title: Wavelength Tuneable Frequency Domain Photon Migration Spectrometer for Tissue-like Media

authors: Cletus, Biju

subjects: Photon Migration

abstract: Frequency domain spectrometers use intensity modulated light to quantitatively interrogate turbid media. The modulation frequencies employed are in the radiofrequency range. Intensity modulated light launched into a turbid medium generates photon density fluctuations with wave like character that oscillates at the modulation frequency. These density fluctuations are named diffuse photon density waves, and it has been shown that the amplitude and phase of the photon density wave inside the medium depends on its optical properties. Hence by measuring the amplitude and phase of the photon density wave the optical properties of the medium can be estimated. This is the basic working principle of a frequency domain photon migration spectrometer. 
Frequency domain spectrometers fabricated with laser diodes are limited to discrete wavelengths thereby making compromises on the information about the media under test. In this research a wavelength tuneable frequency domain spectrometer was constructed by modulating the output intensity of a titanium: sapphire laser using an acousto-optic modulator. A low noise avalanche photodiode module in conjunction with a lock-in amplifier was used to measure the amplitude attenuation and phase lag inside a turbid sample. The frequency domain spectrometer was tested for accuracy and precision by estimating the optical properties of an important tissue simulation phantom, Intralipid , at a representative wavelength 790 nm. The results indicated that the spectrometer estimates absorption with an accuracy of 10%. The instrument estimates the absorption and reduced scattering coefficients with a precision of 3% and 6%, respectively. 
Optical properties of Intralipid  were measured from 710-850 nm in the therapeutic window. The results were compared with published data measured by other methods and similar frequency domain techniques. The absorption coefficient agrees within 10% with results from a time domain measurement. The reduced scattering coefficient was within the error limits of other reported measurements. At 750 nm the reduced scattering agrees within 5% with the results from a continuous wave, time domain and within 1% from another frequency domain measurement, and at 811 and 849 nm this agreement is within 9%. A Mie theory prediction of the reduced scattering coefficient based on a measurement of the particle size distribution by a Mastersizer 2000 is larger than the frequency domain results by 6%. 
The spectrometer was used to determine the optical temperature coefficient of Intralipid , exploring its potential as a non invasive temperature monitoring device. The measured minute change in the absorption coefficient suggests a minimum observable temperature change of   4'C, which for most practical applications means that the precision needs to improve. The effect of glucose on the optical properties of Intralipid  indicates that the absorption coefficient decreases steadily at 730 nm up to 1000mg/dL. The reduced scattering coefficient decreases with increasing glucose concentration at most of the wavelengths. 
This work quantified the absorption and reduced scattering of Intralipid  over a larger wavelength range (in the therapeutic window) than before. This is the first time the effects of temperature on the optical properties of a turbid medium monitored with a frequency domain spectrometer.  Specific information about the precision and accuracy which can be achieved with the current technology is documented. Current precision is not sufficient for many applications that would benefit from separation of absorption and scattering.

text: Wavelength Tuneable Frequency Domain Photon Migration Spectrometer for Tissue-like Media Frequency domain spectrometers use intensity modulated light to quantitatively interrogate turbid media. The modulation frequencies employed are in the radiofrequency range. Intensity modulated light launched into a turbid medium generates photon density fluctuations with wave like character that oscillates at the modulation frequency. These density fluctuations are named diffuse photon density waves, and it has been shown that the amplitude and phase of the photon density wave inside the medium depends on its optical properties. Hence by measuring the amplitude and phase of the photon density wave the optical properties of the medium can be estimated. This is the basic working principle of a frequency domain photon migration spectrometer. 
Frequency domain spectrometers fabricated with laser diodes are limited to discrete wavelengths thereby making compromises on the information about the media under test. In this research a wavelength tuneable frequency domain spectrometer was constructed by modulating the output intensity of a titanium: sapphire laser using an acousto-optic modulator. A low noise avalanche photodiode module in conjunction with a lock-in amplifier was used to measure the amplitude attenuation and phase lag inside a turbid sample. The frequency domain spectrometer was tested for accuracy and precision by estimating the optical properties of an important tissue simulation phantom, Intralipid , at a representative wavelength 790 nm. The results indicated that the spectrometer estimates absorption with an accuracy of 10%. The instrument estimates the absorption and reduced scattering coefficients with a precision of 3% and 6%, respectively. 
Optical properties of Intralipid  were measured from 710-850 nm in the therapeutic window. The results were compared with published data measured by other methods and similar frequency domain techniques. The absorption coefficient agrees within 10% with results from a time domain measurement. The reduced scattering coefficient was within the error limits of other reported measurements. At 750 nm the reduced scattering agrees within 5% with the results from a continuous wave, time domain and within 1% from another frequency domain measurement, and at 811 and 849 nm this agreement is within 9%. A Mie theory prediction of the reduced scattering coefficient based on a measurement of the particle size distribution by a Mastersizer 2000 is larger than the frequency domain results by 6%. 
The spectrometer was used to determine the optical temperature coefficient of Intralipid , exploring its potential as a non invasive temperature monitoring device. The measured minute change in the absorption coefficient suggests a minimum observable temperature change of   4'C, which for most practical applications means that the precision needs to improve. The effect of glucose on the optical properties of Intralipid  indicates that the absorption coefficient decreases steadily at 730 nm up to 1000mg/dL. The reduced scattering coefficient decreases with increasing glucose concentration at most of the wavelengths. 
This work quantified the absorption and reduced scattering of Intralipid  over a larger wavelength range (in the therapeutic window) than before. This is the first time the effects of temperature on the optical properties of a turbid medium monitored with a frequency domain spectrometer.  Specific information about the precision and accuracy which can be achieved with the current technology is documented. Current precision is not sufficient for many applications that would benefit from separation of absorption and scattering.

