Inverse techniques: problems in optics and gas sensing

In this thesis, two, seemingly different, classes of problems are discussed: locating gas sources from downwind gas concentration measurements and designing diffractive optics (i.e. computer generated holograms), which on illumination will produce a desired light beam in the far field. The similarity between these problems is that they are both “inverse problems” and we discuss the use of inverse techniques to solve them. In many instances within science, it is possible to calculate accurately a set of consequences which result from defined events. In most cases, however, it is math- ematically impossible to analytically calculate the unique set of events which led to the observed consequences. Such problems are termed “inverse problems”. Taking the example of gas dispersion, one sees that a known source leads to a calculable set of downwind concentrations. However, given a single concentration measurement it is impossible to distinguish a specific source and location from a larger, more distant source that would have given the same measured concentration. This is an example of the same consequence resulting from two, or more, different events. Key to solving inverse problems are iterative algorithms which randomly trial different possible events to find those which best describe the observed consequences. Such algorithms use a search method to postulate possible events, apply a forward model to calculate the anticipated consequences and then use a cost function to compare the postulated with the known consequences. The process is iterated until the optimum value of the cost function is found, at which point the current set of postulated events are taken to be the best estimate of the real events. In this thesis I apply similar iterative algorithms to solve the two classes of problem. The current demand on the world’s oil resources have encouraged the development of new prospecting techniques. LightTouch is one such solution which is discussed in this thesis and was developed with Shell Global Solutions. LightTouch uses the fact that oil reserves, through microseepages, leak hydrocarbons to their surface. Detection of these hydrocarbons can indicate the presence of oil reserves. LightTouch measures Ethane to sub-part-per-billion sensitivity at multiple positions across a survey area. Locating the source of the Ethane from the sparse downwind concentration measurements is an inverse problem and we deploy algorithms of the type discussed above to locate the Ethane sources. The algorithm is written in LabView and the software, Recon, is currently used by Shell Global Solutions to solve this problem. In appendix B the Recon user interface is shown. We investigate both the impact of choice of cost function (chapter 3) and forward model (chapter 4), which in this inverse problem is a gas dispersion model, on the algorithm’s ability to locate the gas sources. We find that the choice of cost function is more important to the success of the algorithm than the choice of forward model. Optical tweezers trap and manipulate particles with light beams. In order to manipulate the particles in a desired way it is necessary for the shape and position of the light beam to be controlled. One way of achieving a desired light beam is to use a spatial light modulator (SLM) which displays a phase pattern (referred to as a computer generated hologram), off which the light is diffracted. Calculating the phase pattern which will result in the desired light beam is an inverse problem and is referred to as holographic light shaping. The forward model in this case is a Fourier transform. In this thesis we use an algorithm similar to that used to solve the gas location problem and the Gerchberg-Saxton algorithm to calculate phase patterns with applications in optical tweezers. Within an optical tweezers system the highest trap resolution (the smallest distance between neighboring traps) that can be achieved is conventionally dictated by the diffraction limit. In this thesis we investigate two possible ways of beating the diffraction limit: superresolution and evanescent waves. In chapter 5 we investigate the application of inverse techniques to calculating phase patterns which produce superresolution optical traps. We calculate theoreti- cally the improvements to both relative trap stiffness and trap resolution using the superresolution optical traps. Although both are improved it comes at a cost to trap strength. In chapter 7 we simulate evanescent wave fields and demonstrate shaping three dimensional evanescent optical traps. Similar light shaping techniques are used in chapter 6 to shape light beams which after being disturbed will self-reconstruct

Simulated holographic three-dimensional intensity shaping of evanescent-wave fields

The size of bright structures in traveling-wave light fields is limited by diffraction. This in turn limits a number of technologies, for example, optical trapping. One way to beat the diffraction limit is to use evanescent waves instead of traveling waves. Here we apply a holographic algorithm, direct search, to the shaping of complex evanescent-wave fields. We simulate three-dimensional intensity shaping of evanescent-wave fields using this approach, and we investigate some of its limitations. (c) 2008 Optical Society of America.</p

