James Renwick BeattieJ Renwick Beattie Consulting
James Renwick Beattie
BSc, PhD
About
51
Publications
117,568
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1,513
Citations
Citations since 2017
Introduction
I am a consultant data scientist specialising in real world data, with a primary focus on biomedical applications. I assist with strategy, methodology, data handling, processing and interpretation. I have guided two scientific products to market, Osentia (bone health test) and Kerus (clinical trial simulator for optimising clinical trials).
Additional affiliations
May 2014 - April 2017
Exploristics Ltd
Position
- R&D Manager
Description
- As Product Owner, I led the development of a web based SaaS platform for simulating real world complex clinical trials of biotech products, called KERUS. This required developing strategy and managing a team of agile programmers and testers.
October 2011 - April 2014
Crescent Diagnostics Ltd, UCD-NOVA, Dublin, Ireland
Position
- Research Officer
Description
- Developing a Raman spectroscopy based diagnostic for fracture risk in postmenopausal women using finger/toe nail clippings.
November 2006 - June 2010
Publications
Publications (51)
Increasing use of real‐world experiments embeds scientific study in settings relevant to everyday life but brings a number of complications. Traditional study design has evaluated experimental risk based on a limited number of factors that are tightly controlled while others are standardised. In real‐world data, many unstandardised factors risk con...
Detailed methods for J.R. Beattie. “Reflections of the real-world in the unreal, using simulation to design complex real-world validation studies for spectroscopy”. J. Raman Spectrosc. John Wiley & Sons, Ltd, 2021. jrs.6240. 10.1002/JRS.6240
Spectroscopy rapidly captures a large amount of data that is not directly interpretable. Principal Components Analysis (PCA) is widely used to simplify complex spectral datasets into comprehensible information by identifying recurring patterns in the data with minimal loss of information. The linear algebra underpinning PCA is not well understood b...
Laser-induced breakdown spectroscopy (LIBS), Fourier transform mid-infrared (FT-IR) and Raman spectroscopy combined with chemometrics were investigated to quantify calcium (Ca) content in infant formula powder (INF). INF samples (n=51) with calcium content levels (ca. 6.5-30 mg Ca/100kJ) were prepared in accordance with the guidelines of Commission...
Pharmacological therapy of osteoporosis reduces bone loss and risk of fracture in patients. Modulation of bone mineral density cannot explain all effects. Other aspects of bone quality affecting fragility and ways to monitor them need to be better understood. Keratinous tissue acts as surrogate marker for bone protein deterioration caused by oestro...
Studies have shown that Raman spectroscopic analysis of fingernail clippings can help differentiate between post-menopausal women who have and who have not suffered a fracture. However, all studies to date have been retrospective in nature, comparing the proteins in nails sourced from women, post-fracture. The objective of this study was to investi...
Osteoporosis is a common disease characterised by reduced bone mass and an increased risk of fragility fractures. Low bone mineral density is known to significantly increase the risk of osteoporotic fractures, however, the majority of non-traumatic fractures occur in individuals with a bone mineral density too high to be classified as osteoporotic....
Patients diagnosed with osteoporosis have reported loss of fingernail resilience as the disease progresses. Keratin is the predominant protein in human nail tissue, and its structure has been postulated to be different in fingernails clipped from subjects who have sustained fragility fractures and those who have not, which may offer a window into t...
Raman spectroscopy was applied to nail clippings from 633 postmenopausal British and Irish women, from six clinical sites, of whom 42% had experienced a fragility fracture. The objective was to build a prediction algorithm for fracture using data from four sites (known as the calibration set) and test its performance using data from the other two s...
Supplementary Table 1. The significance of different variable clinical risk factors for fracture and their correlation with the Raman based fracture score.
Real-world experiments are becoming increasingly more complex, needing techniques capable of tracking this complexity. Signal based measurements are often used to capture this complexity, where a signal is a record of a sample’s response to a parameter (e.g. time, displacement, voltage, wavelength) that is varied over a range of values. In signals...
Vertebra Common fracture sites DXA Measurement sites Lumbar Femoral Neck Total hip Figure 6 Human skeletal system showing the location of the measurements performed using DXA (left hand side, blue) and the main fracture sites in fragility fractures (right hand side in red) DXA Age BMI Height Exploiting human fingernail as a surrogate marker of frac...
The present study is designed to understand further implications of using multivariate loadings for the correction of back-ground signal, which has previously been shown to be highly reproducible even for very low quality signals. Singular value decomposition (SVD)-based background correction was compared with the traditional per-signal paradigm fo...
