The use of ultrasound to create tissue hyperthermia to support the treatment of cancer

The value of mild hyperthermia in improving the outcome of radiotherapy and chemotherapy treatments is well established. However, clinical applications are currently restricted to accessible tumours, with the application of controlled hyperthermia in solid tumours deep within the body presenting an unresolved problem. Ultrasound is an attractive heating technique because of its ability to create a focus at depth which can be steered around the tumour volume. However, despite considerable research no clinically usable transducers for deep tumour applications have resulted. In this thesis the underlying principles that govern the characteristics of phased array transducers have been examined. The concept of an idealised phased array has been introduced, and analysis of simulated fields from such arrays has enabled a new set of equations to be defined which relate the geometry of the field to the fundamental array design parameters (including the array diameter, radius of curvature and frequency of operation). Further simulations have examined the impact of secondary array design parameters (such as the individual element size, number density and layout geometry) which modify the field from that of the idealised case. Analysis of these has enabled an upper limit to be placed on the element size within any planar array in order to prevent undesirable changes in the characteristics of the focal region. A fifteen element phased array with a random element distribution has been constructed based on the design principles established in the simulation work. Measurements of the inter-element cross-coupling have been made, demonstrating that acoustic coupling dominated for inter-element pitches of less than 8 mm, while electrical coupling dominated at larger inter-element pitches. The field produced by the array in an acoustic tank has been characterised and compared against simulation predictions, showing good agreement in terms of the geometries of the focal region and the grating lobes. However, a number of differences have also been identified. In particular, the focal region was closer to the surface of the physical transducer in the measured fields compared to the simulation results, and there were numerous small high intensity regions between the surface of the transducer and the focus which were absent from the simulated fields. A sensitivity analysis, using a simulated factorial experiment, has been performed to identify the origin of these differences, with the results indicating that the presence of a secondary vibrational mode within the elements of the array was the principal causative factor. Finally, calculations have been performed which demonstrate the feasibility of manufacturing an array suitable for the application of mild hyperthermia in deep tumours based on the array design scheme presented in this thesis. Potential extensions of the array design have also been described which would improve the behaviour of the array under steering and provide further increase in the focal intensity

Inaccuracies in plasma oxytocin extraction and enzyme immunoassay techniques

Numerous studies have reported extensive associations between plasma oxytocin (OXT) concentrations and various human physiological and neurobehavioral processes. Measurement of OXT is fraught with difficulty due to its low molecular weight and plasma concentrations, with no consensus as to the optimal conditions for pre-analytical sample extraction, standards for immunoassay validation or the ideal protease inhibitors to prevent OXT degradation. Previous attempts at determining the efficacy of various purification techniques such as solid phase extraction (SPE) or ultrafiltration have only utilized human plasma samples, making it difficult to dissect out whether the effect of interference comes from the extraction process itself or cross-reactivity with other proteins. By testing these on pure OXT solutions, we demonstrate poor recovery efficacy and reliability of reversed phase SPE (maximum 58.1%) and ultrafiltration (<1%) techniques, and the potential for the former to introduce interference into enzyme immunoassay (EIA) measurements. The clonality of antibodies used in EIA kits also potentially contributes to the differences in the readings obtained, and we validate an EIA kit which did not require pre-analytical sample extraction with low cross-reactivity and high reliability (intraclass correlation coefficient 0.980 (95% CI 0.896–0.999). Biochemical techniques used for measuring plasma OXT concentrations must therefore be internally validated prior to translation into clinical studies

The use of ultrasound to create tissue hyperthermia to support the treatment of cancer

