1,380 results on '"Millar, David"'
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2. Tracking oscillatory signals through the flaring solar atmosphere
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Millar, David C. L.
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QB Astronomy ,QC Physics - Abstract
Fluctuations in the light we receive from the Sun happen constantly. Much of this variation can be thought of as random, however within solar timeseries there are many true periodic signals to be found, if one knows where to look. Identifying the source of these oscillations can give us a wealth of information about the underlying physical environment of the solar atmosphere. One area which has been particularly exploited is the search for oscillations due to solar flares which can be short-lived, bursty, and variable. Periodic signals detected during solar flares can help us understand the physics of flares, as well as how they interact with the lower layers of the atmosphere. The lower layers of the atmosphere have been known to present periodic fluctuations on timescales of a few minutes in quiet Sun conditions, and there have been some recent reports of energetic events such as flares affecting the quiescent oscillations, even exciting them. This thesis aims to investigate the effect of flares on the lower atmosphere by identifying and categorising oscillatory signals in a variety of solar data. In Chapter 1 an overview of necessary background physics is given. The layers of the Sun's atmosphere and the standard model of solar flares are described. An introduction to different periodic signals which are present in solar data is given, including quiet Sun periodicities and those observed during transient phenomena. The methods used throughout the thesis are presented in Chapter 2, starting with descriptions of the instrumentation which obtained the analysed datasets. A discussion is presented on best practices when searching for oscillations in data, and the spectral fitting method is outlined. Techniques used to obtain physical solar parameters from observations are also introduced. In Chapter 3, a study of chromospheric intensity oscillations in a flaring active region is presented. Maps were produced showing the oscillatory signals which were present before and after the occurrence of the flare. When comparing the results after the flare to those before, oscillations were found to have changed their locations and typical periods in the vicinity of a sunspot located near the flare ribbons. These changes were interpreted as the result of a changing magnetic environment connected to the flare. The interpretations of these results were investigated using magnetohydrodynamic simulations in Chapter 4. Three different sets of simulations were carried out, to identify the most likely effect to have been responsible for the results of Chapter 3. The sets of simulations were concerned with the magnetic field inclination, the chromospheric temperature profile, and the length of the chromospheric cavity. The inclination angle was found to be the most likely of these three effects to change the periodic signals. Chapter 5 presents analysis of a second dataset, from an active region which featured much less powerful flare activity than the event from Chapter 3. A similar analysis was performed, and extended to also feature Doppler velocity data. Velocity oscillations were identified in pixels which exhibited some of the strongest flare heating. The possible cause of the induced velocity oscillations was explored using measurements of the magnetic field from spectropolarimetric observations, and inversions using the STiC code. In Chapter 6 concluding remarks are made, including a summary of the main results of the thesis and descriptions of possible future avenues for investigation.
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- 2023
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3. Line-field Coherent Sensing with LED Illumination
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Yurdakul, Celalettin, Millar, David S., Mansour, Hassan, Wang, Pu, Kojima, Keisuke, Koike-Akino, Toshiaki, Parsons, Kieran, and Orlik, Philip V.
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Physics - Optics ,Physics - Instrumentation and Detectors - Abstract
We describe a method of low-coherence interferometry based optical profilometry using standard light-emitting diode (LED) illumination and complementary metal-oxide-semiconductor (CMOS) image sensors. A line-field illumination strategy allows for the simultaneous measurement of many points in space. Micron scale accuracy and resolution are achieved and demonstrated using a variety of targets.
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- 2022
4. DNN-assisted optical geometric constellation shaped PSK modulation for PAM4-to-QPSK format conversion gateway node
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Kodama, Takahiro, Koike-Akino, Toshiaki, Millar, David S., Kojima, Keisuke, and Parsons, Kieran
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Electrical Engineering and Systems Science - Signal Processing - Abstract
An optical gateway to convert four-level pulse amplitude modulation to quadrature phase shift keying modulation format having shaping gain was proposed for flexible intensity to phase mapping which exploits non-uniform phase noise. The power consumption of the optical modulation format conversion can save by making a DNN-based decision on the receiver side for the generated QPSK signal with non-uniform phase noise. A proof-of-principle experiment has shown that an optically geometric constellation shaped QPSK modulated signals generated from regular PAM4 signals with Gaussian-distributed noise. The shaped QPSK signal shows BER and generalized mutual information improvement by 1dB gain through the use of digital neural network signal recovery.
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- 2021
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5. Cosmovisions and critical sustainability sciences
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Millar, David, primary, Santuah, Niagia F., additional, and Tengolzor, Maxwell Ba-an, additional
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- 2023
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6. Huffman-Coded Sphere Shaping for Extended-Reach Single-Span Links
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Skvortcov, Pavel, Phillips, Ian, Forysiak, Wladek, Koike-Akino, Toshiaki, Kojima, Keisuke, Parsons, Kieran, and Millar, David S.
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Electrical Engineering and Systems Science - Signal Processing - Abstract
Huffman-coded sphere shaping (HCSS) is an algorithm for finite-length probabilistic constellation shaping, which provides nearly optimal energy efficiency at low implementation complexity. In this paper, we experimentally study the nonlinear performance of HCSS employing dual-polarization 64-ary quadrature amplitude modulation (DP-64QAM) in an extended reach single-span link comprising 200 km of standard single mode fiber (SSMF). We investigate the effects of shaping sequence length, dimensionality of symbol mapping, and shaping rate. We determine that the na\"ive approach of Maxwell-Boltzmann distribution matching - which is optimal in the additive white Gaussian noise channel - provides a maximum achievable information rate gain of 0.18 bits/4D-symbol in the infinite length regime. Conversely, HCSS can achieve a gain of 0.37 bits/4Dsymbol using amplitude sequence lengths of 32, which may be implemented without multiplications, using integer comparison and addition operations only. Coded system performance, with a net data rate of approximately 425 Gb/s for both shaped and uniform inputs, is also analyzed., Comment: 13 pages and 16 figures
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- 2020
7. The effect of a solar flare on chromospheric oscillations
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Millar, David C. L., Fletcher, Lyndsay, and Milligan, Ryan O.
