Stable and fast techniques for unambiguous compound phase coding

Phase shift methods have proven to be very robust and accurate for photometric 3D reconstruction. One problem of these approaches is the existence of ambiguities arising from the periodicity of the fringe patterns. While several techniques for disambiguation exist, all of them require the projection of a significant number of additional patterns. For instance, a global Gray coding sequence or supplemental sinusoidal patterns of different periods are commonly used to complement the basic phase shift technique. In this paper we propose four new coding strategies that encode the index of the projected column using several phases and that mix the resulting phases into a controllable number of projected patterns from which the position can be recovered with subpixel precision. One notable characteristic of the proposed approaches is that we can allocate the additional number of patterns specifically to improve precision or provide higher robustness to noise. The proposed approaches are analyzed and compared with the state of the art, showing their ability to be tuned towards high precision in low noise conditions or robustness with respect to noise

Bottom-Up Design Approach for OBOC Peptide Libraries

One-bead-one-compound peptide libraries, developed following the top-down experimental approach, have attracted great interest in the identification of potential ligands or active peptides. By exploiting a reverse experimental design approach based on the bottom-up strategy, we aimed to develop simplified, maximally diverse peptide libraries that resulted in the successful characterization of mixture components. We show that libraries of 32 and 48 components can be successfully detected in a single run using chromatography coupled to mass spectrometry (UPLC-MS). The proposed libraries were further theoretically evaluated in terms of their composition and physico-chemical properties. By combining the knowledge obtained on single libraries we can cover larger sequence spaces and provide a controlled exploration of the peptide chemical space both theoretically and experimentally. Designing libraries by using the bottom-up approach opens up the possibility of rationally fine-tuning the library complexity based on the available analytical methods

Rapid and Precise Determination of Zero-Field Splittings by Terahertz Time-Domain Electron Paramagnetic Resonance Spectroscopy

Zero-field splitting (ZFS) parameters are fundamentally tied to the geometries of metal ion complexes. Despite their critical importance for understanding the magnetism and spectroscopy of metal complexes, they are not routinely available through general laboratory-based techniques, and are often inferred from magnetism data. Here we demonstrate a simple tabletop experimental approach that enables direct and reliable determination of ZFS parameters in the terahertz (THz) regime. We report time-domain measurements of electron paramagnetic resonance (EPR) signals associated with THz-frequency ZFSs in molecular complexes containing high-spin transition-metal ions. We measure the temporal profiles of the free-induction decays of spin resonances in the complexes at zero and nonzero external magnetic fields, and we derive the EPR spectra via numerical Fourier transformation of the time-domain signals. In most cases, absolute values of the ZFS parameters are extracted from the measured zero-field EPR frequencies, and the signs can be determined by zero-field measurements at two different temperatures. Field-dependent EPR measurements further allow refined determination of the ZFS parameters and access to the g-factor. The results show good agreement with those obtained by other methods. The simplicity of the method portends wide applicability in chemistry, biology and material science.Comment: 36 pages, 30 figures, 1 tabl

Millimeter-wave Communication and Radar Sensing — Opportunities, Challenges, and Solutions

