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					Enclosure 6

List of Publications

(Note: Abstracts to these publications are at the end of this enclosure)

A. Peer-reviewed Publications

    1. Baki P. and Mito C. (2009), “The spectral analysis of X-ray binaries from the
       XMM-Newton space craft data using SAS software”, African Skies/Cieux
       Africains, 13: pp 18-19

    2. Niyibizi A. “Current trends in laser technology and applications”, Submitted to
       Africa Journal of Science & Technology, (October 2008)

B. MSc Theses

    1. Makokha J. W., “Radiative Characterization of Atmospheric Aerosols Over
       Selected Urban, Rural, and Maritime Sites of Kenya Using Sun
       Spectrophotometry”, Thesis to be defended in September 2010

C. Internal Reports

    1. Kimari John Wangai, “Development of a Diode Laser Spectrometer for Trace Gas
       Measurements”, (Ph.D. Progress Report)

    2. Gathoni Robinson Ndegwa, “Diode laser Absorption spectroscopy for molecular
       oxygen in scattering media”, (Ph.D. Progress Report)

    3. Cheruiyot Elijah, “Simulation of the Upwelling and Downwelling mean radiance
       of the Kenyan Coastal Region, („Advanced Laboratory Techniques‟ Report)

    4. Gitau Elias Thuo, “CNC Machine Controller for Laser Tool Control”, (Advanced
       Laboratory Techniques Report)

    5. Maina Walter, “Direct Digital Frequency Synthesizer Modeling Using SystemC”,
       (M.Sc. Progress Report)

    6. Memeu Daniel Maitethia, “Image Processing Techniques for Detection and
       Quantification of Plasmodium Parasites in Blood Sample Images”, (Advanced
       Laboratory Techniques Report)

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    7. Omucheni Dickson Linani, “Multispectral Imaging Microscopy of Human Blood
       Media Applied to Malaria Diagnostics”, (M.Sc. Progress Report)

    8. Onyango Michael Otieno, “Detection of Oxygen and Nitrogen Oxide
       Concentration Using Tunable Diode Laser Absorption Spectroscopy and
       Multispectral Image Analysis Using Principal Component Analysis”, (Advanced
       Labortory Techniques Report)

    9. Mukhono Pauline, “Analysis of Nitrogen dioxide and Oxygen Gases Using
       Absorption Spectroscopy Techniques and Multipectral Image Analysis of
       Microspheres using Principal Component Analysis”, („Advanced Laboratory
       Techniques‟ Report)

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                             2
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       Published in: African Skies/Cieux Africains, No.13, October 2009, pp. 18 – 19

 The Spectral Analysis of X-Ray Binaries from the XMM-Newton Space Craft Data
                                           using SAS Software
                                           Baki P. and Mito C.O.


A spectral data analysis on a luminous object of sky-coordinates 12h52m24.28s-
29d115‟02.3‟12.6 arcsec using Science Analysis Software (SAS) is presented. The
analysis, based on data acquired by the Reflection Grating Spectrometer (RGS) camera
aboard the XMM-Newton Space satellite, shows that the primary constituents of the X-
ray source are Fe (Iron) and O (oxygen). This suggests that the source may be a
magnetized plasma in a binary system and as this magnetic field accelerates the cooling
of a star, one may speculate that this may be a compact star in its last stages of a
thermonuclear fusion process.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                               3
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                     Submitted to: African Journal of Science and Technology
                                          (October 2008)

        Current trends in laser technology and applications: A literature review

                                           Alphonse Niyibizi


The laser is no longer a „scientific gadget‟, but an „industrial or a medical tool‟ from
which an investor expects financial returns. The present presentation will try to give a
literature overview of the state of affairs and trends regarding the most important types of
industrial and commercial lasers worldwide and their applications.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                                   4
Enclosure 6

 Radiative Characterization of Atmospheric Aerosols Over Selected Urban, Rural,
           and Maritime Sites of Kenya Using Sun Spectrophotometry

                   (M.Sc. Thesis Report – to be defended in September 2010)

