Mid-Infrared Integrated Devices for Optical Chemical Sensing

The mid-infrared (MIR) spectral range is of special interest for establishing optical chemical sensor technologies by allowing specific molecular identification and quantification, whether the sample is in a liquid, gas or solid form, in addition to providing highly sensitive, rapid, reagent-free and non-destructive detection. This thesis explores four different liquid- and gas- sensing applications and methods using MIR spectroscopy by integrating it with other technologies, such as microfluidics and fibre-optics. Firstly, fibre-optic integrated microfluidic devices were developed and tested for con- tinuous fluid monitoring. These showed good sensing capabilities for online, continuous and real-time liquid sensing in hard-to-reach locations. Next, this thesis presents the establishment and clinical testing of a novel method for continuous monitoring of the brain chemistry of traumatically brain-injured patients by MIR transmission spectroscopy. Here, the outlet of a cerebral microdialysis catheter is cou- pled to a micro flow-cell and the flowing microdialysate is continuously analysed. Clinical studies were carried out and showed the capability of this system for performing continuous patient monitoring over several hours. With further optimisation, the implementation of this system could lead to improved patient outcome. This thesis also presents a novel method and system based on MIR fibre-optic evanescent- wave spectroscopy, which enables enhanced detection of volatile organic compounds (VOCs). Here, a nanoporous silicon cladding was used to reversibly concentrate molecules close to the fibre surface, thus enhancing VOC detection. A significant increase in sen- sitivity was seen compared to that of an uncoated fibre and successful detection of three different VOCs, both independently and in binary mixtures, was achieved. Finally, this thesis introduces a simple and relatively low-cost fibre-optic sensor for in-line, real-time bioprocess monitoring. The sensor was successfully able to monitor varying concentrations of product (sophorolipids) in fermentation broth and was able to distinguish between the two types of generated product (acidic and lactonic sophorolipids). The work presented in this thesis showed that MIR-integrated sensors have great potential to provide novel and/or enhanced sensing solutions in a wide range of applications, including medical, industrial and environmental

Assessment of a Microfluidic Intravenous Oxygen Generating Platform to Aid Acute Respiratory Failure

Acute respiratory failure is associated with a high mortality rate, despite the advances in conventional treatments. This work presents the development of a proof-of-concept device for assessing the viability of an oxygen-generating catheter, deployed intravenously, to temporarily sustain a patient who is suffering from acute respiratory failure. The assessment device mimics the interface between the catheter and bloodstream (deoxygenated water substitutes the blood), and consists of two parallel channels separated from each other by an oxygen-permeable membrane that simulates the catheter material. Several polydimethylsiloxane membranes with enhanced permeability were developed and tested on the device according to their permeation rates. The highest permeation rate achieved was 3.6×10-7 cm3/s (equivalent in-blood value) considering the device’s surface area and applied pressure. However, the extrapolation of this value to a catheter with increased surface area demonstrated a predicted oxygen permeation rate of 1.6×10-3 cm3/s. Although the oxygen permeation rates achieved here do not yet reach the minimum required rate to sustain a patient with only 30 % of their lungs functional (1.6 cm3/s O2), it may be enhanced further by improving certain parameters such as material permeability, surface area and applied pressure. The ability to administer oxygen or other gases directly into the bloodstream may portray a technique for short-term rescue of severely hypoxemic patients to increase whole body or at-risk organ oxygenation

Measurement of transpiration restriction under high vapor pressure deficit for sorghum mapping population parents

Limiting transpiration rate under high vapor pressure deficit (VPD) and/or progressive soil drying conditions are soil water conservation mechanisms that can play an important drought-adaptive role if water is limiting to support crops at its full potential. In this study, these two important physiological mechanisms were measured on parental pairs of existing Recombinant Inbred Lines (RILs) of sorghum mapping populations; both in experiments run in the glasshouse and growth chambers, and outdoors. In controlled environmental conditions, the RIL1, RIL2, RIL6 and RIL8 showed contrasting transpiration response to increasing VPD. The difference in the soil moisture fractions of transpirable soil water threshold where transpiration initiated a decline were high in RIL1, RIL3 and RIL8 respectively. The exploration of the variation of the evapotranspiration response to VPD was also carried out in a high throughput phenotyping facility in which plants were grown similar to field density conditions. Under high VPD conditions, the RIL parental pairs showed usual transpiration peak during the midday period. At this time period, genotypic differences within parental pairs were observed in RIL1, RIL2, RIL6 and RIL8. The donor parent had lower transpiration than the recurrent parents during the midday/high VPD period. Also, we found variation among parental pairs in leaf area normalized with received radiation and measured plant architecture traits. Across studied genotypes, RIL1, RIL2 and RIL8 showed differences in the plant canopy architecture and the transpiration response to an increasing VPD. Collectively, these results open the opportunity to phenotype the RIL progenies of contrasting parents and genetically map the traits controlling plant water use. In turn, this can act as an important genetic resource for identification and incorporation of terminal drought tolerance components in marker-assisted breeding

LeasyScan: 3D scanning of crop canopy plus seamless monitoring of water use to harness the genetics of key traits for drought adaptation

