The beetle, Agrilus planipennis Fairmaire, was introduced to Michigan in 2002 and has since spread to many other states. In recent years, it has been reported in parts of New York. The fluctuations in satellite data signal associated with indices describing ash tree health, such as leaf area index (LAI) and Normalized Difference Vegetation Index (NVDI) as reported by the MODIS, have been studied. The fraction of Photosynthetically Active Radiation (FPAR) data was also studied. MODIS hyperspectral data, as calibrated to winged aircraft hyperspectral data, was used for ash tree characterization.
Digital solar image data is available to users with access to standard, mass-market software. Many scientific
projects utilize the Flexible Image Transport System (FITS) format, which requires specialized software
typically used in astrophysical research. Data in the FITS format includes photometric and spatial calibration
information, which may not be useful to researchers working with self-calibrated, comparative approaches. This
project examines the advantages of using mass-market software with readily downloadable image data from the
Solar Dynamics Observatory for comparative analysis over with the use of specialized software capable of
reading data in the FITS format. Comparative analyses of brightness statistics that describe the solar disk in the
study of magnetic energy using algorithms included in mass-market software have been shown to give results
similar to analyses using FITS data. The entanglement of magnetic energy associated with solar eruptions, as
well as the development of such eruptions, has been characterized successfully using mass-market software. The
proposed algorithm would help to establish a publicly accessible, computing network that could assist in
exploratory studies of all FITS data. The advances in computer, cell phone and tablet technology could
incorporate such an approach readily for the enhancement of high school and first-year college space weather
education on a global scale. Application to ground based data such as that contained in the Baryon Oscillation
Spectroscopic Survey is discussed.
The fluctuations of leaf area index (LAI) and Fraction of Photosynthetically Active Radiation (FPAR) as
reported by the MODIS 8-day product MOD15A2 over a section of Harriman State Park, New York were
studied with reference to another nearby local park. The area selected for study, a seven km square grid with one
km resolution, is known for its biodiversity. Time series data points were generated using the sums of the grid's
49 pixel measurements for each of the 46 entries that make up the annual time series. A quadratic relation has
been observed that suggests that LAI/FPAR is proportional to FPAR if FPAR is considered as the forcing
parameter via chlorophyll (a, b, c, d and f), in an application model for the study of biodiversity. The LAI annual
time series from 2000 to 2009 follows the corresponding FPAR annual time series as expected, but with different
proportionality ratios in different seasons. The fractal analysis results of the time series data suggest that the LAI
sequences have a lower fractal dimension (~1.35) than those of the FPAR sequences (~1.55), consistent with the
idea that biological systems are capable of regulating fluctuation. The regression of LAI sequence fractal
dimension versus FPAR sequence fractal dimension exhibits an R-square of about 0.7 (N =10). The observed
regression outlier for the year 2009 could be indicative of the presence of additional factors. Synchrotron
EXAFS and XANES investigations of leaf samples reveal data consistent with metal absorption under stress.
Further studies of absorption under stress using remote sensing data are warranted.
The deep water chlorophyll concentration fluctuation from 2003 to 2007 has been studied using fractal analysis.
The SeaWiFS global daily mean chlorophyll concentration time series were used. The Higuchi fractal algorithm
was used to calculate fractal dimension, which is given by the slope of an associated length versus the lag. Short
range fluctuation investigation using a six point slope gives fractal dimensions from 1.80 to 1.85, suggesting the
presence of correlation, which was confirmed by computer simulations. The gradual increase of fractal
dimension to 1.9 in about 15 lag-days suggests that a long-range de-correlation mechanism favoring random
fluctuation is present. The 2007 times series shows a relatively low overall fractal dimension and exhibits a
peculiar multi-fractal behavior. This phenomenon and the observed low accumulated cyclone energy in 2007
support the interpretation that cyclone energy can promote deep-water chlorophyll concentration fluctuation. A
regression of fractal dimension at 10 lag-days versus the log of cyclone energy gives an R2 value of 0.75 (N =
5)., which suggests the presence of additional or related de-correlation mechanisms.