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Astrophysics - Solar and Stellar Astrophysics - Abstract
Oscillations in the solar atmosphere have long been observed in quiet conditions, and increasingly also in data taken during solar flares. The chromosphere is known for its 3-minute signals, which are particularly strong over sunspot umbrae. These signals are thought to be driven by photospheric disturbances and their periods determined by the chromosphere's acoustic cut-off frequency. A small number of observations have shown the chromospheric 3-minute signals to be affected by energetic events such as solar flares, however the link between flare activity and these oscillatory signals remains unclear. In this work we present evidence of changes to the oscillatory structure of the chromosphere over a sunspot which occurs during the impulsive phase of an M1 flare. Using imaging data from the CRISP instrument across the H$\alpha$ and Ca II 8542 {\AA} spectral lines, we employed a method of fitting models to power spectra to produce maps of areas where there is evidence of oscillatory signals above a red noise background. Comparing results taken before and after the impulsive phase of the flare, we found that the oscillatory signals taken after the start of the flare differ in two ways: the locations of oscillatory signals had changed and the typical periods of the oscillations had tended to increase (in some cases increasing from $\lt$100s to $\sim$200s). Both of these results can be explained by a restructuring of the magnetic field in the chromosphere during the flare activity, which is backed up by images of coronal loops showing clear changes to magnetic connectivity. These results represent one of the many ways that active regions can be affected by solar flare events.
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- 2020
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8. Huffman-coded Sphere Shaping and Distribution Matching Algorithms via Lookup Tables
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Fehenberger, Tobias, Millar, David S., Koike-Akino, Toshiaki, Kojima, Keisuke, Parsons, Kieran, and Griesser, Helmut
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Electrical Engineering and Systems Science - Signal Processing ,Computer Science - Information Theory - Abstract
In this paper, we study amplitude shaping schemes for the probabilistic amplitude shaping (PAS) framework as well as algorithms for constant-composition distribution matching (CCDM). Huffman-coded sphere shaping (HCSS) is discussed in detail, which internally uses Huffman coding to determine the composition to be used and relies on conventional CCDM algorithms for mapping and demapping. Numerical simulations show that HCSS closes the performance gap between distribution matching schemes and sphere shaping techniques such as enumerative sphere shaping (ESS). HCSS is based on an architecture that is different from the trellis-based setup of ESS. It allows to tailor the used HCSS compositions to the transmission channel and to take into account complexity constraints. We further discuss in detail multiset ranking (MR) and subset ranking (SR) as alternatives to arithmetic-coding (AC) CCDM. The advantage of MR over AC is that it requires less sequential operations for mapping. SR operates on binary alphabets only, which can introduce some additional rate loss when a nonbinary-to-binary transformation is required. However, the binomial coefficients required for SR can be precomputed and stored in a lookup table (LUT). We perform an analysis of rate loss and decoding performance for the proposed techniques and compare them to other prominent amplitude shaping schemes. For medium to long block lengths, MR-HCSS and SR-HCSS are shown to have similar performance to ESS. SR-HCSS and uniform 64QAM are compared in additive white Gaussian noise simulations and shaping gains of 0.5 dB and 1 dB are demonstrated with 1 kbit and 100 kbit LUT size, respectively., Comment: The work has been partially funded by the German Ministry of Education and Research in the project PEARLS (contract #13N14937)
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- 2020
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9. Analysis of Nonlinear Fiber Interactions for Finite-Length Constant-Composition Sequences
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Fehenberger, Tobias, Millar, David S., Koike-Akino, Toshiaki, Kojima, Keisuke, Parsons, Kieran, and Griesser, Helmut
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Electrical Engineering and Systems Science - Signal Processing ,Computer Science - Information Theory - Abstract
In order to realize probabilistically shaped signaling within the probabilistic amplitude shaping (PAS) framework, a shaping device outputs sequences that follow a certain nonuniform distribution. In case of constant-composition (CC) distribution matching (CCDM), the sequences differ only in the ordering of their constituent symbols, whereas the number of occurrences of each symbol is constant in every output block. Recent results by Amari \textit{et al.} have shown that the CCDM block length can have a considerable impact on the effective signal-to-noise ratio (SNR) after fiber transmission. So far, no explanation for this behavior has been presented. Furthermore, the block-length dependence of the SNR seems not to be fully aligned with previous results in the literature. This paper is devoted to a detailed analysis of the nonlinear fiber interactions for CC sequences. We confirm in fiber simulations the inverse proportionality of SNR with CCDM block length and present two explanations. The first one, which only holds in the short-length regime, is based on how two-dimensional symbols are generated from shaped amplitudes in the PAS framework. The second, more general explanation relates to an induced shuffling within a sequence, or equivalently a limited concentration of identical symbols, that is an inherent property for short CC blocks, yet not necessarily present for long blocks. This temporal property results in weaker nonlinear interactions, and thus higher SNR, for short CC sequences. For a typical multi-span fiber setup, the SNR difference is numerically demonstrated to be up to 0.7dB. Finally, we evaluate a heuristic figure of merit that captures the number of runs of identical symbols in a concatenation of several CC sequences. For moderate block lengths up to approximately 100 symbols, this metric suggests that limiting the number of identical-symbol runs can be beneficial., Comment: The work was supported in part by the German Ministry of Education and Research in the projects SpeeD (contract #13N1374) and PEARLS (contract #13N14937)
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- 2020
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10. How to treat travel medicine
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Millar, David
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- 2003
11. Neural Turbo Equalization: Deep Learning for Fiber-Optic Nonlinearity Compensation
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Koike-Akino, Toshiaki, Wang, Ye, Millar, David S., Kojima, Keisuke, and Parsons, Kieran
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Electrical Engineering and Systems Science - Signal Processing ,Computer Science - Information Theory ,Computer Science - Machine Learning - Abstract
