Statistical modeling of protein lysate array data

The protein lysate array is an emerging technology for quantifying the protein concentration ratios in multiple biological samples. It is gaining popularity, and has the potential to answer questions about post-translational modifications and protein pathway relationships. Statistical inference for a parametric quantification procedure has been inadequately addressed in the literature, mainly due to two challenges: the increasing dimension of the parameter space and the need to account for dependence in the data. Each chapter of this thesis addresses one of these issues. In Chapter 1, an introduction to the protein lysate array quantification is presented, followed by the motivations and goals for this thesis work. In Chapter 2, we develop a multi-step procedure for the Sigmoidal models, ensuring consistent estimation of the concentration level with full asymptotic efficiency. The results obtained in this chapter justify inferential procedures based on large-sample approximations. Simulation studies and real data analysis are used to illustrate the performance of the proposed method in finite-samples. The multi-step procedure is simpler in both theory and computation than the single-step least squares method that has been used in current practice. In Chapter 3, we introduce a new model to account for the dependence structure of the errors by a nonlinear mixed effects model. We consider a method to approximate the maximum likelihood estimator of all the parameters. Using the simulation studies on various error structures, we show that for data with non-i.i.d. errors the proposed method leads to more accurate estimates and better confidence intervals than the existing single-step least squares method.

Rapid hydrothermal cooling above the axial melt lens at fast-spreading mid-ocean ridge

Axial melt lenses sandwiched between the lower oceanic crust and the sheeted dike sequences at fast-spreading mid-ocean ridges are assumed to be the major magma source of oceanic crust accretion. According to the widely discussed "gabbro glacier'' model, the formation of the lower oceanic crust requires efficient cooling of the axial melt lens, leading to partial crystallization and crystal-melt mush subsiding down to lower crust. These processes are believed to be controlled by periodical magma replenishment and hydrothermal circulation above the melt lens. Here we quantify the cooling rate above melt lens using chemical zoning of plagioclase from hornfelsic recrystallized sheeted dikes drilled from the East Pacific at the Integrated Ocean Drilling Program Hole 1256D. Weestimate the cooling rate using a forward modelling approach based on CaAl-NaSi interdiffusion in plagioclase. The results show that cooling from the peak thermal overprint at 1000-10506 degrees C to 6006 degrees C are yielded within about 10-30 years as a result of hydrothermal circulation above melt lens during magma starvation. The estimated rapid hydrothermal cooling explains how the effective heat extraction from melt lens is achieved at fast-spreading mid-ocean ridges.

Spatial and temporal measurements using polyoxometalate, enzymatic and biofilm layers on a CMOS 0.35 μm 64 X 64-pixel I.S.F.E.T. array sensor

This thesis presents the achievements and scientific work conducted using a previously designed and fabricated 64 x 64-pixel ion camera with the use of a 0.35 μm CMOS technology. We used an array of Ion Sensitive Field Effect Transistors (ISFETs) to monitor and measure chemical and biochemical reactions in real time. The area of our observation was a 4.2 x 4.3 mm silicon chip while the actual ISFET array covered an area of 715.8 x 715.8 μm consisting of 4096 ISFET pixels in total with a 1 μm separation space among them. The ion sensitive layer, the locus where all reactions took place was a silicon nitride layer, the final top layer of the austriamicrosystems 0.35 μm CMOS technology used. Our final measurements presented an average sensitivity of 30 mV/pH. With the addition of extra layers we were able to monitor a 65 mV voltage difference during our experiments with glucose and hexokinase, whereas a difference of 85 mV was detected for a similar glucose reaction mentioned in literature, and a 55 mV voltage difference while performing photosynthesis experiments with a biofilm made from cyanobacteria, whereas a voltage difference of 33.7 mV was detected as presented in literature for a similar cyanobacterial species using voltamemtric methods for detection. To monitor our experiments PXIe-6358 measurement cards were used and measurements were controlled by LabVIEW software. The chip was packaged and encapsulated using a PGA-100 chip carrier and a two-component commercial epoxy. Printed circuit board (PCB) has also been previously designed to provide interface between the chip and the measurement cards.

