proteins expressed in mammalian cells, in particular if high volumetric yields are to be achieved. In his report, Buessow surveys recent structures of proteins produced using stable mammalian cells and summarizes both well-established and novel approaches to facilitate stable cell-line generation for structural biology applications. The ambition of many biologists is to observe a protein's structure in the native environment of the cell itself. Until recently, this seemed to be more of a dream than a reality. Advances in nuclear magnetic resonance (NMR) spectroscopy techniques, however, have now made possible the observation of mechanistic events at the molecular level of protein structure. Smith and colleagues, in an exciting contribution, review emerging ‘in-cell NMR’ techniques that demonstrate the potential to monitor biological activities by NMR in real time in native physiological environments. A current drawback of NMR as a structure determination tool derives from size limitations of the molecule under investigation and the structures of large proteins and their complexes are therefore typically intractable by NMR. A solution to this challenge is the use of selective isotope labeling of the target protein, which results in a marked reduction of the complexity of NMR spectra and allows dynamic processes even in very large proteins and even ribosomes to be investigated. Kerfah and co-workers introduce methyl-specific isotopic labeling as a molecular tool-box, and review its applications to the solution NMR analysis of large proteins. Tyagi and Lemke next examine single-molecule FRET and crosslinking following the co-translational incorporation of non-canonical amino acids (ncAAs); the goal here is to move beyond static snap-shots of proteins and their complexes and to observe them as dynamic entities. The encoding of ncAAs through codon-suppression technology allows biomolecules to be investigated with diverse structural biology methods. In their article, Tyagi and Lemke discuss these approaches and speculate on the design of improved host organisms for ‘integrative structural biology research’. Our volume concludes with two contributions that resolve particular bottlenecks in the protein structure determination pipeline. The contribution by Crepin and co-workers introduces the concept of polyproteins in contemporary structural biology. Polyproteins are widespread in nature. They represent long polypeptide chains in which individual smaller proteins with different biological function are covalently linked together. Highly specific proteases then tailor the polyprotein into its constituent proteins. Many viruses use polyproteins as a means of organizing their proteome. The concept of polyproteins has now been exploited successfully to produce hitherto inaccessible recombinant protein complexes. For instance, by means of a self-processing synthetic polyprotein, the influenza polymerase, a high-value drug target that had remained elusive for decades, has been produced, and its high-resolution structure determined. In the contribution by Desmyter and co-workers, a further, often imposing, bottleneck in high-resolution protein structure determination is addressed: The requirement to form stable three-dimensional crystal lattices that diffract incident X-ray radiation to high resolution. Nanobodies have proven to be uniquely useful as crystallization chaperones, to coax challenging targets into suitable crystal lattices. Desmyter and co-workers review the generation of nanobodies by immunization, and highlight the application of this powerful technology to the crystallography of important protein specimens including G protein-coupled receptors (GPCRs). Recombinant protein production has come a long way since Peter Lobban's hypothesis in the late 1960s, with recombinant proteins now a dominant force in structural biology. The contributions in this volume showcase an impressive array of inventive approaches that are being developed and implemented, ever increasing the scope of recombinant technology to facilitate the determination of elusive protein structures. Powerful new methods from synthetic biology are further accelerating progress. Structure determination is now reaching into the living cell with the ultimate goal of observing functional molecular architectures in action in their native physiological environment. We anticipate that even the most challenging protein assemblies will be tackled by recombinant technology in the near future.

Ultralong fiber lasers with coding in free-spectral range for secure key Distribution

We present experimental results on a 50km fiber laser switching among four different values of the free-spectral range for possible applications in secure key-distribution. © 2014 OSA.

Demonstration of phase-conjugated subcarrier coding for fiber nonlinearity compensation in CO-OFDM transmission

In this paper, we demonstrate through computer simulation and experiment a novel subcarrier coding scheme combined with pre-electrical dispersion compensation (pre-EDC) for fiber nonlinearity mitigation in coherent optical orthogonal frequency division multiplexing (CO-OFDM) systems. As the frequency spacing in CO-OFDM systems is usually small (tens of MHz), neighbouring subcarriers tend to experience correlated nonlinear distortions after propagation over a fiber link. As a consequence, nonlinearity mitigation can be achieved by encoding and processing neighbouring OFDM subcarriers simultaneously. Herein, we propose to adopt the concept of dual phase conjugated twin wave for CO-OFDM transmission. Simulation and experimental results show that this simple technique combined with 50% pre-EDC can effectively offer up to 1.5 and 0.8 dB performance gains in CO-OFDM systems with BPSK and QPSK modulation formats, respectively.