Diatom bioactivity has been reported to be responsible for about 20% of carbon fixation globally and together
with other photosynthetic organisms, the bioactivity can be monitored via satellite ocean imaging. The bioinformatics
embedded in the nucleotide fluctuations of photosynthesis and bio-silicate genes in diatoms were
studied. The recently reported phosphoenolpyruvate carboxylase PEPC1 and PEPC2 C4-like photosynthesis
genes in Phaeodactylum tricornutum were found to have similar fractal dimensions of about 2.01. In
comparison, the green alga Chlamydomonas reinhardtii PEPC1 and PEPC2 genes have fractal dimensions of
about 2.05. The PEPC CpG dinucleotide content is 8% in P. tricornutum and 10% in C. reinhardtii. Further
comparison of the cell wall protein gene showed that the VSP1 gene sequence in C. reinhardtii has a fractal
dimension of 2.03 and the bio-silica formation silaffin gene in Thalassiosira pseudonana has a fractal dimension
of 2.01. The phosphoenolpyruvate carboxylase PPC1 and PPC2 in T. pseudonana were found to have fractal
dimensions and CpG dinucleotide content similar to that of P. tricornutum. The fractal dimension of the dnaB
replication helicase gene is about 1.98 for both diatoms as well as for the alga Heterosigma akashiwo. In
comparison, the E. coli dnaB gene has a fractal dimension of about 2.03. Given that high fractal dimension and
CpG dinucleotide content sequences have been associated with the presence of selective pressures, the relatively
low fractal dimension gene sequences of the two unique properties of Earth-bound diatoms (photosynthesis and
bio-silica cell wall) suggests the potential for the development of high fractal dimension sequences for adaptation
in harsh environments.
KEYWORDS: Fractal analysis, Organisms, Monte Carlo methods, Statistical analysis, Proteins, Image information entropy, Resistance, Biological research, Information science, Genetics
We have characterized function related DNA sequences of various organisms using informatics techniques,
including fractal dimension calculation, nucleotide and multi-nucleotide statistics, and sequence fluctuation
analysis. Our analysis shows trends which differentiate extremophile from non-extremophile organisms, which
could be reproduced in extraterrestrial life. Among the systems studied are radiation repair genes, genes involved
in thermal shocks, and genes involved in drug resistance. We also evaluate sequence level changes that have
occurred during short term evolution (several thousand generations) under extreme conditions.
A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton
number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution
and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the RecA
repair gene of Psychrobacter cryohalolentis K5, Psychrobacter arcticus 273-4, and Psychrobacter sp. PRwf-1.
The fractal dimension was found to correlate with the gene's operating temperature with the highest fractal
dimension associated with P. cryohalolentis K5 living at the low temperatures found in Siberian permafrost.
The CpG dinucleotide content was found to be about 5% for the three species of Psychrobacters, which is
substantially lower than that of Deinococcus radiodurans at about 12%. The average nucleotide pair-wise free
energy was found to be lowest for Psychrobacter sp. PRwf-1, the species with the lowest fractal dimension of
the three, consistent with the recent finding that Psychrobacter sp. PRw-f1 has a temperature growth maximum
of 15-20°C higher than P. arcticus 273-4 and P. cryohaloentis K5. The results suggest that microbial vitality in
extreme environments is associated with fractal dimension as well as high CpG dinucleotide content, while the
average nucleotide pair-wise free energy is related to the operating environment. Evidence that extreme
temperature operation would impose constraints measurable by Shannon entropy is also discussed. A
quantitative estimate of an entropy-based measure having the characteristics of a mechanical pressure shows that
the Psychrobacter RecA sequence experiences lower pressure than that of the human HAR1 sequence.
Cultures of the methane-producing archaea Methanosarcina, have recently been isolated from Alaskan
sediments. It has been proposed that methanogens are strong candidates for exobiological life in extreme
conditions. The spatial environmental gradients, such as those associated with the polygons on Mars' surface,
could have been produced by past methanogenesis activity. The 16S rRNA gene has been used routinely to
classify phenotypes. Using the fractal dimension of nucleotide fluctuation, a comparative study of the 16S
rRNA nucleotide fluctuation in Methanosarcina acetivorans C2A, Deinococcus radiodurans, and E. coli was
conducted. The results suggest that Methanosarcina acetivorans has the lowest fractal dimension, consistent
with its ancestral position in evolution. Variation in fluctuation complexity was also detected in the transcription
factors. The transcription factor B (TFB) was found to have a higher fractal dimension as compared to
transcription factor E (TFE), consistent with the fact that a single TFB in Methanosarcina acetivorans can code
three different TATA box proteins. The average nucleotide pair-wise free energy of the DNA repair genes was
found to be highest for Methanosarcina acetivorans, suggesting a relatively weak bonding, which is consistent
with its low prevalence in pathology. Multitasking capacity comparison of type-I and type-II topoisomerases
has been shown to correlate with fractal dimension using the methicillin-resistant strain MRSA 252. The
analysis suggests that gene adaptation in a changing chemical environment can be measured in terms of
bioinformatics. Given that the radiation resistant Deinococcus radiodurans is a strong candidate for an extraterrestrial
origin and that the cold temperature Psychrobacter cryohalolentis K5 can function in Siberian
permafrost, the fractal dimension comparison in this study suggests that a chemical resistant methanogen could
exist in extremely cold conditions (such as that which existed on early Mars) where demands on gene activity are
low. In addition, the comparative study of the Methanococcoides burtonii cold shock domain sequence has
provided further support for the correlation between multitasking capacity and fractal dimension.