Using a voxel-based krogh cylinder array to simulate microvascular contrast enhancement

The goal of this study is to better simulate microscopic and voxel-based dynamic contrast enhancement in magnetic resonance imaging. Specifically, errors imposed by the traditional two-compartment model are reduced by introducing a novel Krogh cylinder network. The two-compartment model was developed for macroscopic pharmacokinetic analysis of dynamic contrast enhancement and generalizing it to voxel dimensions, due to the significant decrease in scale, imposes physiologically unrealistic assumptions. In the project, a system of microscopic exchange between plasma and extravascular-extracellular space is built while numerically simulating the local contrast agent flow between and inside image elements. To do this, tissue parameter maps were created, contrast agent was introduced to the tissue via a flow lattice, and various data sets were simulated. The effects of sources, tissue heterogeneity, and the contribution of individual tissue parameters to an image are modeled. Further, the study attempts to demonstrate the effects of a priori flow maps on image contrast, indicating that flow data is as important as permeability data when analyzing tumor contrast enhancement. In addition, the simulations indicate that it may be possible to obtain tumor-type diagnostic information by acquiring both flow and permeability data.

Ocean bottom pressure records from the Cascadia array and short surface gravity waves

The ocean bottom pressure records from eight stations of the Cascadia array are used to investigate the properties of short surface gravity waves with frequencies ranging from 0.2 to 5 Hz. It is found that the pressure spectrum at all sites is a well-defined function of the wind speed U10 and frequency f, with only a minor shift of a few dB from one site to another that can be attributed to variations in bottom properties. This observation can be combined with the theoretical prediction that the ocean bottom pressure spectrum is proportional to the surface gravity wave spectrum E(f) squared, times the overlap integral I(f) which is given by the directional wave spectrum at each frequency. This combination, using E(f) estimated from modeled spectra or parametric spectra, yields an overlap integral I(f) that is a function of the local wave age inline image. This function is maximum for f∕fPM = 8 and decreases by 10 dB for f∕fPM = 2 and f∕fPM = 30. This shape of I(f) can be interpreted as a maximum width of the directional wave spectrum at f∕fPM = 8, possibly equivalent to an isotropic directional spectrum, and a narrower directional distribution toward both the dominant low frequencies and the higher capillary-gravity wave frequencies.

The outset of mental torture. Through the lens of the Ticking Time Bomb Scenario

No doubt shall be placed when qualifying torture as one of the cruellest crime offences against human beings. It is widely known that the first torture practices go back to the Middle Ages, where torture mechanisms and devices were used as a legitimate means of punishment, extraction of confessions or executions. Brutal techniques such as ‘Judas Cradle’, ‘The Rack’ or the ‘Rat Torture’ were indeed, the ones commonly used. Moreover, some centuries onwards, torture warrants were permitted and authorised by Privy Councils in legislations such as the English one. However, examples like that were the only ones which public accountability was given to, whereas off-the-book practices remained in silence in other countries for long lasting years. Nowadays, in the 21st century, there are innumerable enforced laws and provisions that prohibit the act of torture, to be precise, physical and psychological torture. Nonetheless, not only are these legislations necessary for fighting torture, but also ad hoc courts and specialised committees continuously report the existence of this crime offence.

Biomimetic accommodating intraocular lens

The crystalline lens allows the eye to focus on near and far objects. During the aging process, it loses its ability to focus and often becomes cloudy during cataract formation. At this point, traditional medical therapy replaces the lens with an artificial replacement lens. Although replacement lenses for the crystalline lens have been implanted since 1949 for cataract surgery, none of the FDA-approved lenses mimic the anatomy of the natural lens. Hence, they are not able to focus in a manner similar to the youthful lens. Instead, they function in a manner similar to the aged lens and only provide vision at a single distance or at a very limited range of focal distances. Patients with the newest implants are often obliged to use reading glasses when using near vision, or suffer from optical aberrations, halos, or glare. Therefore, there is a need to provide youthful vision after lens surgery in terms of focusing ability, accurate optical power, and sharp focus without distortion or optical aberrations.

