Coding Strategies and Implementations of Compressive Sensing

This dissertation studies the coding strategies of computational imaging to overcome the limitation of conventional sensing techniques. The information capacity of conventional sensing is limited by the physical properties of optics, such as aperture size, detector pixels, quantum efficiency, and sampling rate. These parameters determine the spatial, depth, spectral, temporal, and polarization sensitivity of each imager. To increase sensitivity in any dimension can significantly compromise the others.

This research implements various coding strategies subject to optical multidimensional imaging and acoustic sensing in order to extend their sensing abilities. The proposed coding strategies combine hardware modification and signal processing to exploiting bandwidth and sensitivity from conventional sensors. We discuss the hardware architecture, compression strategies, sensing process modeling, and reconstruction algorithm of each sensing system.

Optical multidimensional imaging measures three or more dimensional information of the optical signal. Traditional multidimensional imagers acquire extra dimensional information at the cost of degrading temporal or spatial resolution. Compressive multidimensional imaging multiplexes the transverse spatial, spectral, temporal, and polarization information on a two-dimensional (2D) detector. The corresponding spectral, temporal and polarization coding strategies adapt optics, electronic devices, and designed modulation techniques for multiplex measurement. This computational imaging technique provides multispectral, temporal super-resolution, and polarization imaging abilities with minimal loss in spatial resolution and noise level while maintaining or gaining higher temporal resolution. The experimental results prove that the appropriate coding strategies may improve hundreds times more sensing capacity.

Human auditory system has the astonishing ability in localizing, tracking, and filtering the selected sound sources or information from a noisy environment. Using engineering efforts to accomplish the same task usually requires multiple detectors, advanced computational algorithms, or artificial intelligence systems. Compressive acoustic sensing incorporates acoustic metamaterials in compressive sensing theory to emulate the abilities of sound localization and selective attention. This research investigates and optimizes the sensing capacity and the spatial sensitivity of the acoustic sensor. The well-modeled acoustic sensor allows localizing multiple speakers in both stationary and dynamic auditory scene; and distinguishing mixed conversations from independent sources with high audio recognition rate.

Investigating the Structure of FtsZ to Understand its Functional Role in Bacterial Cell Division

FtsZ, a bacterial tubulin homologue, is a cytoskeleton protein that plays key roles in cytokinesis of almost all prokaryotes. FtsZ assembles into protofilaments (pfs), one subunit thick, and these pfs assemble further to form a “Z ring” at the center of prokaryotic cells. The Z ring generates a constriction force on the inner membrane, and also serves as a scaffold to recruit cell-wall remodeling proteins for complete cell division in vivo. FtsZ can be subdivided into 3 main functional regions: globular domain, C terminal (Ct) linker, and Ct peptide. The globular domain binds GTP to assembles the pfs. The extreme Ct peptide binds membrane proteins to allow cytoplasmic FtsZ to function at the inner membrane. The Ct linker connects the globular domain and Ct peptide. In the present studies, we used genetic and structural approaches to investigate the function of Escherichia coli (E. coli) FtsZ. We sought to examine three questions: (1) Are lateral bonds between pfs essential for the Z ring? (2) Can we improve direct visualization of FtsZ in vivo by engineering an FtsZ-FP fusion that can function as the sole source of FtsZ for cell division? (3) Is the divergent Ct linker of FtsZ an intrinsically disordered peptide (IDP)?

One model of the Z ring proposes that pfs associate via lateral bonds to form ribbons; however, lateral bonds are still only hypothetical. To explore potential lateral bonding sites, we probed the surface of E. coli FtsZ by inserting either small peptides or whole FPs. Of the four lateral surfaces on FtsZ pfs, we obtained inserts on the front and back surfaces that were functional for cell division. We concluded that these faces are not sites of essential interactions. Inserts at two sites, G124 and R174 located on the left and right surfaces, completely blocked function, and were identified as possible sites for essential lateral interactions. Another goal was to find a location within FtsZ that supported fusion of FP reporter proteins, while allowing the FtsZ-FP to function as the sole source of FtsZ. We discovered one internal site, G55-Q56, where several different FPs could be inserted without impairing function. These FtsZ-FPs may provide advances for imaging Z-ring structure by super-resolution techniques.