With the development of communication and radar sensing technology, people are able to seek for a more convenient life and better experiences. The fifth generation (5G) mobile network provides high speed communication and internet services with a data rate up to several gigabit per second (Gbps). In addition, 5G offers great opportunities of emerging applications, for example, manufacture automation with the help of precise wireless sensing. For future communication and sensing systems, increasing capacity and accuracy is desired, which can be realized at millimeter-wave spectrum from 30 GHz to 300 GHz with several tens of GHz available bandwidth. Wavelength reduces at higher frequency, this implies more compact transceivers and antennas, and high sensing accuracy and imaging resolution. Challenges arise with these application opportunities when it comes to realizing prototype or demonstrators in practice. This thesis proposes some of the solutions addressing such challenges in a laboratory environment.High data rate millimeter-wave transmission experiments have been demonstrated with the help of advanced instrumentations. These demonstrations show the potential of transceiver chipsets. On the other hand, the real-time communication demonstrations are limited to either low modulation order signals or low symbol rate transmissions. The reason for that is the lack of commercially available high-speed analog-to-digital converters (ADCs); therefore, conventional digital synchronization methods are difficult to implement in real-time systems at very high data rates. In this thesis, two synchronous baseband receivers are proposed with carrier recovery subsystems which only require low-speed ADCs [A][B].Besides synchronization, high-frequency signal generation is also a challenge in millimeter-wave communications. The frequency divider is a critical component of a millimeter-wave frequency synthesizer. Having both wide locking range and high working frequencies is a challenge. In this thesis, a tunable delay gated ring oscillator topology is proposed for dual-mode operation and bandwidth extension [C]. Millimeter-wave radar offers advantages for high accuracy sensing. Traditional millimeter-wave radar with frequency-modulated continuous-wave (FMCW), or continuous-wave (CW), all have their disadvantages. Typically, the FMCW radar cannot share the spectrum with other FMCW radars.\ua0 With limited bandwidth, the number of FMCW radars that could coexist in the same area is limited. CW radars have a limited ambiguous distance of a wavelength. In this thesis, a phase-modulated radar with micrometer accuracy is presented [D]. It is applicable in a multi-radar scenario without occupying more bandwidth, and its ambiguous distance is also much larger than the CW radar. Orthogonal frequency-division multiplexing (OFDM) radar has similar properties. However, its traditional fast calculation method, fast Fourier transform (FFT), limits its measurement accuracy. In this thesis, an accuracy enhancement technique is introduced to increase the measurement accuracy up to the micrometer level [E]

A Probabilistic Approach for Spatio-Temporal Phase Unwrapping in Multi-Frequency Phase-Shift Coding

Multi-frequency techniques with temporally encoded pattern sequences are used in phase-measuring methods of 3D optical metrology to suppress phase noise but lead to ambiguities that can only be resolved by phase unwrapping. However, classical phase unwrapping methods do not use all the information to unwrap all measurements simultaneously and do not consider the periodicity of the phase, which can lead to errors. We present an approach that optimally reconstructs the phase on a pixel-by-pixel basis using a probabilistic modeling approach. The individual phase measurements are modeled using circular probability densities. Maximizing the compound density of all measurements yields the optimal decoding. Since the entire information of all phase measurements is simultaneously used and the wrapping of the phases is implicitly compensated, the reliability can be greatly increased. In addition, a spatio-temporal phase unwrapping is introduced by a probabilistic modeling of the local pixel neighborhoods. This leads to even higher robustness against noise than the conventional methods and thus to better measurement results

Rakenteellisen tiedon johtaminen koodaamattomista ribonukleiinihapoista massaspektrometrialla

The purpose of this study is to describe the development of application of mass spectrometry for the structural analyses of non-coding ribonucleic acids during past decade. Mass spectrometric methods are compared of traditional gel electrophoretic methods, the characteristics of performance of mass spectrometric, analyses are studied and the future trends of mass spectrometry of ribonucleic acids are discussed. Non-coding ribonucleic acids are short polymeric biomolecules which are not translated to proteins, but which may affect the gene expression in all organisms. Regulatory ribonucleic acids act through transient interactions with key molecules in signal transduction pathways. Interactions are mediated through specific secondary and tertiary structures. Posttranscriptional modifications in the structures of molecules may introduce new properties to the organism, such as adaptation to environmental changes or development of resistance to antibiotics. In the scope of this study, the structural studies include i) determination of the sequence of nucleobases in the polymer chain, ii) characterisation and localisation of posttranscriptional modifications in nucleobases and in the backbone structure, iii) identification of ribonucleic acid-binding molecules and iv) probing of higher order structures in the ribonucleic acid molecule. Bacteria, archaea, viruses and HeLa cancer cells have been used as target organisms. Synthesised ribonucleic acids consisting of structural regions of interest have been frequently used. Electrospray ionisation (ESI) and matrix-assisted laser desorption ionisation (MALDI) have been used for ionisation of ribonucleic analytes. Ammonium acetate and 2-propanol are common solvents for ESI. Trihydroxyacetophenone is the optimal MALDI matrix for ionisation of ribonucleic acids and peptides. Ammonium salts are used in ESI buffers and MALDI matrices as additives to remove cation adducts. Reverse phase high performance liquid chromatography has been used for desalting and fractionation of analytes either off-line of on-line, coupled with ESI source. Triethylamine and triethylammonium bicarbonate are used as ion pair reagents almost exclusively. Fourier transform ion cyclotron resonance analyser using ESI coupled with liquid chromatography is the platform of choice for all forms of structural analyses. Time-of-flight (TOF) analyser using MALDI may offer sensitive, easy-to-use and economical solution for simple sequencing of longer oligonucleotides and analyses of analyte mixtures without prior fractionation. Special analysis software is used for computer-aided interpretation of mass spectra. With mass spectrometry, sequences of 20-30 nucleotides of length may be determined unambiguously. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Sequencing in conjunction with other structural studies enables accurate localisation and characterisation of posttranscriptional modifications and identification of nucleobases and amino acids at the sites of interaction. High throughput screening methods for RNA-binding ligands have been developed. Probing of the higher order structures has provided supportive data for computer-generated three dimensional models of viral pseudoknots. In conclusion. mass spectrometric methods are well suited for structural analyses of small species of ribonucleic acids, such as short non-coding ribonucleic acids in the molecular size region of 20-30 nucleotides. Structural information not attainable with other methods of analyses, such as nuclear magnetic resonance and X-ray crystallography, may be obtained with the use of mass spectrometry. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Ligand screening may be used in the search of possible new therapeutic agents. Demanding assay design and challenging interpretation of data requires multidisclipinary knowledge. The implement of mass spectrometry to structural studies of ribonucleic acids is probably most efficiently conducted in specialist groups consisting of researchers from various fields of science