Coding together at scale:GitHub as a collaborative social network

GitHub is the most popular repository for open source code (Finley 2011). It has more than 3.5 million users, as the company declared in April 2013, and more than 10 million repositories, as of December 2013. It has a publicly accessible API and, since March 2012, it also publishes a stream of all the events occurring on public projects. Interactions among GitHub users are of a complex nature and take place in different forms. Developers create and fork repositories, push code, approve code pushed by others, bookmark their favorite projects and follow other developers to keep track of their activities. In this paper we present a characterization of GitHub, as both a social network and a collaborative platform. To the best of our knowledge, this is the first quantitative study about the interactions happening on GitHub. We analyze the logs from the service over 18 months (between March 11, 2012 and September 11, 2013), describing 183.54 million events and we obtain information about 2.19 million users and 5.68 million repositories, both growing linearly in time. We show that the distributions of the number of contributors per project, watchers per project and followers per user show a power-law-like shape. We analyze social ties and repository-mediated collaboration patterns, and we observe a remarkably low level of reciprocity of the social connections. We also measure the activity of each user in terms of authored events and we observe that very active users do not necessarily have a large number of followers. Finally, we provide a geographic characterization of the centers of activity and we investigate how distance influences collaboration.

Radio-frequency spectrum coding in ultra-long fibre laser based cryptography

We propose a new approach for secret key exchange involving the variation of the cavity length of an ultra-long fibre laser. The scheme is based on the realisation that the free spectral range of the laser cavity can be used as an information carrier. We present a proof-of-principle demonstration of this new concept using a 50-km-long fibre laser to link two users, both of whom can randomly add an extra 1-km-long fibre segment.

Probabilistic Models in Cryptography, Coding Theory and Tests for PRNG

2000 Mathematics Subject Classification: 94A29, 94B70

Advanced digital signal processing for coherent optical OFDM transmissions

Coherent optical orthogonal frequency division multiplexing (CO-OFDM) has been actively considered as a potential candidate for long-haul transmission and 400 Gb/s to 1 Tb/s Ethernet transport because of its high spectral efficiency, efficient implementation, flexibility and robustness against linear impairments such as chromatic dispersion and polarization mode dispersion. However, due to the long symbol duration and narrow subcarrier spacing, CO-OFDM systems are sensitive to laser phase noise and fibre nonlinearity induced penalties. As a result, the development of CO-OFDM transmission technology crucially relies on efficient techniques to compensate for the laser phase noise and fibre nonlinearity impairments. In this thesis, high performance and low complexity digital signal processing techniques for laser phase noise and fibre nonlinearity compensation in CO-OFDM transmissions are demonstrated. For laser phase noise compensation, three novel techniques, namely quasipilot-aided, decision-directed-free blind and multiplier-free blind are introduced. For fibre nonlinear compensation, two novel techniques which are referred to as phase conjugated pilots and phase conjugated subcarrier coding, are proposed. All these abovementioned digital signal processing techniques offer high performances and flexibilities while requiring relatively low complexities in comparison with other existing phase noise and nonlinear compensation techniques. As a result of the developments of these digital signal processing techniques, CO-OFDM technology is expected to play a significant role in future ultra-high capacity optical network. In addition, this thesis also presents preliminary study on nonlinear Fourier transform based transmission schemes in which OFDM is a highly suitable modulation format. The obtained result paves the way towards a truly flexible nonlinear wave-division multiplexing system that allows the current nonlinear transmission limitations to be exceeded.

Space time coding for polynomial phase modulated signals

Polynomial phase modulated (PPM) signals have been shown to provide improved error rate performance with respect to conventional modulation formats under additive white Gaussian noise and fading channels in single-input single-output (SISO) communication systems. In this dissertation, systems with two and four transmit antennas using PPM signals were presented. In both cases we employed full-rate space-time block codes in order to take advantage of the multipath channel. For two transmit antennas, we used the orthogonal space-time block code (OSTBC) proposed by Alamouti and performed symbol-wise decoding by estimating the phase coefficients of the PPM signal using three different methods: maximum-likelihood (ML), sub-optimal ML (S-ML) and the high-order ambiguity function (HAF). In the case of four transmit antennas, we used the full-rate quasi-OSTBC (QOSTBC) proposed by Jafarkhani. However, in order to ensure the best error rate performance, PPM signals were selected such as to maximize the QOSTBC’s minimum coding gain distance (CGD). Since this method does not always provide a unique solution, an additional criterion known as maximum channel interference coefficient (CIC) was proposed. Through Monte Carlo simulations it was shown that by using QOSTBCs along with the properly selected PPM constellations based on the CGD and CIC criteria, full diversity in flat fading channels and thus, low BER at high signal-to-noise ratios (SNR) can be ensured. Lastly, the performance of symbol-wise decoding for QOSTBCs was evaluated. In this case a quasi zero-forcing method was used to decouple the received signal and it was shown that although this technique reduces the decoding complexity of the system, there is a penalty to be paid in terms of error rate performance at high SNRs.