This thesis presents an approach to restoring youthful vision after lens replacement. An intraocular lens (IOL) that can provide accurate visual acuity along with focusing ability is proposed. This IOL relies on the natural anatomy and physiology of the eye, and therefore is actuated in a manner identical to the natural lens. In addition, the lens has the capability for adjustment during or after implantation to provide high-acuity vision throughout life.

The natural anatomy and physiology of the eye is described, along with lens replacement surgery. A lens design is proposed to address the unmet need of lens-replacement patients. Specific care in the design is made for small surgical incisions, high visual acuity, adjustable acuity over years, and the ability to focus similar to the natural lens. Methods to test the IOL using human donor tissue are developed based upon prior experiments on the ex vivo natural lens. These tools are used to demonstrate efficacy of the newly developed accommodating intraocular lens.

To further demonstrate implant feasibility, materials and processes for building the lens are evaluated for biocompatibility, endurance, repeatable manufacture, and stability. The lens biomechanics are determined after developing an artificial anatomy testing setup inspired by the natural anatomy of the human focusing mechanism. Finally, based upon a mechanical and optical knowledge of the lens, several improved lens concepts are proposed and demonstrated for efficacy.

the plenoptic sensor

In this thesis, we will introduce the innovative concept of a plenoptic sensor that can determine the phase and amplitude distortion in a coherent beam, for example a laser beam that has propagated through the turbulent atmosphere.. The plenoptic sensor can be applied to situations involving strong or deep atmospheric turbulence. This can improve free space optical communications by maintaining optical links more intelligently and efficiently. Also, in directed energy applications, the plenoptic sensor and its fast reconstruction algorithm can give instantaneous instructions to an adaptive optics (AO) system to create intelligent corrections in directing a beam through atmospheric turbulence. The hardware structure of the plenoptic sensor uses an objective lens and a microlens array (MLA) to form a mini “Keplerian” telescope array that shares the common objective lens. In principle, the objective lens helps to detect the phase gradient of the distorted laser beam and the microlens array (MLA) helps to retrieve the geometry of the distorted beam in various gradient segments. The software layer of the plenoptic sensor is developed based on different applications. Intuitively, since the device maximizes the observation of the light field in front of the sensor, different algorithms can be developed, such as detecting the atmospheric turbulence effects as well as retrieving undistorted images of distant objects. Efficient 3D simulations on atmospheric turbulence based on geometric optics have been established to help us perform optimization on system design and verify the correctness of our algorithms. A number of experimental platforms have been built to implement the plenoptic sensor in various application concepts and show its improvements when compared with traditional wavefront sensors. As a result, the plenoptic sensor brings a revolution to the study of atmospheric turbulence and generates new approaches to handle turbulence effect better.

The scientific rationale, design and implementation plan for a Biogeochemical-Argo float array