\u3ci\u3eIn Vitro\u3c/i\u3e Stable Isotope Labeling for Discovery of Novel Metabolites by Liquid Chromatography-Mass Spectrometry: Confirmation of γ-Tocopherol Metabolism in Human A549 Cell

A general approach for discovering novel catabolic metabolites from a parent biocompound was developed and validated on metabolism of γ-tocopherol in human A549 cell. Method is based on LC-MS analysis of in vitro stable isotope labeled metabolites and assumes that a parent compound and its metabolites share a common functional group that can be derivatized by well-documented reagents. In this method, two equal aliquots of extracted metabolites are separately derivatized with isotope-coded (heavy) and non-isotope-coded (light) form of derivatizing reagent, mixed at 1:1 ratio and analyzed using LC-MS. The metabolites with common functional group are then easily recognized by determination of a chromatographically co-eluted pair of isotopomers (MS doublet peaks) with similar peak intensities and mass difference corresponding to the mass difference between heavy and light form of derivatization reagent. The feasibility of this approach was demonstrated and validated by identification of products of γ-tocopherol catabolism in human A549 cell culture media using N-methyl-nicotinic acid N-hydroxysuccinimide ester (C1-NANHS) and Nmethyl- d3-nicotinic acid N-hydroxysuccinimide ester (C1-d3-NANHS) derivatizing reagent. Overall four γ-tocopherol metabolites were identified including 9\u27-COOH, 11\u27-COOH, 13\u27-COOH and 13\u27-OH. In addition, the developed LC-MS method can also be used for the fast and sensitive quantitative analysis of γ-tocopherol and other forms of vitamin E related compounds

A combined NMR crystallographic and PXRD investigation of the structure-directing role of water molecules in orotic acid and its lithium and magnesium salts

Despite the abundance of hydrates, their multifaceted nature and hydration/dehydration behaviour is still not fully understood. For the example of orotic acid monohydrate and its lithium and magnesium hydrate salts, we show how NMR crystallography, namely a combination of solid-state NMR with a focus here on 1H Magic Angle Spinning (MAS) NMR experiments and first-principles DFT GIPAW (gauge-including projector augmented wave) calculations, can play a valuable role in the characterization of hydrate systems. Starting from lithium orotate monohydrate, a rigid system with a limited number of tightly bound water molecules, the general feasibility of this approach was demonstrated. Moving onto more complex hydrate structures, mobility in the orotic acid monohydrate was observed, while for the most complex hydrate, magnesium orotate octahydrate, a loss of associated water molecules was observed after an overnight MAS NMR experiment. A combined study by experimental MAS NMR, powder X-ray diffraction (PXRD) and thermogravimetric analysis (TGA) revealed changes after vacuum drying as well as after storage of a vacuum dried sample under ambient conditions. Specifically, TGA showed the vacuum dried sample to correspond to a dihydrate, for which no structure has yet been determined by single-crystal diffraction. An NMR crystallography analysis showed that a combination of putative symmetric and asymmetric dihydrate structures explains the observed changes in the experimental MAS NMR spectra