Recently, data-driven approaches motivated by modern deep learning have been applied to optical communications in place of traditional model-based counterparts. The application of deep neural networks (DNN) allows flexible statistical analysis of complicated fiber-optic systems without relying on any specific physical models. Due to the inherent nonlinearity in DNN, various equalizers based on DNN have shown significant potentials to mitigate fiber nonlinearity. In this paper, we propose a turbo equalization (TEQ) based on DNN as a new alternative framework to deal with nonlinear fiber impairments for future coherent optical communications. The proposed DNN-TEQ is constructed with nested deep residual networks (ResNet) to train extrinsic likelihood given soft-information feedback from channel decoding. Through extrinsic information transfer (EXIT) analysis, we verify that our DNN-TEQ can accelerate decoding convergence to achieve a significant gain in achievable throughput by 0.61b/s/Hz. We also demonstrate that optimizing irregular low-density parity-check (LDPC) codes to match EXIT chart of the DNN-TEQ can improve achievable rates by up to 0.12 b/s/Hz., Comment: 7 pages, 13 figures
- Published
- 2019
12. Parallel-Amplitude Architecture and Subset Ranking for Fast Distribution Matching
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Fehenberger, Tobias, Millar, David S., Koike-Akino, Toshiaki, Kojima, Keisuke, and Parsons, Kieran
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Electrical Engineering and Systems Science - Signal Processing - Abstract
A distribution matcher (DM) maps a binary input sequence into a block of nonuniformly distributed symbols. To facilitate the implementation of shaped signaling, fast DM solutions with high throughput and low serialism are required. We propose a novel DM architecture with parallel amplitudes (PADM) for which m component DMs, each with a different binary output alphabet, are operated in parallel in order to generate a shaped sequence with m amplitudes. With negligible rate loss compared to a single nonbinary DM, PA-DM has a parallelization factor that grows linearly with m, and the component DMs have reduced output lengths. For such binary-output DMs, a novel constant-composition DM (CCDM) algorithm based on subset ranking (SR) is proposed. We present SR-CCDM algorithms that are serial in the minimum number of occurrences of either binary symbol for mapping and fully parallel in demapping. For distributions that are optimized for the additive white Gaussian noise (AWGN) channel, we numerically show that PA-DM combined with SR-CCDM can reduce the number of sequential processing steps by more than an order of magnitude, while having a rate loss that is comparable to conventional nonbinary CCDM with arithmetic coding., Comment: 10 pages, 6 figures/
- Published
- 2019
13. Labour's byzantine processes
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Millar, David
- Published
- 1990
14. Multiset-Partition Distribution Matching
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Fehenberger, Tobias, Millar, David S., Koike-Akino, Toshiaki, Kojima, Keisuke, and Parsons, Kieran
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Electrical Engineering and Systems Science - Signal Processing - Abstract
Distribution matching is a fixed-length invertible mapping from a uniformly distributed bit sequence to shaped amplitudes and plays an important role in the probabilistic amplitude shaping framework. With conventional constantcomposition distribution matching (CCDM), all output sequences have identical composition. In this paper, we propose multisetpartition distribution matching (MPDM) where the composition is constant over all output sequences. When considering the desired distribution as a multiset, MPDM corresponds to partitioning this multiset into equal-size subsets. We show that MPDM allows to address more output sequences and thus has lower rate loss than CCDM in all nontrivial cases. By imposing some constraints on the partitioning, a constructive MPDM algorithm is proposed which comprises two parts. A variable-length prefix of the binary data word determines the composition to be used, and the remainder of the input word is mapped with a conventional CCDM algorithm, such as arithmetic coding, according to the chosen composition. Simulations of 64-ary quadrature amplitude modulation over the additive white Gaussian noise channel demonstrate that the block-length saving of MPDM over CCDM for a fixed gap to capacity is approximately a factor of 2.5 to 5 at medium to high signal-to-noise ratios (SNRs)., Comment: 9 pages, 8 figures
- Published
- 2018
15. Modeling dynamic soil carbon attributes among common southern New England land uses
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Millar, David, Stolt, Mark, Amador, José, and Paolucci, Andrew
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- 2022
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16. Novel III-V compound semiconductor technologies for low power digital logic applications
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Millar, David Alan John
- Subjects
621.3815 ,T Technology (General) ,TK Electrical engineering. Electronics Nuclear engineering - Abstract
As silicon (Si) complementary metal oxide semiconductor (CMOS) technology continues to scale into the 10 nm node, chip power consumption is approaching 200 W/cm2 and any further increase is unsustainable. Incorporating III-V compound semiconductor n-type devices into future CMOS generations could allow for the the reduction in supply voltage, and therefore, power consumption, while simultaneously improving on-state performance. The advanced state of Si CMOS places stringent demands on III-V devices, however: the current 14 nm Si tri-gate devices employ high aspect ratio, densely spaced fins which serve to significantly increase current per chip surface area. III-V devices need to significantly out perform state of the art Si devices in order to merit their disruptive incorporation into the well established CMOS process. This necessitates that they too exploit the vertical dimension. To this end, this thesis reports on the fabrication, measurement and analysis of high aspect ratio junctionless InGaAs FinFETs. The junctionless architecture was first demonstrated in 2010 and was shown to circumvent pro- hibitive fabrication challenges for devices with ultra short gate lengths. This work investigated the impact of fin width on both the on and off-state performance of 200 nm gate length devices, with nominal fin widths of 10, 15 and 20 nm. Excellent subthreshold performance was demonstrated, with the narrowest fin width exhibiting a minimum subthreshold swing (SS) of 73 mV/Dec., and an average SS of 80 mV/Dec. over two decades of current. A maximum on-current, Ion, of 80.51 μA/cm2 was measured at a gate overdrive of 0.5 V from an off-state current, Ioff, of 100 nA/cm2 and a drain voltage, Vd, of 0.5 V, with current normalised by gated perimeter. This is competitive with other III-V junctionless devices at similar gate lengths. With current normalised to base fin width, however, Ion increases to 371.8 μA/cm2, which is a record value among equivalently normalised non-planar III-V junctionless devices at any gate length. This technology, therefore, clearly demonstrates the feasibility of incorporating scaled, etched InGaAs fins into future logic generations. Perhaps the greatest bottleneck to the incorporation of III-V compounds into future CMOS technology nodes, however, is the lack of a suitable III-V PMOS candidate: co-integrating different material systems onto a common substate incurs great fabrication complexity, and therefore, cost. III-V antimonides, however, have recently emerged as promising candidates for III-V PMOS and exhibit the highest bulk electron mobility of all III-Vs in addition to a hole mobility second only to germanium. InGaSb ternary compounds have been shown to offer the best combined performance