Biogeochemical-Argo is the extension of the Argo array of profiling floats to include floats that are equipped with biogeochemical sensors for pH, oxygen, nitrate, chlorophyll, suspended particles, and downwelling irradiance. Argo is a highly regarded, international program that measures the changing ocean temperature (heat content) and salinity with profiling floats distributed throughout the ocean. Newly developed sensors now allow profiling floats to also observe biogeochemical properties with sufficient accuracy for climate studies. This extension of Argo will enable an observing system that can determine the seasonal to decadal-scale variability in biological productivity, the supply of essential plant nutrients from deep-waters to the sunlit surface layer, ocean acidification, hypoxia, and ocean uptake of CO2. Biogeochemical-Argo will drive a transformative shift in our ability to observe and predict the effects of climate change on ocean metabolism, carbon uptake, and living marine resource management. Presently, vast areas of the open ocean are sampled only once per decade or less, with sampling occurring mainly in summer. Our ability to detect changes in biogeochemical processes that may occur due to the warming and acidification driven by increasing atmospheric CO2, as well as by natural climate variability, is greatly hindered by this undersampling. In close synergy with satellite systems (which are effective at detecting global patterns for a few biogeochemical parameters, but only very close to the sea surface and in the absence of clouds), a global array of biogeochemical sensors would revolutionize our understanding of ocean carbon uptake, productivity, and deoxygenation. The array would reveal the biological, chemical, and physical events that control these processes. Such a system would enable a new generation of global ocean prediction systems in support of carbon cycling, acidification, hypoxia and harmful algal blooms studies, as well as the management of living marine resources. In order to prepare for a global Biogeochemical-Argo array, several prototype profiling float arrays have been developed at the regional scale by various countries and are now operating. Examples include regional arrays in the Southern Ocean (SOCCOM ), the North Atlantic Sub-polar Gyre (remOcean ), the Mediterranean Sea (NAOS ), the Kuroshio region of the North Pacific (INBOX ), and the Indian Ocean (IOBioArgo ). For example, the SOCCOM program is deploying 200 profiling floats with biogeochemical sensors throughout the Southern Ocean, including areas covered seasonally with ice. The resulting data, which are publically available in real time, are being linked with computer models to better understand the role of the Southern Ocean in influencing CO2 uptake, biological productivity, and nutrient supply to distant regions of the world ocean. The success of these regional projects has motivated a planning meeting to discuss the requirements for and applications of a global-scale Biogeochemical-Argo program. The meeting was held 11-13 January 2016 in Villefranche-sur-Mer, France with attendees from eight nations now deploying Argo floats with biogeochemical sensors present to discuss this topic. In preparation, computer simulations and a variety of analyses were conducted to assess the resources required for the transition to a global-scale array. Based on these analyses and simulations, it was concluded that an array of about 1000 biogeochemical profiling floats would provide the needed resolution to greatly improve our understanding of biogeochemical processes and to enable significant improvement in ecosystem models. With an endurance of four years for a Biogeochemical-Argo float, this system would require the procurement and deployment of 250 new floats per year to maintain a 1000 float array. The lifetime cost for a Biogeochemical-Argo float, including capital expense, calibration, data management, and data transmission, is about $100,000. A global Biogeochemical-Argo system would thus cost about $25,000,000 annually. In the present Argo paradigm, the US provides half of the profiling floats in the array, while the EU, Austral/Asia, and Canada share most the remaining half. If this approach is adopted, the US cost for the Biogeochemical-Argo system would be ~$12,500,000 annually and ~$6,250,000 each for the EU, and Austral/Asia and Canada. This includes no direct costs for ship time and presumes that float deployments can be carried out from future research cruises of opportunity, including, for example, the international GO-SHIP program (http://www.go-ship.org). The full-scale implementation of a global Biogeochemical-Argo system with 1000 floats is feasible within a decade. The successful, ongoing pilot projects have provided the foundation and start for such a system.

Optimization of Energy Distribution in Solar Panel Array Configurations by Graph Theory and Minkowski’s Paths

Nowadays, the development of the photovoltaic (PV) technology is consolidated as a source of renewable energy. The research in the topic of maximum improvement on the energy efficiency of the PV plants is today a major challenge. The main requirement for this purpose is to know the performance of each of the PV modules that integrate the PV field in real time. In this respect, a PLC communications based Smart Monitoring and Communications Module, which is able to monitor at PV level their operating parameters, has been developed at the University of Malaga. With this device you can check if any of the panels is suffering any type of overriding performance, due to a malfunction or partial shadowing of its surface. Since these fluctuations in electricity production from a single panel affect the overall sum of all panels that conform a string, it is necessary to isolate the problem and modify the routes of energy through alternative paths in case of PV panels array configuration.

Simultaneous determination of carotenoids and tocochromanols from palm hybrid oil by hplc with photodiode array and fluorescence detectors.

2016

Analyzing Tidal Fluctuations in the Big Pine Key Freshwater Lens with Time-Lapse Resistivity

The tidal influence on the Big Pine Key saltwater/freshwater interface was analyzed using time-lapse electrical resistivity imaging and shallow well measurements. The transition zone at the saltwater/freshwater interface was measured over part of a tidal cycle along three profiles. The resistivity was converted to salinity by deriving a formation factor for the Miami Oolite. A SEAWAT model was created to attempt to recreate the field measurements and test previously established hydrogeologic parameters. The results imply that the tide only affects the groundwater within 20 to 30 m of the coast. The effect is small and caused by flooding from the high tide. The low relief of the island means this effect is very sensitive to small changes in the magnitude. The SEAWAT model proved to be insufficient in modeling this effect. The study suggests that the extent of flooding is the largest influence on the salinity of the groundwater.