Simulation of superresolution holography for optical tweezers

Optical tweezers manipulate microscopic particles using foci of light beams. Their performance is therefore limited by diffraction. Using computer simulations of a model system, we investigate the application of superresolution holography for two-dimensional (2D) light shaping in optical tweezers, which can beat the diffraction limit. We use the direct-search and Gerchberg algorithms to shape the center of a light beam into one or two bright spots; we do not constrain the remainder of the beam. We demonstrate that superresolution algorithms can significantly improve the normalized stiffness of an optical trap and the minimum separation at which neighboring traps can be resolved. We also test if such algorithms can be used interactively, as is desirable in optical tweezers

Comment on “Discovery of davemaoite, CaSiO₃-perovskite, as a mineral from the lower mantle”

Tschauner et al. (Reports, 11 November 2021, p. 891) present evidence that diamond GRR-1507 formed in the lower mantle. Instead, the data support a much shallower origin in cold, subcratonic lithospheric mantle. X-ray diffraction data are well matched to phases common in microinclusion-bearing lithospheric diamonds. The calculated bulk inclusion composition is too imprecise to uniquely confirm CaSiO₃ stoichiometry and is equally consistent with inclusions observed in other lithospheric diamonds

Embodied Knowledge: Writing Researchers’ Bodies Into Qualitative Health Research

After more than a decade of postpositivist health care research and an increase in narrative writing practices, social scientific, qualitative health research remains largely disembodied. The erasure of researchers’ bodies from conventional accounts of research obscures the complexities of knowledge production and yields deceptively tidy accounts of research. Qualitative health research could benefit significantly from embodied writing that explores the discursive relationship between the body and the self and the semantic challenges of writing the body by incorporating bodily details and experiences into research accounts. Researchers can represent their bodies by incorporating autoethnographic narratives, drawing on all of their senses, interrogating the connections between their bodily signifiers and research processes, and experimenting with the semantics of self and body. The author illustrates opportunities for embodiment with excerpts from an ethnography of a geriatric oncology team and explores implications of embodied writing for the practice of qualitative health research

Rediscovering the value of families for psychiatric genetics research

As it is likely that both common and rare genetic variation are important for complex disease risk, studies that examine the full range of the allelic frequency distribution should be utilized to dissect the genetic influences on mental illness. The rate limiting factor for inferring an association between a variant and a phenotype is inevitably the total number of copies of the minor allele captured in the studied sample. For rare variation, with minor allele frequencies of 0.5% or less, very large samples of unrelated individuals are necessary to unambiguously associate a locus with an illness. Unfortunately, such large samples are often cost prohibitive. However, by using alternative analytic strategies and studying related individuals, particularly those from large multiplex families, it is possible to reduce the required sample size while maintaining statistical power. We contend that using whole genome sequence (WGS) in extended pedigrees provides a cost-effective strategy for psychiatric gene mapping that complements common variant approaches and WGS in unrelated individuals. This was our impetus for forming the “Pedigree-Based Whole Genome Sequencing of Affective and Psychotic Disorders” consortium. In this review, we provide a rationale for the use of WGS with pedigrees in modern psychiatric genetics research. We begin with a focused review of the current literature, followed by a short history of family-based research in psychiatry. Next, we describe several advantages of pedigrees for WGS research, including power estimates, methods for studying the environment, and endophenotypes. We conclude with a brief description of our consortium and its goals

Lifespan extension and the doctrine of double effect

Recent developments in biogerontology—the study of the biology of ageing—suggest that it may eventually be possible to intervene in the human ageing process. This, in turn, offers the prospect of significantly postponing the onset of age-related diseases. The biogerontological project, however, has met with strong resistance, especially by deontologists. They consider the act of intervening in the ageing process impermissible on the grounds that it would (most probably) bring about an extended maximum lifespan—a state of affairs that they deem intrinsically bad. In a bid to convince their deontological opponents of the permissibility of this act, proponents of biogerontology invoke an argument which is grounded in the doctrine of double effect. Surprisingly, their argument, which we refer to as the ‘double effect argument’, has gone unnoticed. This article exposes and critically evaluates this ‘double effect argument’. To this end, we first review a series of excerpts from the ethical debate on biogerontology in order to substantiate the presence of double effect reasoning. Next, we attempt to determine the role that the ‘double effect argument’ is meant to fulfil within this debate. Finally, we assess whether the act of intervening in ageing actually can be justified using double effect reasoning

Humoral and cellular responses to SARS-CoV-2 in patients with B-cell haematological malignancies improve with successive vaccination