for electrons and holes in the same material, and as such, have the potential to the enable the most simplistic incarnation of III-V CMOS; provided, of course, that is possible to form a gate stack to both device polarities with sufficient electrical properties. To date, however, there has been no investigation into the high-k dielectric interface to InGaSb. To this end, this thesis presents results of the first investigation into the impact of in-situ H2 plasma exposure on the electrical properties of the p/n-In0.3Ga0.7Sb-Al2O3 interface. The parameter space was explored systematically in terms of H2 plasma power and exposure time, and further, the impact of impact of in-situ trimethylaluminium (TMA) pre-cleaning and annealing in forming gas was assessed. Metal oxide semiconductor capacitors (MOSCAPs) were fabricated subsequent to H2 plasma processing and Al2O3 deposition, and the correspond- ing capacitance-voltage and conductance-voltage measurements were analysed both qualita- tively and quantitatively via the simulation of an equivalent circuit model. X-Ray photoelectron spectroscopy (XPS) analysis of samples processed as part of the plasma power series revealed a combination of ex-situ HCl cleaning and in-situ H2 plasma exposure to completely remove In and Sb sub oxides, with the Ga-O content reduced to Ga-O:InGaSb < 0.1. The optimal process, which included ex-situ HCl surface cleaning, in-situ H2 plasma and TMA pre-cleaning, and a post gate metal forming gas anneal, was unequivocally demonstrated to yield a fully unpinnned MOS interface with both n and p-type MOSCAPs explicitly demonstrating a genuine minority carrier response. Interface state and border trap densities were extracted, with a minimum Dit of 1.73x1012 cm-2 eV-1 located at ~110 meV below the conduction band edge and peak border trap densities approximately aligned with the valence and conduction band edges of 3x1019 cm-3 eV-1 and 6.5x1019 cm-3 eV-1 respectively. These results indicate that the optimal gate stack process is indeed applicable to both p and n- type InGaSb MOSFETs, and therefore, represent a critical advancement towards achieving high performance III-V CMOS.
- Published
- 2018
17. The Barren Berry Phenotype: Untangling Cranberry (Vaccinium macrocarpon Ait.) Genetic Contamination in Central Wisconsin and Beyond
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Lazar, F., primary, Lopez-Moreno, H., additional, Wiesman, E., additional, Torre, F. La, additional, Verhulst, P., additional, Sojka, J., additional, Maureira, I., additional, Millar, David, additional, Kennedy, C., additional, Mura, J., additional, and Zalapa, J., additional
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- 2024
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18. Stealth transgenes enable CAR-T cells to evade host immune responses
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Grauwet, Korneel, primary, Berger, Trisha, additional, Kann, Michael C, additional, Silva, Harrison, additional, Larson, Rebecca, additional, Leick, Mark B, additional, Bailey, Stefanie R, additional, Bouffard, Amanda A, additional, Millar, David, additional, Gallagher, Kathleen, additional, Turtle, Cameron J, additional, Frigault, Matthew J, additional, and Maus, Marcela V, additional
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- 2024
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19. DSP for Optical Transponders
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Savory, Seb J., Millar, David S., Mukherjee, Biswanath, editor, Tomkos, Ioannis, editor, Tornatore, Massimo, editor, Winzer, Peter, editor, and Zhao, Yongli, editor
- Published
- 2020
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20. PERFORMANCE IN MATHEMATICS OF STUDENTS ENTERING UNIVERSITY IN IRELAND : HAS CURRICULUM REFORM CONTRIBUTED TO A DECLINE IN STANDARDS?
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Shiel, Gerry, Millar, David, and Cunningham, Rachel
- Published
- 2020
21. Why compensating fibre nonlinearity will never meet capacity demands
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Lavery, Domanic, Maher, Robert, Millar, David, Alvarado, Alex, Savory, Seb J., and Bayvel, Polina
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Physics - Optics ,Computer Science - Information Theory - Abstract
Current research efforts are focussed on overcoming the apparent limits of communication in single mode optical fibre resulting from distortion due to fibre nonlinearity. It has been experimentally demonstrated that this Kerr nonlinearity limit is not a fundamental limit; thus it is pertinent to review where the fundamental limits of optical communications lie, and direct future research on this basis. This paper details recently presented results. The work herein briefly reviews the intrinsic limits of optical communication over standard single mode optical fibre (SMF), and shows that the empirical limits of silica fibre power handling and transceiver design both introduce a practical upper bound to the capacity of communication using SMF, on the order of 1 Pbit/s. Transmission rates exceeding 1 Pbit/s are shown to be possible, however, with currently available optical fibres, attempts to transmit beyond this rate by simply increasing optical power will lead to an asymptotically zero fractional increase in capacity., Comment: 4 pages, 2 figures
- Published
- 2015
22. Psychological factors influencing technology adoption: A case study from the oil and gas industry
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Roberts, Ruby, Flin, Rhona, Millar, David, and Corradi, Luca
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- 2021
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23. A DEAD-box protein acts through RNA to promote HIV-1 Rev-RRE assembly
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Lamichhane, Rajan, Hammond, John A, Pauszek, Raymond F, Anderson, Rae M, Pedron, Ingemar, van der Schans, Edwin, Williamson, James R, and Millar, David P
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Biological Sciences ,Bioinformatics and Computational Biology ,HIV/AIDS ,Genetics ,Binding Sites ,Biological Transport ,Carbocyanines ,DEAD-box RNA Helicases ,Fluorescence Resonance Energy Transfer ,Fluorescent Dyes ,Gene Expression ,Genes ,env ,HIV-1 ,Host-Pathogen Interactions ,Humans ,Nucleic Acid Conformation ,Protein Binding ,RNA ,Messenger ,RNA ,Viral ,Recombinant Fusion Proteins ,Rhodamines ,Single Molecule Imaging ,Staining and Labeling ,Sulfonic Acids ,Virus Assembly ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
The HIV-1 Rev protein activates nuclear export of unspliced and partially spliced viral RNA transcripts, which encode the viral genome and the genes encoding viral structural proteins, by binding to and oligomerizing on the Rev Response Element (RRE). The human DEAD-box protein 1 (DDX1) enhances the RNA export activity of Rev through an unknown mechanism. Using a single-molecule assembly assay and various DDX1 mutants, we show that DDX1 acts through the RRE RNA to specifically accelerate the nucleation step of the Rev-RRE assembly process. Single-molecule Förster resonance energy transfer (smFRET) experiments using donor-labeled Rev and acceptor-labeled DDX1 show that both proteins can associate with a single RRE molecule. However, simultaneous interaction is only observed in a subset of binding events and does not explain the extent to which DDX1 promotes the nucleation step of Rev-RRE assembly. Together, these results are consistent with a model wherein DDX1 acts as an RNA chaperone, remodeling the RRE into a conformation that is pre-organized to bind the first Rev monomer, thereby promoting the overall Rev-RRE assembly process.