The Ct linker is the most divergent region of FtsZ in both sequence and length. In E. coli FtsZ the Ct linker is 50 amino acids (aa), but for other FtsZ it can be as short as 37 aa or as long as 250 aa. The Ct linker has been hypothesized to be an IDP. In the present study, circular dichroism confirmed that isolated Ct linkers of E. coli (50 aa) and C. crescentus (175 aa) are IDPs. Limited trypsin proteolysis followed by mass spectrometry (LC-MS/MS) confirmed Ct linkers of E. coli (50 aa) and B. subtilis (47 aa) as IDPs even when still attached to the globular domain. In addition, we made chimeras, swapping the E. coli Ct linker for other peptides and proteins. Most chimeras allowed for normal cell division in E. coli, suggesting that IDPs with a length of 43 to 95 aa are tolerated, sequence has little importance, and electrostatic charge is unimportant. Several chimeras were purified to confirm the effect they had on pf assembly. We concluded that the Ct linker functions as a flexible tether allowing for force to be transferred from the FtsZ pf to the membrane to constrict the septum for division.

Photoacoustic tomography: principles and advances.

Photoacoustic tomography (PAT) is an emerging imaging modality that shows great potential for preclinical research and clinical practice. As a hybrid technique, PAT is based on the acoustic detection of optical absorption from either endogenous chromophores, such as oxy-hemoglobin and deoxy-hemoglobin, or exogenous contrast agents, such as organic dyes and nanoparticles. Because ultrasound scatters much less than light in tissue, PAT generates high-resolution images in both the optical ballistic and diffusive regimes. Over the past decade, the photoacoustic technique has been evolving rapidly, leading to a variety of exciting discoveries and applications. This review covers the basic principles of PAT and its different implementations. Strengths of PAT are highlighted, along with the most recent imaging results.

Ultracompact Retrodirective Antenna Arrays With Superdirective Radiation Patterns

It is shown that the direction-of-arrival (DoA) information carried by an incident electromagnetic (EM) wave can be encoded into the evanescent near field of an electrically small resonance antenna array with a spatial rate higher than that of the incident field oscillation rate in free space. Phase conjugation of the received signal leads to the retrodirection of the near field in the antenna array environment, which in turn generates a retrodirected far-field beam toward the original DoA. This EM phenomenon enables electrically small retrodirective antenna arrays with superdirective, angular super-resolution, auto-pointing properties for an arbitrary DoA. A theoretical explanation of the phenomenon based on first principal observations is given and full-wave simulations demonstrate a realizability route for the proposed retrodirective terminal that is comprised of resonance dipole antenna elements. Specifically, it is shown that a three-element disk-loaded retrodirective dipole array with 0.15\lambda spacings can achieve a 3.4-dBi maximal gain, 3-dBi front-to-back ratio, and 13% return loss fractional bandwidth (at the 10-dB level). Then, it is demonstrated that the radiation gain of a three-element array can be improved to approximately 6 dBi at the expense of the return loss fractional bandwidth reduction (2%).

Actin dynamics provides membrane tension to merge fusing vesicles into the plasma membrane

Vesicle fusion is executed via formation of an Ω-shaped structure (Ω-profile), followed by closure (kiss-and-run) or merging of the Ω-profile into the plasma membrane (full fusion). Although Ω-profile closure limits release but recycles vesicles economically, Ω-profile merging facilitates release but couples to classical endocytosis for recycling. Despite its crucial role in determining exocytosis/endocytosis modes, how Ω-profile merging is mediated is poorly understood in endocrine cells and neurons containing small ∼30-300 nm vesicles. Here, using confocal and super-resolution STED imaging, force measurements, pharmacology and gene knockout, we show that dynamic assembly of filamentous actin, involving ATP hydrolysis, N-WASP and formin, mediates Ω-profile merging by providing sufficient plasma membrane tension to shrink the Ω-profile in neuroendocrine chromaffin cells containing ∼300 nm vesicles. Actin-directed compounds also induce Ω-profile accumulation at lamprey synaptic active zones, suggesting that actin may mediate Ω-profile merging at synapses. These results uncover molecular and biophysical mechanisms underlying Ω-profile merging.