The value of mild hyperthermia in improving the outcome of radiotherapy and chemotherapy treatments is well established. However, clinical applications are currently restricted to accessible tumours, with the application of controlled hyperthermia in solid tumours deep within the body presenting an unresolved problem. Ultrasound is an attractive heating technique because of its ability to create a focus at depth which can be steered around the tumour volume. However, despite considerable research no clinically usable transducers for deep tumour applications have resulted. In this thesis the underlying principles that govern the characteristics of phased array transducers have been examined. The concept of an idealised phased array has been introduced, and analysis of simulated fields from such arrays has enabled a new set of equations to be defined which relate the geometry of the field to the fundamental array design parameters (including the array diameter, radius of curvature and frequency of operation). Further simulations have examined the impact of secondary array design parameters (such as the individual element size, number density and layout geometry) which modify the field from that of the idealised case. Analysis of these has enabled an upper limit to be placed on the element size within any planar array in order to prevent undesirable changes in the characteristics of the focal region. A fifteen element phased array with a random element distribution has been constructed based on the design principles established in the simulation work. Measurements of the inter-element cross-coupling have been made, demonstrating that acoustic coupling dominated for inter-element pitches of less than 8 mm, while electrical coupling dominated at larger inter-element pitches. The field produced by the array in an acoustic tank has been characterised and compared against simulation predictions, showing good agreement in terms of the geometries of the focal region and the grating lobes. However, a number of differences have also been identified. In particular, the focal region was closer to the surface of the physical transducer in the measured fields compared to the simulation results, and there were numerous small high intensity regions between the surface of the transducer and the focus which were absent from the simulated fields. A sensitivity analysis, using a simulated factorial experiment, has been performed to identify the origin of these differences, with the results indicating that the presence of a secondary vibrational mode within the elements of the array was the principal causative factor. Finally, calculations have been performed which demonstrate the feasibility of manufacturing an array suitable for the application of mild hyperthermia in deep tumours based on the array design scheme presented in this thesis. Potential extensions of the array design have also been described which would improve the behaviour of the array under steering and provide further increase in the focal intensity.EThOS - Electronic Theses Online ServiceEngineering and Physical Sciences Research Council (Great Britain) (EPSRC)GBUnited Kingdo

Gypsophile chemistry unveiled: Fourier transform infrared (FTIR) spectroscopy provides new insight into plant adaptations to gypsum soils

Gypsum soils are among the most restrictive and widespread substrates for plant life. Plants living on gypsum are classified as gypsophiles (exclusive to gypsum) and gypsovags (non-exclusive to gypsum). The former have been separated into wide and narrow gypsophiles, each with a putative different ecological strategy. Mechanisms displayed by gypsum plants to compete and survive on gypsum are still not fully understood. The aim of this study was to compare the main chemical groups in the leaves of plants with different specificity to gypsum soils and to explore the ability of Fourier transform infrared (FTIR) spectra analyzed with neural network (NN) modelling to discriminate groups of gypsum plants. Leaf samples of 14 species with different specificity to gypsum soils were analysed with FTIR spectroscopy coupled to neural network (NN) modelling. Spectral data were further related to the N, C, S, P, K, Na, Ca, Mg and ash concentrations of samples. The FTIR spectra of the three groups analyzed showed distinct features that enabled their discrimination through NN models. Wide gypsophiles stood out for the strong presence of inorganic compounds in their leaves, particularly gypsum and, in some species, also calcium oxalate crystals. The spectra of gypsovags had less inorganic chemical species, while those of narrow gypsum endemisms had low inorganics but shared with wide gypsophiles the presence of oxalate. Gypsum and calcium oxalate crystals seem to be widespread amongst gypsum specialist plants, possibly as a way to tolerate excess Ca and sulphate. However, other mechanisms such as the accumulation of sulphates in organic molecules are also compatible with plant specialization to gypsum. While gypsovags seem to be stress tolerant plants that tightly regulate the uptake of S and Ca, the ability of narrow gypsum endemisms to accumulate excess Ca as oxalate may indicate their incipient specialization to gypsum

A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping: an example using rice root-growth QTLs