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- 2017
24. A DEAD-Box Helicase Mediates an RNA Structural Transition in the HIV-1 Rev Response Element
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Hammond, John A, Lamichhane, Rajan, Millar, David P, and Williamson, James R
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Microbiology ,Biochemistry and Cell Biology ,Biological Sciences ,HIV/AIDS ,Genetics ,Infection ,DEAD-box RNA Helicases ,DNA Helicases ,Gene Expression Regulation ,Viral ,HIV-1 ,Nucleic Acid Conformation ,RNA Splicing ,RNA ,Viral ,Response Elements ,Virus Replication ,rev Gene Products ,Human Immunodeficiency Virus ,RNA structure ,RRE ,Rev ,Medicinal and Biomolecular Chemistry ,Biochemistry & Molecular Biology ,Biochemistry and cell biology - Abstract
Nuclear export of partially spliced or unspliced HIV-1 RNA transcripts requires binding of the viral protein regulator of expression of virion (Rev) to the Rev response element (RRE) and subsequent oligomerization in a cooperative manner. Cellular DEAD-box helicase DEAD-box protein 1 (DDX1) plays a role in HIV replication, interacting with and affecting Rev-containing HIV transcripts in vivo, interacting directly with the RRE and Rev in vitro, and promoting Rev oligomerization in vitro. Binding of DDX1 results in enhancement of Rev oligomerization on the RRE that is correlated with an RNA structural change within the RRE that persists even after dissociation of DDX1. Furthermore, this structural transition is likely located within the three-way junction of stem II of the RRE that is responsible for initial Rev binding. This discovery of the stem II structural transition leads to a model wherein DDX1 can act as an RNA chaperone, folding stem IIB into a proper Rev binding conformation.
- Published
- 2017
25. Dynamic conformational changes in the rhesus TRIM5α dimer dictate the potency of HIV-1 restriction
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Lamichhane, Rajan, Mukherjee, Santanu, Smolin, Nikolai, Pauszek, Raymond F, Bradley, Margret, Sastri, Jaya, Robia, Seth L, Millar, David, and Campbell, Edward M
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Medical Microbiology ,Biomedical and Clinical Sciences ,HIV/AIDS ,Amino Acid Sequence ,Animals ,Carrier Proteins ,Cell Line ,Dimerization ,Disease Models ,Animal ,HIV Infections ,HIV-1 ,Humans ,Macaca mulatta ,Mutation ,Protein Conformation ,Single molecule FRET ,TRIM5alpha ,Molecular dynamics simulation ,smFRET ,Restriction factor ,Coiled coil ,Dimer ,Tripartite Motif ,Biological Sciences ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Virology ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
The TRIM5α protein from rhesus macaques (rhTRIM5α) mediates a potent inhibition of HIV-1 infection via a mechanism that involves the abortive disassembly of the viral core. We have demonstrated that alpha-helical elements within the Linker 2 (L2) region, which lies between the SPRY domain and the Coiled-Coil domain, influence the potency of restriction. Here, we utilize single-molecule FRET analysis to reveal that the L2 region of the TRIM5α dimer undergoes dynamic conformational changes, which results in the displacement of L2 regions by 25 angstroms relative to each other. Analysis of restriction enhancing or abrogating mutations in the L2 region reveal that restriction defective mutants are unable to undergo dynamic conformational changes and do not assume compact, alpha-helical conformations in the L2 region. These data suggest a model in which conformational changes in the L2 region mediate displacement of CA bound SPRY domains to induce the destabilization of assembled capsid during restriction.
- Published
- 2017
26. Impacts of genotype, edaphic factors, and plant nutrients on yield and fruit quality for a perennial specialty crop (Vaccinium macrocarpon Ait.).
