Ashwin Sachdeva

The inherent problem of transflection-mode infrared spectroscopic microscopy and the ramifications for biomedical single point and imaging applications

Transflection-mode FTIR spectroscopy has become a popular method of measuring spectra from biomedical and other samples due to the relative low cost of substrates compared to transmission windows, and a higher absorbance due to a double pass through the same sample approximately doubling the effective path length. In this publication we state an optical description of samples on multilayer low-e reflective substrates. Using this model we are able to explain in detail the so-called electric-field standing wave effect and rationalise the non-linear change in absorbance with sample thickness. The ramifications of this non-linear change, for imaging and classification systems, where a model is built from tissue sectioned at a particular thickness and compared with tissue of a different thickness are discussed. We show that spectra can be distorted such that classification fails leading to inaccurate tissue segmentation which may have subsequent implications for disease diagnostics applications.

FTIR microscopy of biological cells and tissue: data analysis using resonant Mie scattering (RMieS) EMSC algorithm

Transmission and transflection infrared microscopy of biological cells and tissue suffer from significant baseline distortions due to scattering effects, predominantly resonant Mie scattering (RMieS). This scattering can also distort peak shapes and apparent peak positions making interpretation difficult and often unreliable. A correction algorithm, the resonant Mie scattering extended multiplicative signal correction (RMieS-EMSC), has been developed that can be used to remove these distortions. The correction algorithm has two key user defined parameters that influence the accuracy of the correction. The first is the number of iterations used to obtain the best outcome. The second is the choice of the initial reference spectrum required for the fitting procedure. The choice of these parameters influences computational time. This is not a major concern when correcting individual spectra or small data sets of a few hundred spectra but becomes much more significant when correcting spectra from infrared images obtained using large focal plane array detectors which may contain tens of thousands of spectra. In this paper we show that, classification of images from tissue can be achieved easily with a few (<10) iterations but a reliable interpretation of the biochemical differences between classes could require more iterations. Regarding the choice of reference spectrum, it is apparent that the more similar it is to the pure absorption spectrum of the sample, the fewer iterations required to obtain an accurate corrected spectrum. Importantly however, we show that using three different non-ideal reference spectra, the same unique correction solution can be obtained.

Whole organ cross-section chemical imaging using label-free mega-mosaic FTIR microscopy

FTIR chemical imaging has been demonstrated as a promising technique to construct automated systems to complement histopathological evaluation of biomedical tissue samples. The rapid chemical imaging of large areas of tissue has previously been a limiting factor in this application. Consequently, smaller areas of tissue have previously had to be sampled, possibly introducing sampling bias and potentially missing diagnostically important areas. In this report a high spatial resolution chemical image of a whole prostate cross section is shown comprising 66 million pixels. Each pixel represents an area 5.5 × 5.5 μm(2) of tissue and contains a full infrared spectrum providing a chemical fingerprint. The data acquisition time was 14 hours, thus showing that a clinical time frame of hours rather than days has been achieved.

Substrate contributions in micro-ATR of thin samples: implications for analysis of cells, tissue and biological fluids

Low-e microscope slides are a common substrate for biological samples. Typically they are used for transflection infrared microspectroscopy but increasingly they are also being used for micro-ATR experiments since it is assumed that the FTIR-ATR absorbance spectra of cells and tissue on low-e substrates will not contain any spectral contributions from the substrate materials. This, in part, is due to the expectation that all the infrared light will be reflected at the highly reflective surface. At low sample thicknesses, however (e.g. less than 2 μm) the electric field does indeed penetrate through the substrate layers and undergoes absorption, from the glass supporting layer making up the majority of the slide. In this paper we show experimental evidence of the substrate contributions in ATR spectra and also a theoretical model giving insight into the spectral contributions of the substrate as a function of sample thickness.

Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging

Fourier transform infrared (FT-IR) chemical imaging has been demonstrated as a promising technique to complement histopathological assessment of biomedical tissue samples. Current histopathology practice involves preparing thin tissue sections and staining them using hematoxylin and eosin (H&E) after which a histopathologist manually assess the tissue architecture under a visible microscope. Studies have shown that there is disagreement between operators viewing the same tissue suggesting that a complementary technique for verification could improve the robustness of the evaluation, and improve patient care. FT-IR chemical imaging allows the spatial distribution of chemistry to be rapidly imaged at a high (diffraction-limited) spatial resolution where each pixel represents an area of 5.5 × 5.5 μm2 and contains a full infrared spectrum providing a chemical fingerprint which studies have shown contains the diagnostic potential to discriminate between different cell-types, and even the benign or malignant state of prostatic epithelial cells. We report a label-free (i.e. no chemical de-waxing, or staining) method of imaging large pieces of prostate tissue (typically 1 cm × 2 cm) in tens of minutes (at a rate of 0.704 × 0.704 mm2 every 14.5 s) yielding images containing millions of spectra. Due to refractive index matching between sample and surrounding paraffin, minimal signal processing is required to recover spectra with their natural profile as opposed to harsh baseline correction methods, paving the way for future quantitative analysis of biochemical signatures. The quality of the spectral information is demonstrated by building and testing an automated cell-type classifier based upon spectral features.

Allogeneic blood transfusion in bilateral lung transplantation: impact on early function and mortality

OBJECTIVES Blood transfusion is associated with higher morbidity and mortality after general cardiothoracic surgery but its impact within the transplant population is unclear. We investigated the profile of blood product transfusion in the bilateral lung transplant population and its impact on function and mortality. METHODS Three hundred and eleven adult patients who underwent bilateral lung transplant between 2003 and 2013 were retrospectively reviewed. Patients were stratified according to pretransplant diagnoses and amount of blood products transfused within 24 h of transplant. All-cause mortality at the 1-year follow-up was analysed using a Cox proportional hazards regression model. RESULTS One hundred and seventy-four male patients and 137 female patients (mean age = 41.4 ± 14.0 years) underwent bilateral lung transplant using cardiopulmonary bypass for cystic fibrosis (48.9%), fibrotic lung disease (12.2%), emphysema (27.0%), bronchiectasis (5.8%), pulmonary hypertension (1.3%) and others (4.5%). The median number of red blood cells in the first 24 h was 3 (0-40) units, fresh frozen plasma (FFP) = 2 (0-26) units and platelets = 1 (0-7) units. The unadjusted all-cause mortality at the 1-year follow-up did not appear to be different between patient subgroups stratified by the median number of units of red blood cells (P = 0.827) or FFP transfused (P = 0.456). However, 1-year mortality was adversely affected when more than the median number of units of platelets was transfused (P = 0.010). Upon adjustment for confounding variables, 1-year mortality was noted to be greater among patients transfused more than the median unit of platelets (adjusted hazard ratios: 2.3, 95% confidence interval: 1.15-4.61, P = 0.019) and those with longer bypass times (P = 0.046). No significant difference in the number of units transfused was noted when patients were stratified by pretransplant diagnosis. Predicted lung function at 3 and 6 months was not significantly affected by greater blood product use. CONCLUSIONS Unlike general cardiothoracic surgery, blood transfusion had no effect on all-cause mortality, whereas a greater administration of platelets was observed to be associated with higher adjusted 1-year mortality. Transfusion rates were not significantly influenced by pretransplant diagnoses. Interestingly, lung function at 3 and 6 months was similar for patients who received more blood product transfusion.

Predominant Asymmetrical Stem Cell Fate Outcome Limits the Rate of Niche Succession in Human Colonic Crypts

Stem cell (SC) dynamics within the human colorectal crypt SC niche remain poorly understood, with previous studies proposing divergent hypotheses on the predominant mode of SC self-renewal and the rate of SC replacement. Here we use age-related mitochondrial oxidative phosphorylation (OXPHOS) defects to trace clonal lineages within human colorectal crypts across the adult life-course. By resolving the frequency and size distribution of OXPHOS-deficient clones, quantitative analysis shows that, in common with mouse, long-term maintenance of the colonic epithelial crypt relies on stochastic SC loss and replacement mediated by competition for limited niche access. We find that the colonic crypt is maintained by ~5 effective SCs. However, with a SC loss/replacement rate estimated to be slower than once per year, our results indicate that the vast majority of individual SC divisions result in asymmetric fate outcome. These findings provide a quantitative platform to detect and study deviations from human colorectal crypt SC niche homeostasis during the process of colorectal carcinogenesis.

Evaluating variation in use of definitive therapy and risk-adjusted prostate cancer mortality in England and the USA.

