Dr. Pat Schneider Profile

Dr. Pat Schneider

at Queensborough Community College

SPIE Involvement:

Author

Publications (27)

Proceedings Article | 26 September 2013 Paper

Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction

Sunil Dehipawala, A. Nguyen, G. Tremberger, E. Cheung, P. Schneider, D. Lieberman, T. Holden, T. Cheung

Proceedings Volume 8865, 88650G (2013) https://doi.org/10.1117/12.2024627

KEYWORDS: Fractal analysis, Proteins, Computer simulations, Astrobiology, Calibration, Dichroic materials, Biomedical optics, Bioinformatics, Analytical research, Image information entropy

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A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene reconstruction studies in astrobiology and also be applicable to the study of point mutation in conformational thermostabilization research with Synchrotron based X-ray data for drug applications such as Parkinson’s disease.

Proceedings Article | 15 October 2012 Paper

Nucleotide fluctuation in extremophilic cold-adapted sequences and their degradation codes

George Tremberger, S. Dehipawala, E. Cheung, Jesaiah Prayor, Rafael Duran, P. Schneider, D. Lieberman, T. Holden, T. Cheung

Proceedings Volume 8521, 85210J (2012) https://doi.org/10.1117/12.929653

KEYWORDS: Fractal analysis, Image information entropy, Data modeling, Bioinformatics, Calibration, Biological research, Astrobiology, Factor analysis, Mode conditioning cables, Atomic layer deposition

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Proceedings Article | 10 March 2012 Paper

Effect of non-homogenous thermal stress during sub-lethal photodynamic antimicrobial chemotherapy

N. Gadura, D. Kokkinos, S. Dehipawala, E. Cheung, R. Sullivan, R. Subramaniam, P. Schneider, G. Tremberger, T. Holden, D. Lieberman, T. Cheung

Proceedings Volume 8211, 82110O (2012) https://doi.org/10.1117/12.909486

KEYWORDS: Fractal analysis, Light sources, Photoacoustic tomography, Thermal effects, Photodynamic therapy, Pathogens, Microscopy, Iron, Oxides, Doping

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Proceedings Article | 23 February 2012 Paper

Optical diffusion property of cerumen from ear canal and correlation to metal content measured by synchrotron x-ray absorption

Todd Holden, Sumudu Dehipawala, E. Cheung, U. Golebiewska, P. Schneider, G. Tremberger, D. Kokkinos, D. Lieberman, Sunil Dehipawala, T. Cheung

Proceedings Volume 8221, 82211L (2012) https://doi.org/10.1117/12.909896

KEYWORDS: Metals, Absorption, Synchrotrons, Pathogens, Microorganisms, Diffusion, Zinc, Ear, Near field optics, Light sources

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Proceedings Article | 9 February 2012 Paper

Optical speckles of blood proteins embedded in porous glassy substrate

T. Holden, S. Dehipawala, D. Kokkinos, A. Berisha, E. Cheung, A. Nguyen, U. Golebiewska, P. Schneider, G. Tremberger, D. Lieberman, T. Cheung

Proceedings Volume 8222, 822207 (2012) https://doi.org/10.1117/12.909503

KEYWORDS: Proteins, Blood, Molecules, Speckle, Speckle pattern, Calibration, Iron, Doping, Diffusion, Molecular interactions

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Proceedings Article | 2 February 2012 Paper

Single mode and sub-cellular fiber probes for cell scattering and density variation measurements

D. Kokkinos, T. Holden, S. Dehipawala, L. Mora, W. Huazhco, N. Gadura, U. Golebiewska, P. Schneider, G. Tremberger, D. Lieberman, T. Cheung

Proceedings Volume 8230, 82301G (2012) https://doi.org/10.1117/12.909911

KEYWORDS: Scattering, Fourier transforms, Refractive index, Single mode fibers, Monte Carlo methods, Correlation function, Microscopy, Yeast, Calibration, Optical testing

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Proceedings Article | 30 January 2012 Paper

Fiber optic based heart-rate and pulse pressure shape monitor

D. Kokkinos, S. Dehipawala, T. Holden, E. Cheung, M. Musa, G. Tremberger, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 8218, 82180V (2012) https://doi.org/10.1117/12.909582

KEYWORDS: Fiber optics sensors, Sensors, Electrocardiography, Fractal analysis, Heart, Fiber optics, Arteries, Single mode fibers, Optical fabrication, Photonic crystal fibers

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Proceedings Article | 23 September 2011 Paper

Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes

Todd Holden, S. Dehipawala, E. Cheung, R. Bienaime, J. Ye, G. Tremberger, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 8152, 81520S (2011) https://doi.org/10.1117/12.893434

KEYWORDS: Fractal analysis, Proteins, Microorganisms, Image information entropy, Sulfur, Biology, Photosynthesis, Metals, Mars, Biological research

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Proceedings Article | 23 September 2011 Paper

Technologically important extremophile 16S rRNA sequence Shannon entropy and fractal property comparison with long term dormant microbes