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Millar, David, Kennedy, Casey, Zalapa, Juan, Jeranyama, Peter, Mupambi, Giverson, Wiegman, Adrian, and Buda, Anthony
- Subjects
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FRUIT yield , *SPECIALTY crops , *FRUIT quality , *PLANT yields , *CROP quality , *CULTIVARS , *PLANT nutrients , *CRANBERRIES - Abstract
Compared to conventional crops, less is known about how genetic and environmental variability affect the yield and quality of specialty crops like cranberry (Vaccinium macrocarpon Ait.). Herein, we performed a multifaceted analysis of six commercial cranberry beds planted to the Stevens cultivar. The six beds included three with above‐average multiyear yields and three that were lower than average. We considered genotype, edaphic factors, and plant nutrient content as driving variables of yield and fruit quality. We found that genetic purity within beds raised the odds of obtaining above‐average yields over an 8‐year period. The highest levels of genetic contamination (38%–75%) were found at the low‐yield beds, where significant differences in yield and fruit quality were observed between genotypes, within beds. Across all beds, focusing only on plots genetically confirmed to be Stevens cultivar, we also found that plot‐scale yield in 2020 was significantly higher for two of three high‐yield beds, suggesting other factors besides genetic contamination influenced differences in bed‐scale yield. A factor analysis of mixed data that jointly included genotype, edaphic variables, and plant tissue nutrient content revealed complex relations among these variables that were tied to grouping plots based on long‐term yield. Findings highlight the need for further research into the complex genetic and environmental factors that control cranberry yield and fruit quality. Core Ideas: Cranberry yield and quality were impacted by genetic and environmental variables across six commercial beds.Genetic contamination negatively impacted long‐term crop yields.Within bed variability in yield and fruit quality arose due to genetic contamination.Phenotypic plasticity caused variation in yield and fruit quality across beds within the Stevens cultivar. [ABSTRACT FROM AUTHOR]
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- 2024
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27. Tailwater recovery systems can improve water quality: An area ripe for research in cranberry agriculture.
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Kennedy, Casey D., Omer, Austin, Wiegman, Adrian R. H., Welsh, Molly K., Millar, David, and Buda, Anthony R.
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- 2024
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28. Characterizing Changes in Cranberry Phenology from 1958 to 2022: Implications for Spring Frost Protection in Massachusetts, United States
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Bhatti, Sandeep, primary, Jeranyama, Peter, additional, Kennedy, Casey D., additional, Buda, Anthony R., additional, Ghantous, Katherine, additional, Millar, David J., additional, and DeMoranville, Carolyn, additional
- Published
- 2024
- Full Text
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29. A tribute to South Africa’s teachers
- Author
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Millar, David J, primary
- Published
- 2021
- Full Text
- View/download PDF
30. The Land Beneath the Ice: The Pioneering Years of Radar Exploration in Antarctica, by David J. Drewry
- Author
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Millar, David, primary
- Published
- 2023
- Full Text
- View/download PDF
31. The Human Gene Mutation Database (HGMD®): optimizing its use in a clinical diagnostic or research setting
- Author
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Stenson, Peter D., Mort, Matthew, Ball, Edward V., Chapman, Molly, Evans, Katy, Azevedo, Luisa, Hayden, Matthew, Heywood, Sally, Millar, David S., Phillips, Andrew D., and Cooper, David N.
- Published
- 2020
- Full Text
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32. Antibody-mediated delivery of viral epitopes to tumors harnesses CMV-specific T cells for cancer therapy
- Author
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Millar, David G., Ramjiawan, Rakesh R., Kawaguchi, Kosuke, Gupta, Nisha, Chen, Jiang, Zhang, Songfa, Nojiri, Takashi, Ho, William W., Aoki, Shuichi, Jung, Keehoon, Chen, Ivy, Shi, Feng, Heather, James M., Shigeta, Kohei, Morton, Laura T., Sepulveda, Sean, Wan, Li, Joseph, Ricky, Minogue, Eleanor, Khatri, Ashok, Bardia, Aditya, Ellisen, Leif W., Corcoran, Ryan B., Hata, Aaron N., Pai, Sara I., Jain, Rakesh K., Fukumura, Dai, Duda, Dan G., and Cobbold, Mark
- Published
- 2020
- Full Text
- View/download PDF
33. Contributors
- Author
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Augustine, Norm, primary, Ausubel, Jesse H., additional, Bassett, Christine, additional, Baygents, Anna Kate, additional, Beaird, Nick, additional, Breece, Matthew, additional, Brown, William Yancey, additional, Chassignet, Eric P., additional, Colwell, Rita, additional, Coniglione, Bob, additional, Cuff, Thomas, additional, Cuker, Benjamin, additional, Curry, Alan, additional, Drake, Thomas G., additional, Englander, John, additional, Fietzek, Peer, additional, Figurskey, Darin, additional, Fischel, Melissa, additional, Flocken, Nicholas I., additional, Freeston, Ben, additional, Garcia-Pineda, Oscar, additional, Gallaudet, Tim, additional, Geerlofs, Simon, additional, Gibson, Deidre, additional, Giron, Alfredo, additional, Glenn, Scott, additional, Gouldman, Carl, additional, Hall, Steve, additional, Hanlon, Jim, additional, Hotaling, Liesl, additional, Jones, Michael, additional, Jugan, Laurie, additional, Keener, Paula, additional, Kildow, Judith T., additional, Kirkpatrick, Barb, additional, Koch, Louisa, additional, Kochevar, Randy, additional, Koehring, Martin, additional, Kohut, Josh, additional, MacKenzie, Bev, additional, Manley, Justin, additional, McLean, Craig, additional, Miles, Travis, additional, Millar, David, additional, Moran, S. Bradley, additional, Nazzaro, Laura, additional, Oliver, Matthew J., additional, Penesis, Irene, additional, Porter, Dwayne E., additional, Puniwai, Noelani, additional, Raso, Perry, additional, Rayner, Ralph, additional, Reiss, A.J., additional, Roffer, Mitch, additional, Ryabinin, Vladimir, additional, Saba, Grace, additional, Sandifer, Paul A., additional, Schofield, Oscar, additional, Scott, Geoffrey I., additional, Scully, Sherry, additional, Skrivanek, Alexandra, additional, Smail, Emily, additional, Snelgrove, Paul, additional, Spinrad, Richard W., additional, Spring, Margaret, additional, Sullivan, Kathryn, additional, Titov, Vasily, additional, Smirren, Jan van, additional, Van Sumeren, Hans, additional, Walker, Samuel, additional, Walsh, Don, additional, Wark, Kevin, additional, Watson-Wright, Wendy, additional, Whitehouse, Sheldon, additional, and Whittington, John, additional