Raman spectroscopy is a noninvasive, nondestructive tool for capturing multiplexed biochemical information across diverse molecular species including proteins, lipids, DNA, and mineralizations. Based on light scattering from molecules, cells, and tissues, it is possible to detect molecular fingerprints and discriminate between subtly different memb...
Osteoporosis is a highly debilitating disease associated with aging and involves weakening of the bones, leading to bone fracture after low-trauma impact. Current methods of diagnosing osteoporosis are poor at predicting those patients who will fracture, with the consequence that many patients undergo unnecessary treatment regimes while many others...
Raman microscopy has become established as a key probe technique in
biology and biomedicine. In combination with imaging and mapping it has
been employed in the investigation of a diverse array of problems
ranging from ex vivo and in vivo single cell studies to elucidation of
the often complex, interacting structures which constitute human and
anim...
Raman microscopy, a rapid nondestructive technique that profiles the composition of biological samples, was used to characterize retinal biochemistry in the retinal dysplasia and degeneration (rdd) and wild-type (wt) chick retina during retinogenesis and at hatching.
Embryonic day (E)13 and posthatch day (P)1 rdd and wt retinal cross-sections (n =...
Raman spectroscopy has been revolutionised in recent decades by major technological advances such as lasers, charge-coupled detectors (CCD) and notch/edge filters. In contrast the development of signal processing algorithms has progressed at a slower pace. Spectroscopic applications increasingly focus on ‘real-world’ applications that are not under...
Raman spectroscopy is an effective probe of advanced glycation end products (AGEs) in Bruch's membrane. However, because it is the outermost layer of the retina, this extracellular matrix is difficult to analyze in vivo with current technology. The sclera shares many compositional characteristics with Bruch's membrane, but it is much easier to acce...
Aging of the human retina is characterized by progressive pathology, which can lead to vision loss. This progression is believed to involve reactive metabolic intermediates reacting with constituents of Bruch's membrane, significantly altering its physiochemical nature and function. We aimed to replace a myriad of techniques following these changes...
The main curative therapy for patients with nonsmall cell lung cancer is surgery. Despite this, the survival rate is only 50%, therefore it is important to more efficiently diagnose and predict prognosis for lung cancer patients. Raman spectroscopy is useful in the diagnosis of malignant and premalignant lesions. The aim of this study is to investi...
Every organ compromises of several different cell types. When studying the effects of a chosen compound within this organ or tissue uptake, localisation, metabolism, and the effect itself can be expected to differ between cells. Using the example of Vitamin E in pulmonary tissue we introduce confocal Raman Microscopy as a superior method to localis...
Spectral signal intensities, especially in ‘real-world’ applications with nonstandardized sample presentation due to uncontrolled variables/factors, commonly require additional spectral processing to normalize signal intensity in an effective way. In this study, we have demonstrated the complexity of choosing a normalization routine in the presence...
The influence of ageing and cooking on the Raman spectrum of porcine longissimus dorsi was investigated. The rich information contained in the Raman spectrum was highlighted, with numerous changes attributed to changes in the environment and conformations of the myofibrillar proteins. Predictions equations for shear force and cooking loss were deve...
Raman microscopy is used to investigate the spectral features of selected compounds known to be involved in the development of the eye disease age-related macular degeneration (AMD). Diagnostic features were identified in synthetic samples of these compounds and in a biological matrix. The study demonstrates the potential of Raman microscopy for th...
The retina is exquisitely sensitive to age-related processes, and, in many cases, these can precipitate progressive and profound loss of vision. Many asymptomatic abnormalities that accrue in the outer retina as we get older can serve as a sinister preamble to age-related macular degeneration (AMD). This condition remains the leading cause of irrev...
The modification of proteins by nonenzymatic glycation leading to accumulation of advanced glycation end products (AGEs) is a well-established phenomenon of aging. In the eyes of elderly patients, these adducts have been observed in retinal pigment epithelium (RPE), particularly within the underlying pentalaminar substrate known as Bruch's membrane...
The aim was twofold; to demonstrate the ability of temperature-controlled Raman microscopy (TRM) to locate mannitol within a frozen system and determine its form; to investigate the annealing behavior of mannitol solutions at -30 degrees C. The different polymorphic forms of anhydrous mannitol as well as the hemihydrate and amorphous form were prep...
In this study multivariate analysis of Raman spectra has been used to classify adipose tissue from four different species (chicken, beef, lamb and pork). The adipose samples were dissected from the carcass and their spectra recorded without further preparation. 102 samples were used to create and compare a range of statistical models, which were th...