Fine mapping can accurately identify positional candidate genes for quantitative trait loci (QTLs) but can be time consuming, costly, and, for small-effect QTLs with low heritability, difficult in practice. We propose an alternative approach, which uses meta-analysis of original mapping data to produce a relatively small confidence interval for target QTLs, lists the underlying positional candidates, and then eliminates them using whole-genome transcriptomics. Finally, sequencing is conducted on the remaining candidate genes allowing identification of allelic variation in either expression or protein sequence. We demonstrate the approach using root-growth QTLs on chromosomes 2, 5, and 9 of the Bala × Azucena rice mapping population. Confidence intervals of 10.5, 9.6, and 5.4 cM containing 189, 322, and 81 genes, respectively, were produced. Transcriptomics eliminated 40% of candidate genes and identified nine expression polymorphisms. Sequencing of 30 genes revealed that 57% of the predicted proteins were polymorphic. The limitations of this approach are discussed

A single-center, observational study of 607 children & young people presenting with Differences in Sex Development (DSD)

Context Differences in sex development (DSD) represent a wide range of conditions presenting at different ages to various health professionals. Establishing a diagnosis, supporting the family and developing a management plan are important. Objective We aimed to better understand the presentation and prevalence of pediatric DSD. Design A retrospective, observational cohort study was undertaken of all children and young people (CYP) referred to a DSD multi-disciplinary team over 25 years (1995-2019). Setting A single tertiary paediatric center. Participants In total, 607 CYP (520 regional referrals) were included. Main Outcome Measures Data were analyzed for diagnosis, sex-assignment, age and mode of presentation, additional phenotypic features, mortality, and approximate point prevalence. Results Amongst the three major DSD categories, sex chromosome DSD was diagnosed in 11.2% (68/607) (most commonly 45, X/46, XY mosaicism), 46, XY DSD in 61.1% (371/607) (multiple diagnoses often with associated features), while 46, XX DSD occurred in 27.7% (168/607) (often 21-hydroxylase deficiency). Most children (80.1%) presented as neonates, usually with atypical genitalia, adrenal insufficiency, undescended testes or herniae. Those presenting later had diverse features. Rarely, the diagnosis was made antenatally (3.8%, n = 23) or following incidental karyotyping/family history (n = 14). Mortality was surprisingly high in 46, XY children, usually due to complex associated features (46, XY girls, 8.3%; 46, XY boys, 2.7%). The approximate point prevalence of neonatal referrals for investigation of DSD was 1 in 6,347 births, and 1 in 5,101 overall throughout childhood. Conclusions DSD represent a diverse range of conditions that can present at different ages. Pathways for expert diagnosis and management are important to optimize care

The prospectivity of a potential shale gas play: An example from the southern Pennine Basin (central England, UK)

During the Serpukhovian (late Mississippian) Stage, the Pennine Basin, now underlying much of northern England, consisted of a series of interlinked sub-basins that developed in response to the crustal extension north of the Hercynic orogenic zone. For the current study, mudstone samples of the Morridge Formation from two sub-basins located in the south-eastern part of the Pennine Basin were collected from the Carsington Dam Reconstruction C3 Borehole (Widmerpool Gulf sub-basin) and the Karenight 1 Borehole (Edale Gulf sub-basin). Detailed palynological analyses indicate that aside from the dominant (often 90% or more) heterogeneous amorphous organic matter (AOM), variable abundances of homogeneous AOM and phytoclasts are present. To complement the palynological dataset, a suite of geochemical and mineralogical techniques were applied to evaluate the prospectivity of these potentially important source rocks. Changes in the carbon isotope composition of the bulk organic fraction (δ13COM) suggest that the lower part (Biozone E2a) of Carsington DR C3 is markedly more influenced by terrigenous kerogen than the upper part of the core (Biozones E2a3–E2b1). The Karenight 1 core yielded more marine kerogen in the lower part (Marine Bands E1–E2b) than the upper part (Marine Band E2b). Present day Rock-Eval™ Total Organic Carbon (TOC) surpasses 2% in most samples from both cores, a proportion suggested by Jarvie (2012) that defines prospective shale gas reservoirs. However, when the pyrolysable component that reflects the generative kerogen fraction is considered, very few samples reach this threshold. The kerogen typing permits for the first time the calculation of an original hydrogen index (HIo) and original total organic carbon (TOCo) for Carboniferous mudstones of the Pennine Basin. The most prospective part of Carsington DR C3 (marine bands E2b1–E2a3) has an average TOCo of 3.2% and an average HIo of 465 mg/g TOCo. The most prospective part of Karenight 1 (242.80–251.89 m) is characterized by an average TOCo of 9.3% and an average HIo of 504 mg/g TOCo. Lastly, X-ray diffraction (XRD) analysis confirms that the siliceous to argillaceous mudstones contain a highly variable carbonate content. The palynological, geochemical and mineralogical proxies combined indicate that marine sediments were continuously being deposited throughout the sampled intervals and were punctuated by episodic turbiditic events. The terrestrial material, originating from the Wales-Brabant High to the south of the Pennine Basin, was principally deposited in the Widmerpool Gulf, with much less terrigenous organic matter reaching the Edale Gulf. As a consequence, the prospective intervals are relatively thin, decimetre-to meter-scale, and further high resolution characterization of these intervals is required to understand variability in prospectivitiy over these limited intervals