- Published
- 2021
- Full Text
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34. Application of two pelvic floor muscle function tests in men following radical prostatectomy: Relationship to urinary incontinence
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Milios, Joanne E, Atkinson, Ceri L, Naylor, Louise H, Millar, David, Thijssen, Dick HJ, Ackland, Timothy R, and Green, Daniel J
- Published
- 2019
35. Pelvic floor muscle assessment in men post prostatectomy: Comparing digital rectal examination and real-time ultrasound approaches
- Author
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Milios, Joanne E, Atkinson, Ceri L, Naylor, Louise H, Millar, David, Thijssen, Dick HJ, Ackland, Timothy R, and Green, Daniel J
- Published
- 2018
36. Intensity and velocity oscillations in a flaring active region
- Author
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Millar, David C L, primary, Fletcher, Lyndsay, additional, and Joshi, Jayant, additional
- Published
- 2023
- Full Text
- View/download PDF
37. Distinct Activation Mechanisms of CXCR4 and ACKR3 Revealed by Single-Molecule Analysis of their Conformational Landscapes
- Author
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Schafer, Christopher T., primary, Pauszek, Raymond F, additional, Gustavsson, Martin, additional, Handel, Tracy M., additional, and Millar, David P., additional
- Published
- 2023
- Full Text
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38. Dowse Art Gallery
- Author
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Millar, David P
- Published
- 1976
39. Displaying : in a private gallery; In a small private gallery
- Author
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Millar, David and Noonan, Anne
- Published
- 1974
40. Dowse Art Gallery, Lower Hutt
- Author
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Millar, David P
- Published
- 1971
41. The application of the dynamic stiffness method for the acoustic fatigue analysis of aircraft engine nacelle structures
- Author
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Millar, David and Ferguson, Neil
- Subjects
620 ,TL Motor vehicles. Aeronautics. Astronautics - Abstract
The subject of acoustic fatigue first came to prominence with the advent of using jet engines on commercial aircraft in the 1950’s. Despite the period of time which has elapsed since then and the work carried out to help develop our understanding of the response of structures subject to high intensity noise, acoustic fatigue problems still occur. The novel contributions which this thesis makes to knowledge in the area have been in the application of the dynamic stiffness method which has been used to predict stress and strain response due to acoustic loading. The dynamic stiffness method can under certain circumstances provide very accurate results for natural frequency and displacement. Indeed for certain configurations it can provide exact solutions. It is largely independent of the number of degrees of freedom necessary to give an accurate result unlike the finite element method. The thesis documents how the dynamic stiffness method can offer a very favourable alternative to available analysis techniques. An alternative method of formulating the dynamic stiffness method is presented and is further extended to the analysis of orthotropic plates. The response of actual structures is discussed and previously unpublished data is also presented.
- Published
- 2012
42. Groundwater dynamics in mountain peatlands with contrasting climate, vegetation, and hydrogeological setting
- Author
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Millar, David J., Cooper, David J., and Ronayne, Michael J.
- Published
- 2018
- Full Text
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43. Variation in Positive End-Expiratory Pressure Levels for Mechanically Ventilated Extremely Low Birth Weight Infants
- Author
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Bamat, Nicolas A., Guevara, James P., Bryan, Matthew, Roberts, Robin S., Yoder, Bradley A., Lemyre, Brigitte, Chiu, Aaron, Millar, David, and Kirpalani, Haresh
- Published
- 2018
- Full Text
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44. Participatory Assessment of Development Interventions: Lessons Learned from a New Evaluation Methodology in Ghana and Burkina Faso
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Pouw, Nicky, Dietz, Ton, Bélemvire, Adame, de Groot, Dieneke, Millar, David, Obeng, Francis, Rijneveld, Wouter, Van der Geest, Kees, Vlaminck, Zjos, and Zaal, Fr
- Abstract
This article presents the principles and findings of developing a new participatory assessment of development (PADev) evaluation approach that was codesigned with Dutch nongovernmental organizations (NGOs) and northern and southern research institutes over a period of 4 years in the context of rural development in Ghana and Burkina Faso. Although participatory approaches in development evaluations have become widely accepted since the 1990s, the PADev approach is different by taking the principles of holism and local knowledge as starting points for its methodological elaboration. The PADev approach is found to have an added value for assessing the differentiated effects of development interventions across different subgroups in a community through intersubjectivity. Moreover, if PADev is taken up by a multitude of stakeholders, including the intended beneficiaries of development interventions and development stakeholders, it can contribute to a process of local history writing, knowledge sharing, capacity development, and providing input into community action plans and the strategies of community-based organizations and NGOs.