Molecular probes for monitoring mitochondrial movement and function

This thesis explores two distinct parts of mitochondrial physiology: the role of mitochondria in generation of reactive oxygen species (ROS) and mitochondrial morphology and dynamics within cells. The first area of research is covered in Chapters 1-8. Mitochondrial biofunctionality and ROS production are discussed in Chapter 1, followed by the strategy of targeting bioactive compounds to mitochondria by linking them to lipophilic triphenylphosphonium cations (TPP) (Chapter 2). ROS sensors relevant to the research are reviewed in Chapter 3. Chapter 4 presents design and synthesis of novel probes for superoxide detection in mitochondria (MitoNeo-D), cytosol (Neo-D) and extracellular environment (ExCellNeo-D). The results of biological validation of MitoNeo-D and Neo-D performed in the MRC MBU in Cambridge are presented in Chapter 5. A dicationic hydrogen peroxide sensor that utilizes in situ click chemistry is discussed in Chapter 6. Preliminary work on the synthesis of mitochondria-targeted superoxide generators, which led to the development of mitochondria-targeted analogue of paraquat, MitoPQ, is presented in Chapter 7. A set of bifunctional probes (BCN-Mal, BCN-E-BCN and Mito-iTag) for assessing the redox states of protein thiols is discussed in Chapter 8 along with their biological validation. The second part of the thesis is aimed at the study of mitochondrial morphology and dynamics and is presented in Chapters 9-11. Chapter 9 provides background on the classes of fluorophores relevant to the research, the phenomenon of fluorescence quenching and the principle of photoactivation with examples of photoactivatable fluorophores. Next, the background on mitochondrial morphology and heterogeneity is presented in Chapter 10, followed by the ways of imaging and tracking mitochondria within cells by conventional fluorophores and by photoactivatable fluorophores exploiting super-resolution microscopy. Chapter 11 presents the design and synthesis of four photoactivatable fluorophores for mitochondrial tracking, MitoPhotoRhod110, MitoPhotoNIR, Photo-E+, MitoPhoto-E+, along with results of biological validation of MitoPhotoNIR. The results and discussion concludes with Chapter 12, which is a summary and suggestions for future work, followed by the chemistry experimental procedures (Chapter 13), materials and methods for biological experiments (Chapter 14) and references.

High-resolution AMS (super 14) C dating of post-bomb peat archives of atmospheric pollutants.

Peat deposits in Greenland and Denmark were investigated to show that high-resolution dating of these archives of atmospheric deposition can be provided for the last 50 years by radiocarbon dating using the atmospheric bomb pulse. (super 14) C was determined in macrofossils from sequential one cm slices using accelerator mass spectrometry (AMS). Values were calibrated with a general-purpose curve derived from annually averaged atmospheric (super 14) CO (sub 2) values in the northernmost northern hemisphere (NNH, 30 degrees -90 degrees N). We present a through review of (super 14) C bomb-pulse data from the NNH including our own measurements made in tree rings and seeds from Arizona as well as other previously published data. We show that our general-purpose calibration curve is valid for the whole NNH producing accurate dates within 1-2 years. In consequence, (super 14) C AMS can precisely date individual points in recent peat deposits within the range of the bomb-pulse (from the mid-1950s on). Comparing the (super 14) C AMS results with the customary dating method for recent peat profiles by (super 210) Pb, we show that the use of (super 137) Cs to validate and correct (super 210) Pb dates proves to be more problematic than previously supposed. As a unique example of our technique, we show how this chronometer can be applied to identify temporal changes in Hg concentrations from Danish and Greenland peat cores.

Very large array detection of radio recombination lines from the radio nucleus of NGC 253: Ionization by a weak active galactic nucleus, an obscured super star cluster, or a compact supernova remnant?

We have imaged the H92alpha and H75alpha radio recombination line (RRL) emissions from the starburst galaxy NGC 253 with a resolution of similar to4 pc. The peak of the RRL emission at both frequencies coincides with the unresolved radio nucleus. Both lines observed toward the nucleus are extremely wide, with FWHMs of similar to200 km s(-1). Modeling the RRL and radio continuum data for the radio nucleus shows that the lines arise in gas whose density is similar to10(4) cm(-3) and mass is a few thousand M., which requires an ionizing flux of (6-20) x 10(51) photons s(-1). We consider a supernova remnant (SNR) expanding in a dense medium, a star cluster, and also an active galactic nucleus (AGN) as potential ionizing sources. Based on dynamical arguments, we rule out an SNR as a viable ionizing source. A star cluster model is considered, and the dynamics of the ionized gas in a stellar-wind driven structure are investigated. Such a model is only consistent with the properties of the ionized gas for a cluster younger than similar to10(5) yr. The existence of such a young cluster at the nucleus seems improbable. The third model assumes the ionizing source to be an AGN at the nucleus. In this model, it is shown that the observed X-ray flux is too weak to account for the required ionizing photon flux. However, the ionization requirement can be explained if the accretion disk is assumed to have a big blue bump in its spectrum. Hence, we favor an AGN at the nucleus as the source responsible for ionizing the observed RRLs. A hybrid model consisting of an inner advection-dominated accretion flow disk and an outer thin disk is suggested, which could explain the radio, UV, and X-ray luminosities of the nucleus.