                                           Makokha John Wanjala


Atmospheric aerosols modulate the radiative budget and ambient air quality of the
atmosphere, thus, there is a need to develop both analytical and computational
methodological techniques that determine their physical, chemical and optical properties
in order to characterize and model their effects. This thesis embodies the results of the
derivation of radiative characteristics of the atmosphere over Nairobi, Mbita and Malindi
using aerosol data obtained from sun spectrophotometry from 2006-2008. Aerosol optical
depths (τ), single scattering albedo (ω), angstrom exponent (α), asymmetry factor ( ),
real ( ) and imaginary ( ) refractive indices at zero Solar Zenith Angle (SZA) were
derived through AErosol RObotic NETwork (AERONET) framework. Temporal and
spatial characteristics in τ and α were investigated using multivariate techniques viz.
Principle Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-
DA), Principle Component Regression (PCR) and Hierarchical Cluster Analysis (HCA).
Annual averages of the optical properties together with selected physico-chemical
properties i.e. aerosol number densities and extinction cross section were determined.
Coupled Ocean and Atmosphere Radiative Transfer (COART) model was used to solve
the radiative transfer equation (RTE) for an atmosphere modulated by aerosols of
different sizes and estimate their radiative impacts.
The use of multivariate chemometric techniques revealed that temporal and spatial
characteristics of both τ and α over the study sites are modulated by rainfall distribution,
relative humidity, temperature, aerosol hygroscopic properties, aerosol burden, aerosol
mode of generation and composition. There was no significant spectral dependence in ω,
   and both         and      at zero SZA over the study sites. Validation of the measured τ and
α from AERONET at λ = 500 nm and 440/675 nm respectively was achieved by utilizing

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                                     5
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Moderate Resolution Imaging Spectrometer (MODIS) data at 550 nm and 470/660 nm.
The values agreed to within 12.4 % and 10.9 % levels of accuracy respectively, showing
consistency in the two remote sensing techniques. There was a declining loss in radiant
energy with increasing aerosol particle sizes over the sites of study which is attributed to
increasing heating effect of the incoming solar radiation. Radiative characteristics
(spectral irradiance, integrated fluxes and reflectance) over Nairobi depicted temporal
variations as influenced by rainfall distribution. There was also an increase in up/down
irradiance ratio of spectral irradiance for 2006-2007 across all wavelength channels of 2.6
%, 6.7 %, 7.2 % and 2.4 % and a drop of the ratio by 2.7 %, 12.2 %, 50.6 % and 25.6 %
for 2007-2008 for λ = 440 nm, λ = 675 nm, λ = 870 nm and λ = 1020 nm respectively as
modulated by amount of rainfall. Up/down integrated flux ratio remained virtually
constant for 2006-2008 over the study sites. Utilizing these data, radiative forcing due to

atmospheric aerosols was estimated, and found to remain relatively constant at 0.46
for all the three sites despite the observed differences in the various aerosol particle
properties dominating the sites.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                                  6
Enclosure 6

       Development of a Diode Laser Spectrometer for Trace Gas Measurements

                                           (Ph.D. Progress Report)

                                            Kimari John Wangai


The design, construction and characterization of a NO2 trace gas instrument is presented.
The gas instrument is based on Diode Laser Absorption spectroscopy with frequency
modulation of the diode current for sensing low (parts per billion per unit volume-ppbv)
concentrations of the NO2 gas. Homemade and factory-made calibration gas cells were
constructed and used in quantifying the ambient NO2 concentration. The homemade gas
cells of nominal concentration 1.87kgm-3 and 187gm-3 were used to test the extremes of
high and low concentrations. The factory-made cells were constructed of 3,6,9 and
12mgm-3 and tested the linearity response of the instrument. The NO2 concentration data
was obtained by means of standard addition of the cells concentration to that of the
ambient NO2 concentration. A MATLAB software based program was developed for
analyzing the absorption profile data. Results obtained show that the instrument has
ability to measure down to gm-3 ambient concentration levels of NO2. This sensitivity is
sufficient to measure background concentrations which occur in the gm-3 regime.
Measurements of ambient concentration of NO2 gas 200m from Chiromo road Nairobi,
Kenya between Feb, 2008 and April, 2008 indicated a range of 31-316gm-3 and a mean
background concentration of 220gm-3. This amount is above the recommended World
Health Organization safe hourly air quality guide of 200 μgm-3.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                               7
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    Diode laser Absorption spectroscopy for molecular oxygen in scattering media

                                           (Ph.D. Progress Report)

                                           Gathoni Robinson Ndegwa


Basic measurements of different aspects related to light propagation and embedded gas in
wood were performed. By shining light through the samples and adding known distances
of ambient air, the gas content in the porous samples could be expressed as an equivalent
mean path length, that is, the path length in air rendering the same absorption as the
encountered oxygen in the material. Measurements of 10-mm-thick polystyrene foam and
10mm thick slab of wood were performed. The equivalent mean path length depends on
the thickness and the porosity of the scattering media and was considered to be
proportional to the gas embedded on the sample. Standard addition methods are used to
obtain the extrapolated equivalent mean path length, from a wavelength modulation
second derivative (2f) signal that was normalized against a diffused light at line center.
This usually compensate against the variation of the detected signal. This is because the
peak-to-peak 2f signal, in the absorption regime, is linearly proportion to the gas-related
differential absorption and to the light intensity reaching the detector. Further, we have
performed the transillimulation of scattering material and used descriptive statistics to
obtain Cachy distribution for 10-mm-thick polystyrene foam and 10mm thick slab of
wood were performed and 19mm -thick polystyrene foam. The HWHM from the three
samples were proportional to the thickness and the porosity of the scattering media.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                                 8
Enclosure 6

Simulation of the Upwelling and Downwelling mean radiance of the Kenyan Coastal

                            (‘Advanced Laboratory Techniques’ Report)

                                           Cheruiyot Elijah


This work reports the determination of the upwelling and downwelling mean radiance of
the Kenyan coastal region.