Long-term efficacy of orthokeratology contact lens wear in controlling the progression of childhood myopia

Purpose: The primary outcome of this study is to compare the axial length growth of white European myopic children wearing orthokeratology contact lenses (OK) to a control group (CT) over a 7-year period. Methods: Subjects 6–12 years of age with myopia −0.75 to −4.00DS and astigmatism ≤1.00DC were prospectively allocated OK or distance single-vision spectacles (SV) correction. Measurements of axial length (Zeiss IOLMaster), corneal topography, and cycloplegic refraction were taken at 6-month intervals over a 2-year period. Subjects were invited to return to the clinic approximately 5 years later (i.e., 7 years after the beginning of the study) for assessment of their ocular refractive and biometric components. The CT consisted of 4 SV and 12 subjects who switched from SV to soft contact lens wear after the initial 2 years of SV lens wear. Changes in axial length relative to baseline over a 7-year period were compared between groups. Results: Fourteen and 16 subjects from the OK and CT groups, respectively, were examined 6.7 ± 0.5 years after the beginning of the study. Statistically significant changes in the axial length were found over time and between groups (both p <0.001), but not for the time*group interaction (p = 0.125). The change in the axial length for the OK group was 22% (p = 0.328), 42% (p = 0.007), 40% (p = 0.020), 41% (p = 0.013), and 33% (p = 0.062) lower than the CT group following 6, 12, 18, 24, and 84 months of lens wear, respectively. Conclusion: A trend toward a reduction in the rate of axial elongation of the order of 33% was found in the OK group in comparison to the CT group following 7 years of lens wear.

Visual outcomes after bilateral trifocal diffractive intraocular lens implantation

Background In recent years new models of intraocular lenses are appearing on the market to reduce requirements for additional optical correction. The purpose of this study is to assess visual outcomes following bilateral cataract surgery and the implant of a FineVision® trifocal intraocular lens (IOL). Methods Prospective, nonrandomized, observational study. Vision was assessed in 44 eyes of 22 patients (mean age 68.4 ± 5.5 years) before and 3 months after surgery. Aberrations were determined using the Topcon KR-1 W wave-front analyzer. LogMAR visual acuity was measured at distance (corrected distance visual acuity, CDVA 4 m), intermediate (distance corrected intermediate visual acuity, DCIVA 60 cm) and near (distance corrected near visual acuity, DCNVA 40 cm). The Pelli-Robson letter chart and the CSV-1000 test were used to estimate contrast sensitivity (CS). Defocus curve testing was performed in photopic and mesopic conditions. Adverse photic phenomena were assessed using the Halo v1.0 program. Results Mean aberration values for a mesopic pupil diameter were: total HOA RMS: 0.41 ± 0.30 μm, coma: 0.32 ± 0.22 μm and spherical aberration: 0.21 ± 0.20 μm. Binocular logMAR measurements were: CDVA −0.05 ± 0.05, DCIVA 0.15 ± 0.10, and DCNVA 0.06 ± 0.10. Mean Pelli-Robson CS was 1.40 ± 0.14 log units. Mean CSV100 CS for the 4 frequencies examined (A: 3 cycles/degree (cpd), B: 6 cpd, C: 12 cpd, D: 18 cpd) were 1.64 ± 0.14, 1.77 ± 0.18, 1.44 ± 0.24 and 0.98 ± 0.24 log units, respectively. Significant differences were observed in defocus curves for photopic and mesopic conditions (p < 0.0001). A mean disturbance index of 0.28 ± 0.22 was obtained. Conclusions Bilateral FineVision IOL implant achieved a full range of adequate vision, satisfactory contrast sensitivity, and a lack of significant adverse photic phenomena. Trial registration Eudract Clinical Trials Registry Number: 2014-003266-2.