The Search for Super-saturation in Chromospheric Emission

We investigate if the super-saturation phenomenon observed at X-ray wavelengths for the corona exists in the chromosphere for rapidly rotating late-type stars. Moderate resolution optical spectra of fast-rotating EUV- and X-ray-selected late-type stars were obtained. Stars in a Per were observed in the northern hemisphere with the Isaac Newton 2.5 m telescope and Intermediate Dispersion Spectrograph. Selected objects from IC 2391 and IC 2602 were observed in the southern hemisphere with the Blanco 4 m telescope and R-C spectrograph at CTIO. Ca II H and K fluxes were measured for all stars in our sample. We find the saturation level for Ca II K at log (L CaK/L bol) = -4.08. The Ca II K flux does not show a decrease as a function of increased rotational velocity or smaller Rossby number as observed in the X-ray. This lack of "super-saturation" supports the idea of coronal stripping as the cause of saturation and super-saturation in stellar chromospheres and coronae, but the detailed underlying mechanism is still under investigation.

Super-luminous Type Ic Supernovae: Catching a Magnetar by the Tail

We report extensive observational data for five of the lowest redshift Super-Luminous Type Ic Supernovae (SL-SNe Ic) discovered to date, namely, PTF10hgi, SN2011ke, PTF11rks, SN2011kf, and SN2012il. Photometric imaging of the transients at +50 to +230 days after peak combined with host galaxy subtraction reveals a luminous tail phase for four of these SL-SNe. A high-resolution, optical, and near-infrared spectrum from xshooter provides detection of a broad He I ?10830 emission line in the spectrum (+50 days) of SN2012il, revealing that at least some SL-SNe Ic are not completely helium-free. At first sight, the tail luminosity decline rates that we measure are consistent with the radioactive decay of 56Co, and would require 1-4 M ? of 56Ni to produce the luminosity. These 56Ni masses cannot be made consistent with the short diffusion times at peak, and indeed are insufficient to power the peak luminosity. We instead favor energy deposition by newborn magnetars as the power source for these objects. A semi-analytical diffusion model with energy input from the spin-down of a magnetar reproduces the extensive light curve data well. The model predictions of ejecta velocities and temperatures which are required are in reasonable agreement with those determined from our observations. We derive magnetar energies of 0.4 <~ E(1051 erg) lsim 6.9 and ejecta masses of 2.3 <~ M ej(M ?) lsim 8.6. The sample of five SL-SNe Ic presented here, combined with SN 2010gx—the best sampled SL-SNe Ic so far—points toward an explosion driven by a magnetar as a viable explanation for all SL-SNe Ic.

Characterizing K2 Planet Discoveries: A super-Earth transiting the bright K-dwarf HIP 116454

We report the first planet discovery from the two-wheeled Kepler (K2) mission: HIP 116454 b. The host star HIP 116454 is a bright (V = 10.1, K = 8.0) K1 dwarf with high proper motion and a parallax-based distance of 55.2 +/- 5.4 pc. Based on high-resolution optical spectroscopy, we find that the host star is metal-poor with [Fe/H]= -0.16 +/- 0.08 and has a radius R-star = 0.716 +/- 0.024 R-circle dot and mass M-star = 0.775 +/- 0.027M(circle dot). The star was observed by the Kepler spacecraft during its Two-Wheeled Concept Engineering Test in 2014 February. During the 9 days of observations, K2 observed a single transit event. Using a new K2 photometric analysis technique, we are able to correct small telescope drifts and recover the observed transit at high confidence, corresponding to a planetary radius of R-p = 2.53 +/- 0.18 R-circle plus. Radial velocity observations with the HARPS-N spectrograph reveal a 11.82 +/- 1.33 M-circle plus planet in a 9.1 day orbit, consistent with the transit depth, duration, and ephemeris. Follow-up photometric measurements from the MOST satellite confirm the transit observed in the K2 photometry and provide a refined ephemeris, making HIP 116454 b amenable for future follow-up observations of this latest addition to the growing population of transiting super-Earths around nearby, bright stars.

Study of the Oceanic Heat Budget Components over the Arabian Sea during the Formation and Evolution of Super Cyclone, Gonu