21 atmospheric profiles from Malindi (Kenyan coastal region) plus 6 in-built profiles are
analyzed using PcLnWin (an atmospheric correction program). FASCODE (Fast
Atmospheric Signature Code) is used to compute spectral transmittance and radiance of a
given path. Upwelling mean radiance is obtained by setting the sensor looking vertically
downwards, while downwelling mean radiance is obtained with the sensor looking
vertically upwards and using the value of the upwelling mean radiance for that profile.
The ratio of upwelling mean radiance to downwelling mean radiance is then compared
with the atmospheric absorptance.

The downwelling mean radiance is slightly higher than the upwelling mean radiance for
every profile, so that their ratio is greater than unity.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                                   9
Enclosure 6

                        CNC Machine Controller for Laser Tool Control
                              (Advanced Laboratory Techniques Report)
                                           Gitau Elias Thuo


Power laser tools are still rare in Africa. This contributes to poor access to competitive
manufacturing technologies in industry.            Central to power laser tools is Compuer
Numerical Control (CNC) machines for the control of the laser tool possibly in 2D or 3D.
A Field Programmable Gate Array (FPGA) based CNC machine controller capable of
interpreting STEP-NC files to manufacturing activities will be developed.
Preliminary work has been done using Modela MDX 20 plotter milling machine and g-
code and limitations of g-code highlighted. G-code is based largely on description of the
manufacturing activities from the perspective of the machine rather than the part to be
manufactured. This makes production sensitive to the machine. STEP-NC on the other
hand provides a description of the part/product to be produced. This make production
relatively independent of the machine.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                               10
Enclosure 6

              Direct Digital Frequency Synthesizer Modeling Using SystemC

                                           (M.Sc. Progress Report)

                                                Maina Walter


This report describes the modeling of a direct digital frequency synthesizer using
systemC. Four models of the signal generator were created, i.e., a model with no dither
signal, with phase dithering only, with amplitude dithering only and one that had a
combination of both phase and amplitude dithering. From these models it was observed
that phase dithering alone offers the best Spurious Free Dynamic Range (SFDR) and the
worst Signal to Noise Ratio (SNR), amplitude dithering alone results in the best SNR,
combining both phase and amplitude dithering leads to average SFDR and SNR
compared to the other two cases of dithering.

The Direct Digital Frequency Synthesis is expected to contribute to the design of wide
frequency range and low cost signal generator for use in both teaching and research labs.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                               11
Enclosure 6

    Image Processing Techniques for Detection and Quantification of Plasmodium
                                   Parasites in Blood Sample Images

                              (Advanced Laboratory Techniques Report)

                                           Memeu Daniel Maitethia


In this work various techniques of segmenting an image of blood sample infected with
malaria parasite were explored with an intention of recommending the best technique for
segmenting images captured under different conditions. It was observed that for images
with a wide dynamic range, the best segmentation technique is thresholding the image
with a suitable threshold value. This yields a binary image whose objects shapes are not
distorted. However, the method is not suitable for images with low contrast.

Images with low dynamic range are best segmented using regional growing or splitting
and merging techniques. However, these techniques introduce distortions to the shapes
of the segmented objects. In addition, they are computationally intensive operations
which take longer execution time.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                             12
Enclosure 6

    Multispectral Imaging Microscopy of Human Blood Media Applied to Malaria

                                           (M.Sc. Progress Report)