With the genomics revolution in full swing, relevant phenotyping is now a main bottleneck. New imaging technologies provide opportunities for easier, faster and more informative phenotyping of many plant parameters. However, it is critical that the development of automated phenotyping be driven by a clear framing of target phenotypes rather than by a technological push, especially for complex constraints. Previous studies on drought adaptation shows the importance of water availability during the grain filling period, which depends on traits controlling the plant water budget at earlier stages. We will then discuss “cause” and “consequence” in phenotypes. Drawing on this, a phenotyping platform (LeasyScan) was developed to target canopy development and conductance traits. Based on a novel 3D scanning technique to capture leaf area development continuously and a scanner-to-plant concept to increase imaging throughput, LeasyScan is also equipped with 1488 analytical scales to measure transpiration seamlessly. Examples of the first applications are presented: (i) to compare the leaf area development pattern of pearl millet breeding material targeted to different agro-ecological zones, (ii) for the mapping of QTLs for vigour traits in chickpea, shown to co-map with an earlier reported “drought tolerance” QTL; (iii) for the mapping of leaf area development in pearl millet; (iv) for assessing the transpiration response to high vapour pressure deficit in different crops. This new platform has the potential to phenotype traits controlling plant water use at a high rate and precision, opening the opportunity to harness their genetics towards breeding improved varieties

Cerebral Microdialysate Metabolite Monitoring using Mid-infrared Spectroscopy.

Funder: Wellcome TrustThe brains of patients suffering from traumatic brain-injury (TBI) undergo dynamic chemical changes in the days following the initial trauma. Accurate and timely monitoring of these changes is of paramount importance for improved patient outcome. Conventional brain-chemistry monitoring is performed off-line by collecting and manually transferring microdialysis samples to an enzymatic colorimetric bedside analyzer every hour, which detects and quantifies the molecules of interest. However, off-line, hourly monitoring means that any subhourly neurochemical changes, which may be detrimental to patients, go unseen and thus untreated. Mid-infrared (mid-IR) spectroscopy allows rapid, reagent-free, molecular fingerprinting of liquid samples, and can be easily integrated with microfluidics. We used mid-IR transmission spectroscopy to analyze glucose, lactate, and pyruvate, three relevant brain metabolites, in the extracellular brain fluid of two TBI patients, sampled via microdialysis. Detection limits of 0.5, 0.2, and 0.1 mM were achieved for pure glucose, lactate, and pyruvate, respectively, in perfusion fluid using an external cavity-quantum cascade laser (EC-QCL) system with an integrated transmission flow-cell. Microdialysates were collected hourly, then pooled (3-4 h), and measured consecutively using the standard ISCUSflex analyzer and the EC-QCL system. There was a strong correlation between the compound concentrations obtained using the conventional bedside analyzer and the acquired mid-IR absorbance spectra, where a partial-least-squares regression model was implemented to compute concentrations. This study demonstrates the potential utility of mid-IR spectroscopy for continuous, automated, reagent-free, and online monitoring of the dynamic chemical changes in TBI patients, allowing a more timely response to adverse brain metabolism and consequently improving patient outcomes

OptiJ: Open-source optical projection tomography of large organ samples

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples

Grain legume production in Europe for food, feed and meat-substitution

Partial shifts from animal-based to plant-based proteins in human diets could reduce environmental pressure from food systems and serve human health. Grain legumes can play an important role here. They are one of the few agricultural commodities for which Europe is not nearly self-sufficient. Here, we assessed area expansion and yield increases needed for European self-sufficiency of faba bean, pea and soybean. We show that such production could use substantially less cropland (4–8%) and reduce GHG emissions (7–22% current meat production) when substituting for animal-derived food proteins. We discuss changes required in food and agricultural systems to make grain legumes competitive with cereals for farmers and how their cultivation can help to increase sustainability of European cropping systems.</p

OptiJ: Open-source optical projection tomography of large organ samples

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples

OptiJ: Open-source optical projection tomography of large organ samples

Abstract: The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples

Contesting the Iranian Revolution: The Green Uprising.

Iran is but one country that gives real-world application to the Orwellian mantra that “history is written by the victors.” Indeed, the militant clerics, who consolidated power at the expense of all the revolutionary factions, have worked tirelessly to present their version of the Iranian Revolution’s history as the only version—one best encapsulated by the state’s preferred revolutionary slogan: “Independence, Freedom, Islamic Republic” (esteqlal, azadi, jomhuri-ye eslami). For years, the Iranian government has presented this one-sided history to the benefit of its ruling class and self-affirming ideology. Just as the events of 1978-79 are far more complex and disputed than the state would like to admit, the historic uprising of 2009 is equally contentious. More than five years after the revolt, the Iranian government continues to refer to the Green Movement as “the sedition”—a conspiracy orchestrated from abroad and without organic roots within the country. Inspired by the studies that contested the “official” narrative of the Iranian Revolution, this work aspires to do the same with the “official” narrative of the uprising in 2009. The events of 2009 are historically consequential not only because they could have dire consequences for the Iranian government in the long-term, but also because of what they tell the reader about the critical juncture in which Iran’s experiment with Islamism finds itself. After 30 years of Islamic rule, a new generation of activists, who were raised under the ideology and authority of the Islamic Republic, challenged that state by co-opting the system’s discourse, history, and symbolism, all of which they reprogrammed with subversive meaning and leveled against the state with a profound sense of purpose. In doing so, activists brought to the fore in a fiery manner the post-Islamist shift that has been taking place in Iran in recent years. This study takes the archival footage from the events in question, interviews, memoirs, diplomatic cables, activist articles, news data, all of which are intertwined with the research material from the history of the Iranian Revolution in order to produce the context necessary to understanding the tectonic shift the uprising in 2009 represents.PhDHistoryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/116777/1/pouya_1.pd