Oceans play a vital role in the global climate system. They absorb the incoming solar energy and redistribute the energy through horizontal and vertical transports. In this context it is important to investigate the variation of heat budget components during the formation of a low-pressure system. In 2007, the monsoon onset was on 28th May. A well- marked low-pressure area was formed in the eastern Arabian Sea after the onset and it further developed into a cyclone. We have analysed the heat budget components during different stages of the cyclone. The data used for the computation of heat budget components is Objectively Analyzed air-sea flux data obtained from WHOI (Woods Hole Oceanographic Institution) project. Its horizontal resolution is 1° × 1°. Over the low-pressure area, the latent heat flux was 180 Wm−2. It increased to a maximum value of 210 Wm−2 on 1st June 2007, on which the system was intensified into a cyclone (Gonu) with latent heat flux values ranging from 200 to 250 Wm−2. It sharply decreased after the passage of cyclone. The high value of latent heat flux is attributed to the latent heat release due to the cyclone by the formation of clouds. Long wave radiation flux is decreased sharply from 100 Wm−2 to 30 Wm−2 when the low-pressure system intensified into a cyclone. The decrease in long wave radiation flux is due to the presence of clouds. Net heat flux also decreases sharply to −200 Wm−2 on 1st June 2007. After the passage, the flux value increased to normal value (150 Wm−2) within one day. A sharp increase in the sensible heat flux value (20 Wm−2) is observed on 1st June 2007 and it decreased there- after. Short wave radiation flux decreased from 300 Wm−2 to 90 Wm−2 during the intensification on 1st June 2007. Over this region, short wave radiation flux sharply increased to higher value soon after the passage of the cyclone.

A high resolution late Holocene palaeo environmental record from the central Adriatic Sea

A multi-proxy study of a Holocene sediment core (RF 93-30) from the western flank of the central Adriatic, in 77 m of water, reveals a sequence of changes in terrestrial vegetation, terrigenous sediment input and benthic fauna, as well as evidence for variations in sea surface temperature spanning most of the last 7000 yr. The chronology of sedimentation is based on several lines of evidence, including AMS 14C dates of foraminifera extracted from the core, palaeomagnetic secular variation, pollen indicators and dated tephra. The temporal resolution increases towards the surface and, for some of the properties measured, is sub-decadal for the last few centuries. The main changes recorded in vegetation, sedimentation and benthic foraminiferal assemblages appear to be directly related to human activity in the sediment source area, which includes the Po valley and the eastern flanks of the central and northern Appenines. The most striking episodes of deforestation and expanding human impact begin around 3600 BP (Late Bronze Age) and 700 BP (Medieval) and each leads to an acceleration in mass sedimentation and an increase in the proportion of terrigenous material, reflecting the response of surface processes to widespread forest clearance and cultivation. Although human impact appears to be the proximal cause of these changes, climatic effects may also have been important. During these periods, signs of stress are detectable in the benthic foram morphotype assemblages. Between these two periods of increased terrigeneous sedimentation there is smaller peak in sedimentation rate around 2400BP which is not associated with evidence for deforestation, shifts in the balance between terrigenous and authigenic sedimentation, or changes in benthic foraminifera. The mineral magnetic record provides a sensitive indicator of changing sediment sources: during forested periods of reduced terrigenous input it is dominated by authigenic bacterial magnetite, whereas during periods of increased erosion, anti-ferromagetic minerals (haematite and/or goethite) become more important, as well as both paramagnetic minerals and super-paramagnetic magnetite. Analysis of the alkenone, U37k′, record provides an indication of possible changes in sea surface temperature during the period, but it is premature to place too much reliance on these inferred changes until the indirect effects of past changes in the depth of the halocline and in circulation have been more fully evaluated. The combination of methods used and the results obtained illustrate the potential value of such high resolution near-shore marine sedimentary sequences for recording wide-scale human impact, documenting the effects of this on marine sedimentation and fauna and, potentially, disentangling evidence for human activities from that for past changes in climate.

High-resolution FTIRS-inferred biogeochemical properties for MIS 11c in the sediment record of core ICDP5011-1 in Lake Elgygytgyn, NE Russia

Here we present a detailed multi-proxy record of the climate and environmental evolution at Lake El'gygytgyn, Far East Russian Arctic during the period 430-395 ka covering the marine isotope stage (MIS) 12/11 transition and the thermal maximum of super interglacial MIS 11c. The MIS 12/11 transition at Lake El'gygytgyn is characterized by initial warming followed by a cold reversal implying similarities to the last deglaciation. The thermal maximum of MIS 11c is characterized by full and remarkably stable interglacial conditions with mean temperatures of the warmest month (MTWM) ranging between ca. 10-15 °C; annual precipitation (PANN) ranging between ca. 300-600 mm; strong in-lake productivity coinciding with dark coniferous forests in the catchment; annual disintegration of the lake ice cover; and full mixis of the water column. Such conditions persisted, according to our age model, for ca. 27 ± 8 kyr between ca. 425-398 ka. The Lake El'gygytgyn record closely resembles the climate pattern recorded in Lake Baikal (SE Siberia) sediments and Antarctic ice cores, implying interhemispheric climate connectivity during MIS 11c.