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- 2017
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45. Energetic materials at extreme conditions
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Millar, David Iain Archibald, Pulham, Colin, and Robertson, Neil
- Subjects
541 ,energetic materials ,RDX ,CL-20 ,azides ,high-pressure - Abstract
In order to effectively model the behaviour of energetic materials under operational conditions it is essential to obtain detailed structural information for these compounds at elevated temperature and/or pressures. The structural characterisation of the high explosives RDX and CL-20 and a series of inorganic azides [Mn+(N3)n] at extreme conditions is described herein. In addition to the characterisation of a highly metastable β -form of RDX (1,3,5- trinitrohexahydro-1,3,5-triazine) at atmospheric pressure, the structure solution of a high-pressure/ high-temperature polymorph is described. This form, obtained above 4.3 GPa and 450 K, has been shown to be distinct from the β -form and has therefore been denoted - RDX. Furthermore, ε -RDX is sufficiently metastable to allow its recovery to ambient pressure at 150 K; it only transforms to the α -form upon warming to 230 K. Finally, the ambient-temperature compression of RDX has been investigated to a maximum pressure of 23.0 GPa, using methanol:ethanol (4:1) as the pressure-transmitting medium; no phase transition was observed under these conditions, other than the α → γ transition at 3.9 GPa. The structure of a high-pressure polymorph of CL-20 (2,4,6,8,10,12- hexanitrohexaazaisowurtzitane) has also been determined by a combination of powder and single-crystal X-ray diffraction. Compression of γ -CL-20 to above 0.7 GPa using Fluorinert (FC-77) as the pressure-transmitting medium results in a phase transition to the ζ -form, which has been found to display structural similarities with both theγ γ - and ε -forms. The high-pressure behaviour of CL-20, however, depends markedly on the starting polymorph and the pressure-transmitting medium selected. Compression of γ -CL-20 in MeOH:EtOH (4:1) results in the formation of a 2:1 CL-20:MeOH solvate at 0.5 GPa. This solvate is stable upon compression to P > 5.0 GPa. It may also be recovered to ambient pressure at 293 K. Meanwhile, no phase transition is observed during the compression of ε -CL-20 to a maximum pressure of 7.2 GPa. Finally, a series of inorganic azides [NaN3, CsN3, TlN3, NH4N3, AgN3 and Pb(N3)2] has been characterised under a range of pressure and temperature conditions. Of the six compounds studied, all displayed at least one polymorphic transition – 5 new forms have been structurally characterised in this work and evidence of another 5 is presented. The combined effect of pressure and temperature results in sodium azide adopting a tetragonal structure common to larger alkali metal azides. Caesium azide has been shown to undergo three phase transitions during compression to 6.0 GPa – the structure of the first high-pressure form is reported. A variable temperature X-ray powder diffraction study of TlN3 has allowed the structural characterisation of the low-temperature TlN3-IV (at 230 K) as well as providing evidence for a phase transition to a high-temperature form above 550 K. The high-pressure form III (obtained above 0.76 GPa) has also been determined by neutron powder diffraction. Silver, ammonium and lead(II) azides have all been shown to undergo a phase transition at high pressures. Compression of silver azide (P > 0.80 GPa) removes an orthorhombic distortion observed at atmospheric pressure, resulting in the tetragonal structure adopted by CsN3 and TlN3 under ambient conditions. Moreover, NH4N3 and Pb(N3)2 have been found to undergo phase transitions at 2.6 GPa, although their high-pressure structures have still to be determined.
- Published
- 2011
46. The role of idiotype-specific immunity in antigen receptor diversity
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Millar, David George
- Subjects
616.99 ,QR180 Immunology ,RC0254 Neoplasms. Tumors. Oncology (including Cancer) - Abstract
Lymphocytes express antigen receptors which are formed by re-arrangement of gene segments. Mutations acquired during this process, predominantly in the complementarity determining regions (CDRs), result in generation of non-germline sequences. Through analysing the CDR3 sequence, this study attempts to determine whether editing of the lymphocyte repertoire is present in an HLA-dependant manner. Data presented demonstrates a decrease frequency of CDR3-derived HLA-A2 binding peptides in HLA-A2+ donors (0.03% (SYFPEITHI) and 0.35% (BIMAS)) compared with HLA-A2- donors (0.24% (SYFPEITHI, p=0.01) and 0.54% (BIMAS, p=0.19)). Trends similar to those seen in HLA-A2 were observed in other HLA alleles as well suggesting that there may be a process by which potentially dangerous B cell populations are edited from the B cell repertoire. Similar analysis of the TCR CDR3 did not reveal any such process in all of the HLA alleles tested suggesting that there is no immunoediting of the T cell repertoire. Simultaneously, this study attempts to determine the processing and presentation of CDR3-derived peptides at the cell surface using lymphocyte antigen receptor models containing CDR3-encoded viral epitopes. The apparent presence of these peptides on the cell surface leads to the hypothesis that antibodies enter the antigen processing pathway and potentially deliver an immunogenic peptide to a target cell. Using antibodies specific for B cells, this study has shown that cells labelled with an antibody-peptide complex are targeted and lysed by cytotoxic CD4+ T cells in a peptide-specific manner. The use of such technology in antibody immunotherapy may be of considerable therapeutic benefit.
- Published
- 2010
47. Mountain Peatlands Range from CO₂ Sinks at High Elevations to Sources at Low Elevations : Implications for a Changing Climate
- Author
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Millar, David J., Cooper, David J., Dwire, Kathleen A., Hubbard, Robert M., and von Fischer, Joseph
- Published
- 2017
48. AN EXPLORATION OF VARIATION IN SUBJECT GRADING, STUDENT SUBJECT SELECTION AND OUTCOMES IN THE LEAVING CERTIFICATE EXAMINATION
- Author
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Millar, David
- Published
- 2017
49. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA
- Author
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Williamson, James, primary, Zhou, Anne, additional, Hammond, John, additional, Sheng, Kai, additional, and Millar, David, additional
- Published
- 2023
- Full Text
- View/download PDF
50. Intensity and velocity oscillations in a flaring active region.
- Author
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Millar, David C L, Fletcher, Lyndsay, and Joshi, Jayant
- Subjects
- *
SOLAR flares , *SOLAR atmosphere , *OSCILLATIONS , *VELOCITY , *SOLAR oscillations , *SOLAR cycle , *MAGNETOHYDRODYNAMIC waves , *AMBIENCE (Environment) , *MAGNETIC fields - Abstract
Chromospheric oscillations can give us insight into the physical environment in the solar atmosphere, both in quiet Sun and flaring conditions. Many authors have reported increases in the prevalence of 3-minute oscillations which are thought to be excited by events which impact the chromosphere such as flares. In this study, we utilized the Ca ii 8542 Å line to study the oscillatory behaviour of the chromosphere in an active region which underwent two B-class flares. We analysed oscillations in both intensity and velocity, and found different behaviours in both. Intensity oscillations were most prevalent over the umbrae of sunspots and magnetic pores in the active region, and the extent of the area which contained significant oscillations was found to decrease when comparing times after the flares to before. By measuring the evolution of the magnetic field, we found that this could be because the areas surrounding the umbrae were becoming more 'penumbral' with an increase to the magnetic field inclination. Velocity oscillations were found across the active region both before and after the flares but were observed clearly in areas which were brightened by the second flare. By comparing to EUV imaging, it was seen that strong chromospheric velocity oscillations with 3–4-minute periods occurred at the same time and location as a flare loop cooling 30 min after the second flare peak. This could be evidence of disturbances in the loop exciting a response from the chromosphere at its acoustic cut-off frequency. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
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