year: 2010

title: Generating species assemblages for restoration and experimentation: A new method that can simultaneously converge on average trait values and maximize functional diversity

authors: Laughlin, Daniel C.

subjects: Science & Technology

abstract: 1. Restoring resilient ecosystems in an era of rapid environmental change requires a flexible framework for selecting assemblages of species based on functional traits. However, current trait‐based models have been limited to algorithms that select species assemblages that only converge on specified average trait values, and could not accommodate the common desire among restoration ecologists to generate functionally diverse assemblages.
2. We have solved this problem by applying a nonlinear optimization algorithm to solve for the species relative abundances that maximize Rao's quadratic entropy (Q) subject to other linear constraints. Rao's Q is a closed‐form algebraic expression of functional diversity that is maximized when the most abundant species are functionally dissimilar.
3. Previous models have maximized species evenness subject to the linear constraints by maximizing the entropy function (H’). Maximizing Q alone produces an undesirable species abundance distribution because species that exhibit extreme trait values have the highest abundances. We demonstrate that the maximization of an objective function that additively combines Q and H’ produces a more even relative abundance distribution across the trait dimension.
4. Some ecological restoration projects aim to restore communities that converge on one set of traits while diverging across another. The selectSpecies r function can derive assemblages for any size species pool that maximizes the diversity of any set of traits, while simultaneously converging on average values of any other set of traits. We demonstrate how the function works through examples using uniformly spaced trait distributions and data with a known structure. We also demonstrate the utility of the function using real trait data collected on dozens of species from three separate ecosystems: serpentine grasslands, ponderosa pine forests, and subtropical rainforests.
5. The quantitative selection of species based on their functional traits for ecological restoration and experimentation must be both rigorous and accessible to practitioners. The selectSpecies function provides ecologists with an easy‐to‐use open‐source solution to objectively derive species assemblages based on their functional traits.

text: Generating species assemblages for restoration and experimentation: A new method that can simultaneously converge on average trait values and maximize functional diversity 1. Restoring resilient ecosystems in an era of rapid environmental change requires a flexible framework for selecting assemblages of species based on functional traits. However, current trait‐based models have been limited to algorithms that select species assemblages that only converge on specified average trait values, and could not accommodate the common desire among restoration ecologists to generate functionally diverse assemblages.
2. We have solved this problem by applying a nonlinear optimization algorithm to solve for the species relative abundances that maximize Rao's quadratic entropy (Q) subject to other linear constraints. Rao's Q is a closed‐form algebraic expression of functional diversity that is maximized when the most abundant species are functionally dissimilar.
3. Previous models have maximized species evenness subject to the linear constraints by maximizing the entropy function (H’). Maximizing Q alone produces an undesirable species abundance distribution because species that exhibit extreme trait values have the highest abundances. We demonstrate that the maximization of an objective function that additively combines Q and H’ produces a more even relative abundance distribution across the trait dimension.
4. Some ecological restoration projects aim to restore communities that converge on one set of traits while diverging across another. The selectSpecies r function can derive assemblages for any size species pool that maximizes the diversity of any set of traits, while simultaneously converging on average values of any other set of traits. We demonstrate how the function works through examples using uniformly spaced trait distributions and data with a known structure. We also demonstrate the utility of the function using real trait data collected on dozens of species from three separate ecosystems: serpentine grasslands, ponderosa pine forests, and subtropical rainforests.
5. The quantitative selection of species based on their functional traits for ecological restoration and experimentation must be both rigorous and accessible to practitioners. The selectSpecies function provides ecologists with an easy‐to‐use open‐source solution to objectively derive species assemblages based on their functional traits.

year: 2018

title: “BODY-SNATCHING”: Changes to coroners legislation and possible Māori responses

authors: Mika, Carl Te Hira

subjects: body-snatcher

abstract: The term body-snatcher has enjoyed a renaissance in the media recently, as various Māori have moved to reclaim their deceased relations. From a Māori perspective, the claiming of bodies has nothing to do with body-snatching, a term that referred to episodes in the West. Indeed, Māori may see some laws themselves as instruments that snatch the body, in contravention of Māori customs. One of these laws, the Coroners Act 2006, may have made some progress by quietly acknowledging these customs in many ways, but that is merely the start of a greater dialogue between Māori and the Crown in relation to proper Māori respect of the dead body.

text: “BODY-SNATCHING”: Changes to coroners legislation and possible Māori responses The term body-snatcher has enjoyed a renaissance in the media recently, as various Māori have moved to reclaim their deceased relations. From a Māori perspective, the claiming of bodies has nothing to do with body-snatching, a term that referred to episodes in the West. Indeed, Māori may see some laws themselves as instruments that snatch the body, in contravention of Māori customs. One of these laws, the Coroners Act 2006, may have made some progress by quietly acknowledging these customs in many ways, but that is merely the start of a greater dialogue between Māori and the Crown in relation to proper Māori respect of the dead body.

year: 2009