Patients with haematological malignancies are more likely to have poor responses to vaccination. Here we provide detailed analysis of the humoral and cellular responses to COVID-19 vaccination in 69 patients with B-cell malignancies. Measurement of anti-spike IgG in serum demonstrated a low seroconversion rate with 27.1% and 46.8% of patients seroconverting after the first and second doses of vaccine, respectively. In vitro pseudoneutralisation assays demonstrated a poor neutralising response, with 12.5% and 29.5% of patients producing a measurable neutralising titre after the first and second doses, respectively. A third dose increased seropositivity to 54.3% and neutralisation to 51.5%, while a fourth dose further increased both seropositivity and neutralisation to 87.9%. Neutralisation titres post-fourth dose showed a positive correlation with the size of the B-cell population measured by flow cytometry, suggesting an improved response correlating with recovery of the B-cell compartment after B-cell depletion treatments. In contrast, interferon gamma ELISpot analysis showed a largely intact T-cell response, with the percentage of patients producing a measurable response boosted by the second dose to 75.5%. This response was maintained thereafter, with only a small increase following the third and fourth doses, irrespective of the serological response at these timepoints

Land degradation neutrality: testing the indicator in a temperate agricultural landscape

Land degradation directly affects around 25% of land globally, undermining progress on most of the UN Sustainable Development Goals (SDG), particularly target 15.3. To assess land degradation, SDG indicator 15.3.1 combines sub-indicators of productivity, soil carbon and land cover. Over 100 countries have set Land Degradation Neutrality (LDN) targets. Here, we demonstrate application of the indicator for a well-established agricultural landscape using the case study of Great Britain. We explore detection of degradation in such landscapes by: 1) transparently evaluating land cover transitions; 2) comparing assessments using global and national data; 3) identifying misleading trends; and 4) including extra sub-indicators for additional forms of degradation. Our results demonstrate significant impacts on the indicator both from the land cover transition evaluation and choice or availability of data. Critically, we identify a misleading improvement trend due to a trade-off between improvement detected by the productivity sub-indicator, and 30-year soil carbon loss trends in croplands (11% from 1978 to 2007). This carbon loss trend would not be identified without additional data from Countryside Survey (CS). Thus, without incorporating field survey data we risk overlooking the degradation of regulating and supporting ecosystem services (linked to soil carbon), in favour of signals from improving provisioning services (productivity sub-indicator). Relative importance of these services will vary between socioeconomic contexts. Including extra sub-indicators for erosion or critical load exceedance, as additional forms of degradation, produced a switch from net area improving (9%) to net area degraded (58%). CS data also identified additional degradation for soil health, including 44% arable soils exceeding bulk density thresholds and 35% of CS squares exceeding contamination thresholds for metals

Genetic Overlap Profiles of Cognitive Ability in Psychotic and Affective Illnesses::A Multi-Site Study of Multiplex Pedigrees

BACKGROUND: Cognitive impairment is a key feature of psychiatric illness, making cognition an important tool for exploring of the genetics of illness risk. It remains unclear which measures should be prioritized in pleiotropy-guided research. Here, we generate profiles of genetic overlap between psychotic and affective disorders and cognitive measures in Caucasian and Hispanic groups. METHODS: Data were from four samples of extended pedigrees (N = 3046). Coefficient of relationship analyses were used to estimate genetic overlap between illness risk and cognitive ability. Results were meta-analyzed. FINDINGS: Psychosis was characterized by cognitive impairments on all measures with a generalized profile of genetic overlap. General cognitive ability shared greatest genetic overlap with psychosis risk (average Endophenotype Ranking Value (ERV) across samples from a random-effects meta-analysis = 0.32) followed by Verbal Memory (ERV = 0.24), Executive Function (ERV = 0.22), and Working Memory (ERV = 0.21). For bipolar disorder, there was genetic overlap with Processing Speed (ERV = 0.05) and Verbal Memory (ERV = 0.11), but these were confined to select samples. Major depression was characterized by enhanced Working and Face Memory performance, as reflected in significant genetic overlap in two samples. INTERPRETATION: There is substantial genetic overlap between risk for psychosis and a range of cognitive abilities (including general intelligence). Most of these effects are largely stable across of ascertainment strategy and ethnicity. Genetic overlap between affective disorders and cognition, on the other hand, tend to be specific to ascertainment strategy, ethnicity, and cognitive test battery