Blue carbon stock of the Bangladesh Sundarban mangroves: what could be the scenario after a century?

The total blue carbon stock of the Bangladesh Sundarban mangroves was evaluated and the probable future status after a century was predicted based on the recent trend of changes in the last 30 years and implementing a hybrid model of Markov Chain and Cellular automata. At present 36.24 Tg C and 54.95 Tg C are stored in the above-ground and below-ground compartments respectively resulting in total blue carbon stock of 91.19 Tg C. According to the prediction 15.88 Tg C would be lost from this region by the year 2115. The low saline species composition classes dominated mainly by Heritiera spp. accounts for the major portion of the carbon sock at present (45.60 Tg C), while the highly saline regions stores only 14.90 Tg C. The prediction shows that after a hundred years almost 22.42 Tg C would be lost from the low saline regions accompanied by an increase of 8.20 Tg C in the high saline regions dominated mainly by Excoecaria sp. and Avicennia spp. The net carbon loss would be due to both mangrove area loss (~ 510 km2) and change in species composition leading to 58.28 Tg of potential CO2 emission within the year 2115

NrCAM, a neuronal system cell-adhesion molecule, is induced in papillary thyroid carcinomas

NrCAM (neuron-glia-related cell-adhesion molecule) is primarily, although not solely, expressed in the nervous system. In the present study, NrCAM expression was analysed in a series (46) of papillary thyroid carcinomas (PTCs) and paired normal tissues (NT). Quantitative reverse transcriptase (QRT)-PCR revealed that NrCAM expression was upregulated in all PTCs compared to normal thyroid, whatever the stage or size of the primary tumour. NrCAM transcript levels were 1.3- to 30.7-fold higher in PTCs than in NT. Immunohistochemistry (IHC) confirmed that the expression of NrCAM was considerably higher in tumours (score 2+/3+) than in adjacent normal paratumoural thyroid tissue. The NrCAM protein was detected in all but three (93.3%) PTC samples, and it was mainly cytoplasmic; in some cases there was additional membranous localisation – basolateral and partly apical. In the normal thyroid and tissues surrounding tumours, focal NrCAM immunolabelling was seen only in follicles containing tall cells, where staining was restricted to the apical pole of thyrocytes. Western blot analysis corroborated the QRT–PCR and IHC results, showing higher NrCAM protein levels in PTCs than in paired NT. The level of overexpression of the NrCAM mRNA in tumourous tissue appeared to be independent of the primary tumour stage (pT) or the size of the PTC. These data provide the first evidence that NrCAM is overexpressed in human PTCs at the mRNA and protein levels, whatever the tumour stage. Thus, the induction and upregulation of NrCAM expression could be implicated in the pathogenesis and behaviour of papillary thyroid cancers