                                           Omucheni Dickson Linani


Imaging System optimization and its application to Malaria diagnostics

Multispectral imaging has found many applications that range from macroscopic remote
sensing to microscopic parasite detection. The amount of data obtained from a
multispectral image is usually very large and may consist of correlated variables.
Multivariate Chemometric tools such as Principal Component Analysis (PCA) and
Cluster Analysis become useful in the analyses of such data. From a macroscopic point of
view, multispectral imaging may be a straight forward process and the only challenge
may be the interpretation of analytical results. However, in multispectral microscopy,
calibration, elimination of non-uniform illumination, reduction of chromatic aberration
and changes in condensor distance from the sample can have a significant effect on the
acquired images. In this work, we have explored these factors on a multispectral imaging
microscope. We have used homogenous polymer microspheres of diameter 10µm to
calibrate the microscope and study the effect of condensor distance from the sample in
order to optimize the microscope. The optimized microscope has then been used to take
images of red blood cell infected with malaria parasites and analyzed using PCA and
cluster analysis. Results show that despite using a cassegrain objective to remove
chromatic aberration, the lenses in the ocular reintroduce it. Focusing behaviour of a
sample can be revealed by studying the microsphere images as the condensor distance is
adjusted. PCA reduces data dimensionality hence few uncorrelated images with high
contrast are obtained. K-means clustering partitions the image to reveal various artefacts
in the sample.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                               13
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Principal Component Analysis

We have explored PCA as a feature extraction tool in MIA. Score matrices have been
visualized both as score images and score plots. By plotting the dominant principal
components, we have used score plots to summarize the dominant spectral features of
malaria infected red blood cells. Different pixels locations in the image with identical
features have identical score value combination. Thus, by plotting the score values of any
two of the first three principal components for each pixel against each other in a scatter
plot, the score combinations form separable clusters in the score plots. To identify pixel
clusters from malaria parasites and red blood cells we have matched the pixel clusters
with the corresponding pixels in the image space. We have done this by repeatedly
placing a mask on a particular cluster and checking the pixels below the mask in the
image space which maps an object in the image.

Cluster Analysis

We have decomposed pixel values into dendrograms by means of Hierachical Cluster
Analysis (HCA). To interpret the dendrograms, we have combined K-means cluster
analysis with HCA to map chemical species in the images. Six clustered images have
shown to map the parasites, red blood cells and the background.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                               14
Enclosure 6

Detection of Oxygen and Nitrogen Oxide Concentration Using Tunable Diode Laser
      Absorption Spectroscopy and Multispectral Image Analysis Using Principal
                                            Component Analysis

                              (Advanced Labortory Techniques Report)

                                           Onyango Michael Otieno


Tunable Diode Laser Absorption Spectroscopy (TDLAS) is a spectroscopic technique for
measuring the concentration of a gaseous species in a gaseous mixture by making use of
semiconductor lasers as the beam source and absorption spectroscopy. Gas in Scattering
Medium Absorption Spectroscopy (GASMAS) employs the method of TDLAS but in
this case, the gas whose concentration is to be detected is in the pores of a porous solid
material. Multispectral Imaging records simultaneously, spatially and spectrally resolved
information about a sample. The image of a sample is taken over a wide range of
wavelengths and this allows the extraction of information about the sample that would
otherwise have been unobservable by the human eye.

TDLAS was used to detect the concentration of Nitrogen Dioxide Gas in the atmosphere.
The setup consisted a Tunable Diode Laser as the laser beam source and the air as
absorption medium. Using known concentrations of Nitrogen Dioxide and studying their
absorption characteristics at specific wavelengths, it was possible to correlate these with
the absorption characteristics of the air to determine the ambient concentration of
Nitrogen Dioxide. The GASMAS system was then used to analyse oxygen embedded in
polystyrene foam

Finally, images of a slide of microspheres were taken at thirteen different wavelengths.
The resultant multispectral image was then processed and information from it analysed
using PCA.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                                     15
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   Analysis of Nitrogen dioxide and Oxygen Gases Using Absorption Spectroscopy
    Techniques and Multipectral Image Analysis of Microspheres using Principal
                                           Component Analysis

                            (‘Advanced Laboratory Techniques’ Report)

                                            Mukhono Pauline


In this report, absorption spectroscopy techniques, namely Tunable Diode Laser
Absorption Spectroscopy (TDLAS) and Gas in Scattering Media Absorption
Spectroscopy (GASMAS) were used to analyze Nitrogen Dioxide (NO2) and molecular
Oxygen gases respectively. Four                NO2 gas cells of different concentrations were
analyzed using a laser beam from a diode laser and the amplitudes of their 2nd harmonic
signals were recorded. The amplitudes and concentrations were used to plot a graph upon
which the path integration of NO2 was calculated. Using GASMAS, oxygen absorption in
the free air was analyzed and both the direct absorption and 2nd harmonic signals were
recorded. They were later used to calculate the GMS of oxygen which gave the
concentration of oxygen in air.

Also, the multispectral imaging microscope was used to capture images of the
microspheres at 13 wavelengths. The multispectral image obtained was analyzed using
the Principal Component Analysis (PCA) technique. The transmission spectrum of the
image was obtained using both MatLab and the spectrometer and the result from the two
instruments were compared and discussed.

6e2c01bd-aadc-4c42-9309-eee7e4cb192c.doc                                                  16