The shape of an exoplanet lightcurve is usually obtained by averaging the noise over multiple datasets. Fractal
analysis has been demonstrated to be an effective tool for the detection of exoplanet transits using lightcurves
summed over all wavelengths sensitive to the detector (G. Tremberger, Jr et. al, 2006 Proc SPIE Vol 6265). The
detection of spectral features would depend on the extent to which the signal was buried in the noise. Different
noise sources would have different fractal characteristics. Also, the signal strength could be discontinuous in
time depending on the exoplanet's local atmospheric environment. Such a discontinuity is unlikely to be
detected with time integrated data. The lightcurve noise and shape information were characterized with fractal
dimension analysis of a noise buried time series signal. Computer simulation revealed that when the noise is
three times that of the signal, the fractal algorithm could detect the signal at about the 87% confidence level.
Application to noise buried time series datasets (HD 209458b lightcurve, HD149026b lightcurve) detected
discontinuities consistent with the results obtained by averaging datasets. Extension to individual wavelength
lightcurves would establish a detection limit for the existence of spectral features at wavelengths important for
exoplanet study. Other applications such as pre-implantation genetic screening spectroscopy and spatially varied
aneuploidy bio-data could use the same analysis principle as well.
The Pacific Ocean deep sea height data around latitude 20 N from Jason-1 satellite was analyzed in terms of
standard deviation (std) and fractal dimension during a 90-day period that included the coronal mass ejection
event of 2003 Oct 29 where a peak solar energetic particles of about 30,000 pfu was measured. The surface
height standard deviation series was observed to have two peaks that corresponded to two typhoon events of Oct
25 and Nov 26, 2003. The cross correlation of the height-std series and average-height series showed a positive
correlation with time delay. The fractal dimension of the height series peaked on Nov 1 (fractal dimension ~1.96
with a background 90-day average of ~ 1.81) and no corresponding peak was observed in the other time series
data. Computer simulation of the fractal dimension of a finite random series suggested a standard deviation of
about 0.071. Annual and long-term trends of the fractal dimensions were also found and investigated. The
possible contribution of coronal mass ejection to the surface height series fractal dimension and the height
correlation to chlorophyll were discussed.
Exoplanet transit time series photometric data usually contain noise levels that are comparable to the transit
signal jumps. The analysis that assumes Gaussian noise and extensive
data averaging calibrated to a reference
star has been the traditionally used algorithm. This paper studied the fractal property of the time series and
found that the fractal dimension changes for time series data that contain transits. The Higuchi fractal method,
where the length of the increment in various time lags is plotted against the lags, was used in this study.
(Higuchi, T., "Approach to an irregular time series on the basis of fractal theory", Physica D, vol 31, 277-283,
1988). The fractal algorithm was calibrated with the Weierstrass function. Simulations using Gaussian noise
suggested that a transit jump signal at about 1-sigma noise level would produce changes in fractal dimension,
while non-Gaussian noise simulations suggested a higher transit jump signal. The fractal algorithm was applied
to data collected on HD 209458 as well as on published data. The transit caused a fractal dimension change of
about 0.06. An over-exposed CCD dataset with much noise was also analyzed and a fractal dimension change of
about 0.02 was obtained. The result suggests that fractal dimension analysis, without the assumption of error
normality, is an alternative method for identifying transits in time series photometric data.
Astronomy is among the most popular courses that students select to fulfill their college science requirement at Queensborough Community College, New York City. Recent advances in photonics now enable us to observe celestial objects from exoplanets to ultra deep space galaxies that are 13 billion light years away. These results are regularly reported in the popular press such as the New York Times and “Sky & Telescope” magazine. We upgraded our astronomy course to keep pace with these advances in optics and photonics. The laboratory hands-on exercises include observations in our observatory using a telescope with digital camera and CCD; spectrum analysis with grating; Java photonics simulation delivered over the Internet; the use of virtual instruments in optics and photonics written with Labview. Advanced techniques such as interferometry are also included as demonstrations in the laboratory. Light is described light as an electromagnetic wave to avoid confusion with the dictionary description. As a result of these teaching designs, the students gain a clearer understanding of the optics and photonics basis of the astronomy instrumentation reported in popular articles.
Access to the requested content is limited to institutions that have purchased or subscribe to SPIE eBooks.
You are receiving this notice because your organization may not have SPIE eBooks access.*
*Shibboleth/Open Athens users─please
sign in
to access your institution's subscriptions.
To obtain this item, you may purchase the complete book in print or electronic format on
SPIE.org.
INSTITUTIONAL Select your institution to access the SPIE Digital Library.
PERSONAL Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.