Quasi-Orthogonal Space-Time Block Coding Using Polynomial Phase Modulation

Recently, polynomial phase modulation (PPM) was shown to be a power- and bandwidth-efficient modulation format. These two characteristics are in high demand nowadays specially in mobile applications, where devices with size, weight, and power (SWaP) constraints are common. In this paper, we propose implementing a full-diversity quasiorthogonal space-time block code (QOSTBC) using polynomial phase signals as modulation format. QOSTBCs along with PPM are used in order to improve the power efficiency of communication systems with four transmit antennas. We obtain the optimal PPM constellations that ensure full diversity and maximize the QOSTBC's minimum coding gain distance. Simulation results show that by using QOSTBCs along with a properly selected PPM constellation, full diversity in flat fading channels and thus low BER at high signal-to-noise ratios (SNR) can be ensured. More importantly, it is also shown that QOSTBCs using PPM achieve a better error performance than those using conventional modulation formats.

The refinement and validation of the critical decision making and problem solving scale moral dilema (CDP-MD)

This thesis extended previous research on critical decision making and problem solving by refining and validating a measure designed to assess the use of critical thinking and critical discussion in sociomoral dilemmas. The purpose of this thesis was twofold: 1) to refine the administration of the Critical Thinking Subscale of the CDP to elicit more adequate responses and for purposes of refining the coding and scoring procedures for the total measure, and 2) to collect preliminary data on the initial reliabilities of the measure. Subjects consisted of 40 undergraduate students at Florida International University. Results indicate that the use of longer probes on the Critical Thinking Subscale was more effective in eliciting adequate responses necessary for coding and evaluating the subjects performance. Analyses on the psychometric properties of the measure consisted of test-retest reliability and inter-rater reliability.

Extended program notes for thesis recital

Chaconne, Transcription for Piano in D minor J.S. Bach (arr. Ferruccio Busoni) Reflets dans l'eau from Images, Book 1 Claude Debussy A la Albeniz Rodion Shchedrin Basso Ostinato from Two Polyphonic Pieces Sonata-Reminiscenza, Op. 38, No. 1 Nikolai Medtner Die Loreley, S. 532 Franz Liszt Hungarian Rhapsody No. 6

A novel lossless compression technique for text data

The focus of this thesis is placed on text data compression based on the fundamental coding scheme referred to as the American Standard Code for Information Interchange or ASCII. The research objective is the development of software algorithms that result in significant compression of text data. Past and current compression techniques have been thoroughly reviewed to ensure proper contrast between the compression results of the proposed technique with those of existing ones. The research problem is based on the need to achieve higher compression of text files in order to save valuable memory space and increase the transmission rate of these text files. It was deemed necessary that the compression algorithm to be developed would have to be effective even for small files and be able to contend with uncommon words as they are dynamically included in the dictionary once they are encountered. A critical design aspect of this compression technique is its compatibility to existing compression techniques. In other words, the developed algorithm can be used in conjunction with existing techniques to yield even higher compression ratios. This thesis demonstrates such capabilities and such outcomes, and the research objective of achieving higher compression ratio is attained.

The bass as a melodic voice in jazz : extended program notes for thesis recital

This thesis discusses the use of the bass as a melodic instrument in jazz. It focuses on seven compositions performed for a Master's recital on March 22, 2010. For each selection, I provide a brief biography of the composer, information about the song and insight on performance practice. I examine the advanced techniques pioneered by innovative bassists and explore ways in which they can be used to further exploit the melodic potential of the bass in a jazz context. A compact disc recording of the recital is included.

Of madness and many-valuedness: an investigation into Suszko's Thesis

Suszko’s Thesis is a philosophical claim regarding the nature of many-valuedness. It was formulated by the Polish logician Roman Suszko during the middle 70s and states the existence of “only but two truth values”. The thesis is a reaction against the notion of many-valuedness conceived by Jan Łukasiewicz. Reputed as one of the modern founders of many-valued logics, Łukasiewicz considered a third undetermined value in addition to the traditional Fregean values of Truth and Falsehood. For Łukasiewicz, his third value could be seen as a step beyond the Aristotelian dichotomy of Being and non-Being. According to Suszko, Łukasiewicz’s ideas rested on a confusion between algebraic values (what sentences describe/denote) and logical values (truth and falsity). Thus, Łukasiewicz’s third undetermined value is no more than an algebraic value, a possible denotation for a sentence, but not a genuine logical value. Suszko’s Thesis is endorsed by a formal result baptized as Suszko’s Reduction, a theorem that states every Tarskian logic may be characterized by a two-valued semantics. The present study is intended as a thorough investigation of Suszko’s thesis and its implications. The first part is devoted to the historical roots of many-valuedness and introduce Suszko’s main motivations in formulating the double character of truth-values by drawing the distinction in between algebraic and logical values. The second part explores Suszko’s Reduction and presents the developments achieved from it; the properties of two-valued semantics in comparison to many-valued semantics are also explored and discussed. Last but not least, the third part investigates the notion of logical values in the context of non-Tarskian notions of entailment; the meaning of Suszko’s thesis within such frameworks is also discussed. Moreover, the philosophical foundations for non-Tarskian notions of entailment are explored in the light of recent debates concerning logical pluralism.