Objectives Prostate cancer mortality (PCM) in the USA is among the lowest in the world, whereas PCM in England is among the highest in Europe. This paper aims to assess the association of variation in use of definitive therapy on risk-adjusted PCM in England as compared with the USA. Design Observational study. Setting Cancer registry data from England and the USA. Participants Men diagnosed with non-metastatic prostate cancer (PCa) in England and the USA between 2004 and 2008. Outcome measures Competing-risks survival analyses to estimate subhazard ratios (SHR) of PCM adjusted for age, ethnicity, year of diagnosis, Gleason score (GS) and clinical tumour (cT) stage. Results 222 163 men were eligible for inclusion. Compared with American patients, English patients were more likely to present at an older age (70–79 years: England 44.2%, USA 29.3%, p<0.001), with higher tumour stage (cT3-T4: England 25.1%, USA 8.6%, p<0.001) and higher GS (GS 8–10: England 20.7%, USA 11.2%, p<0.001). They were also less likely to receive definitive therapy (England 38%, USA 77%, p<0.001). English patients were more likely to die of PCa (SHR=1.9, 95% CI 1.7 to 2.0, p<0.001). However, this difference was no longer statistically significant when also adjusted for use of definitive therapy (SHR=1.0, 95% CI 1.0 to 1.1, p=0.3). Conclusions Risk-adjusted PCM is significantly higher in England compared with the USA. This difference may be explained by less frequent use of definitive therapy in England.

Positive surgical margins and biochemical recurrence following minimally-invasive radical prostatectomy – An analysis of outcomes from a UK tertiary referral centre

BackgroundPositive surgical margins are a strong prognostic marker of disease outcome following radical prostatectomy, though prior evidence is largely from a PSA-screened population. We therefore aim to evaluate the biochemical recurrence in men with positive surgical margins (PSM) after minimally-invasive radical prostatectomy (MIRP) in a UK tertiary centre.MethodsRetrospective study of men undergoing laparoscopic or robotic-assisted radical prostatectomy between 2002 and 2014. Men with positive surgical margins (PSM) were identified and their biochemical recurrence (BCR) rate compared with men without PSM. The primary outcome measures were BCR rates and time to BCR. Cox regression was used to estimate adjusted hazard ratios for biochemical recurrence rate (BCR), accounting for potential confounders.ResultsFive hundred ninety-two men were included for analysis. Pre-operative D’Amico risk stratification showed 37.5%, 53.3% and 9.3% of patients in the low, intermediate and high-risk groups, respectively. On final pathological analysis, the proportion of patients with local staging pT2, pT3a and pT3b was 68.8%, 25.2% and 6.1% respectively. Overall positive margin rate was 30.6%. On multivariate analysis, the only pre-operative factor associated with PSM was age >65years. Patients with PSM were more likely to have higher tumour volume and more advanced pathological local stage. The BCR rate was 10.7% in margin-positive patients and 5.1% in margin-negative patients, at median 4.4-year follow-up. Upon multivariate analysis, high pre-operative PSA and high Gleason group were the only significant predictors of BCR (P<0.05).ConclusionsIn comparison to patients with negative surgical margins, those with PSM do not translate into worse medium-term oncological outcomes in the majority of cases amongst our cohort. We found that high pre-operative PSA and high Gleason group were the only significant predictors of BCR.

Comparison of radical treatment and mortality in patients with nonmetastatic prostate cancer in England and the United States.

46 Background: Prostate-cancer mortality in the U.S. is amongst the lowest globally. Given historical differences in management between England and the U.S., this paper aims to determine if risk-adjusted prostate-cancer mortality is inferior amongst men in England compared to the U.S. Methods: Patients diagnosed with non-metastatic prostate-cancer between 2004 and 2008 were identified using English hospital admission records linked to national cancer registry data, and the American Surveillance, Epidemiology and End Results program. Complete data were available for 222,163 patients. Patients were stratified into low-, intermediate-, and high-risk groups according to disease characteristics. Patient demographics from the two countries were compared using the Chi-square test. Competing-risks survival analyses were used to estimate relative six-year prostate-cancer mortality. Results: In comparison to patients in the U.S., English patients were more likely to present at an older age (70 to 79: England 44.2%,...