Alpha-tocopherol (aT), the predominant form of vitamin E in mammals, is thought to prevent oxidation of polyunsaturated fatty acids. In the lung, aT is perceived to be accumulated in alveolar type II cells and secreted together with surfactant into the epithelial lining fluid. Conventionally, determination of aT and related compounds requires extra...
To characterize the Raman spectra of porcine inner retinal layers, specifically, the inner nuclear, inner plexiform, ganglion cell, and nerve fiber layers.
Raman microscopy was employed at three excitation wavelengths, 785, 633, and 514 nm to measure Raman spectra in a high resolution grid across the inner layers of 4% paraformaldehyde cryoprotecte...
Raman spectroscopy is recognized as a tool for chemometric analysis of biological materials due to the high information content relating to specific physical and chemical qualities of the sample. Thirty cells belonging to two different prostatic cell lines, PNT1A (immortalized normal prostate cell line) and LNCaP (malignant cell line derived from p...
Raman spectroscopy has been used for the first time to predict the FA composition of unextracted adipose tissue of pork, beef, lamb, and chicken. It was found that the bulk unsaturation parameters could be predicted successfully [R
2=0.97, root mean square error of prediction (RMSEP)=4.6% of 4 δ], with cis unsaturation, which accounted for the majo...
Raman microscopy, based upon the inelastic scattering (Raman) of light by molecular species, has been applied as a specific structural probe in a wide range of biomedical samples. The purpose of the present investigation was to assess the potential of the technique for spectral characterization of the porcine outer retina derived from the area cent...
Raman spectroscopy has been used to predict the abundance of the FA in clarified butterfat that was obtained from dairy cows fed a range of levels of rapeseed oil in their diet. Partial least squares regression of the Raman spectra against FA compositions obtained by GC showed that good prediction of the five major (abundance >5%) FA gave R
2=0.74–...
The work presented here is aimed at determining the potential and limitations of Raman spectroscopy for fat analysis by carrying out a systematic investigation of C4−C24 FAME. These provide a simple, well-characterized set of compounds in which the effect of making incremental changes can be studied over a wide range of chain lengths and degrees of...
The results of a study aimed at determining the most important experimental parameters for automated, quantitative analysis of solid dosage form pharmaceuticals (seized and model ‘ecstasy’ tablets) are reported. Data obtained with a macro-Raman spectrometer were complemented by micro-Raman measurements, which gave information on particle size and p...
The potential of Raman spectroscopy for the determination of meat quality attributes has been investigated using data from a set of 52 cooked beef samples, which were rated by trained taste panels. The Raman spectra, shear force and cooking loss were measured and PLS used to correlate the attributes with the Raman data. Good correlations and standa...
Density functional calculations, using B3LPY/6-31G(d) methods, have been used to investigate the conformations and vibrational (Raman) spectra of a series of long-chain, saturated fatty acid methyl esters (FAMEs) with the formula CnH2nO2 (n=5–21) and two series of unsaturated FAMEs. The calculations showed that the lowest energy conformer within th...
Density functional calculations, using B3LPY/6-31G(d) methods, have been used to investigate the conformations and vibrational (Raman) spectra of three short-chain fatty acid methyl esters (FAMEs) with the formula CnH2nO2 (n=3–5). In all three FAMEs, the lowest energy conformer has a simple ‘all-trans’ structure but there are other conformers, with...
Questions
Questions (6)
I need high purity specialist Nylons (1/4,6/2 and 6/6) custom made, but so far have not been able to identify a supplier for the first 2. I first tried Merck then a handful of polymer specialists but none were able to help.
It does need manufactured under GMP and GLP using high purity monomers. The amounts are modest (<<1kg), so small scale synthesis is more suited.
Once the intensity profile of a 785 nm excitation Raman spectrometer has been standardised, e.g. using either white light or NIST SRM-2241, these can be routinely monitored using the same primary standard. However, these aren't ideal candidates for daily monitoring of multiple units in a production environment. It would be preferable to use a custom made-to-requirements secondary standard to measure every single session that would monitor intensity profile. This would then be compared to the primary standard at regular intervals.
Does anyone have any reliable materials that can be dependably sourced to give
1) consistent broadband raw signal
2) remain stable over at least 12 months
3) minimal photobleaching?
I have considered sourcing green glass microscope covers but does anyone manufacture them reproducibly enough? I'm assuming that their intensity profile in a Raman setup is not something they are likely to be analysed for in QC, but maybe their emission spectra are?
Also, I've considered fluorescent polymer sheets, but it isn't easy finding out about quantum efficiency in the NIR, mostly I find only lambda max. I'd also be concerned about photobleaching occurring too fast. Then I imagine the QE of the fluorescence would need to be >10,000x higher than the QE of any Raman modes , preferably 1,000,000x.