Todd Holden, N. Gadura, S. Dehipawala, E. Cheung, M. Tuffour, P. Schneider, G. Tremberger, D. Lieberman, T. Cheung

Proceedings Volume 8152, 81520T (2011) https://doi.org/10.1117/12.893450

KEYWORDS: Fractal analysis, Microorganisms, Image information entropy, Biology, Uranium, Proteins, Rockets, Statistical analysis, Electrodes, Data modeling

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Proceedings Article | 7 September 2010 Paper

Zn-metalloprotease sequences in extremophiles

T. Holden, S. Dehipawala, U. Golebiewska, E. Cheung, G. Tremberger, E. Williams, P. Schneider, N. Gadura, D. Lieberman, T. Cheung

Proceedings Volume 7819, 78190V (2010) https://doi.org/10.1117/12.860091

KEYWORDS: Fractal analysis, Proteins, Organisms, Zinc, Biology, Image information entropy, Calibration, Chemical species, Cadmium sulfide, Astrobiology

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Proceedings Article | 7 September 2010 Paper

Archaeon and archaeal virus diversity classification via sequence entropy and fractal dimension

George Tremberger, Victor Gallardo, Carola Espinoza, Todd Holden, N. Gadura, E. Cheung, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 7819, 78190T (2010) https://doi.org/10.1117/12.860097

KEYWORDS: Fractal analysis, Oceanography, Proteins, Biology, Image information entropy, Organisms, Ecosystems, Databases, Astrobiology, Solar energy

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Proceedings Article | 7 September 2010 Paper

Cyanobacteria gene and protein sequences in diurnal oscillation metabolic processes

George Tremberger, T. Holden, E. Cheung, S. Dehipawala, N. Gadura, U. Golebiewska, K. Valentin, M. Smulczeski, W. Satizabal, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 7819, 78190U (2010) https://doi.org/10.1117/12.860093

KEYWORDS: Fractal analysis, Proteins, Iron, Biology, Photosynthesis, Organisms, Image information entropy, Nitrogen, Astrobiology, Oxygen

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Proceedings Article | 11 September 2009 Paper

Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

Todd Holden, G. Tremberger, E. Cheung, R. Subramaniam, N. Gadura, P. Schneider, R. Sullivan, A. Flamholz, D. Lieberman, T. Cheung

Proceedings Volume 7441, 74410R (2009) https://doi.org/10.1117/12.825827

KEYWORDS: Fractal analysis, Image information entropy, Proteins, Mars, Silver, Bacteria, Resistance, Statistical analysis, Calibration, Gamma radiation

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Proceedings Article | 4 September 2009 Paper

Multi-fractal property of perchlorate reductase gene sequences and DNA photonics application to UV fluorescence detection on Mars-like surfaces

George Tremberger, Eric Cheung, N. Gadura, Todd Holden, Raji Subramaniam, Regina Sullivan, Pat Schneider, Alex Flamholz, David Lieberman, Tak Cheung

Proceedings Volume 7441, 74410G (2009) https://doi.org/10.1117/12.825819

KEYWORDS: Fractal analysis, Image information entropy, Microorganisms, Ultraviolet radiation, Mars, Chemical analysis, Luminescence, DNA photonics, Proteins, Distance measurement

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The discovery of perchlorate on Mars raises the possibility of the existence of perchlorate reduction microbes on that planet. The perchlorate reductase gene sequence fractal dimensions of two Dechloromonas species were compared with five other sequences in the microbial dimethyl sulfoxide (DMSO) reductase family. A nucleotide sequence can be expressed as a numerical sequence where each nucleotide is assigned its proton number. The resulting numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. Analysis of the fractal dimensions for the DMSO reductase family supports phylogenetic analyses that show that the perchlorate reductase gene sequences are members of the same family. A sub-family with roughly the same nucleotide length emerges having the property that the gene fractal dimension is negatively correlated with the Shannon di-nucleotide entropy (R² ~ 0.95, N =5). The gene sequence fractal dimension is found to be positively correlated with the neighbor joining distances reported in a published protein phylogeny tree (R²~ 0.92, N = 5). The multi-fractal property associated with these genes shows that perchlorate reductase has lower dimensionality as compared to the relatively higher dimensionality DNA-break repair genes Rec-A and Rad-A observed in the Dechloromonas aromatica and Deinococcus radiodurans genomes. The studied perchlorate gene sequences show a higher Shannon di-nucleotide entropy (~3.97 bits) relative to Dechloromonas aromatica DNA repair sequences (~3.87 bits Rec-A, ~3.92 bits Rad-A), suggesting that there are fewer constraints on nucleotide variety in the perchorlate sequences . These observations thus allow for the existence of perchlorate reducing microbes on Mars now or in the past. Timeresolved UV fluorescence study near the emission bands of nucleotide sequences could be used for bio-detection on Mars-like surfaces and the results may further constrain the proposed conjectures.

Proceedings Article | 28 August 2008 Paper

Phaeodactylum tricornutum photosynthesis and Thalassiosira pseudonana bio-silica formation genes nucleotide fluctuations

Todd Holden, P. Marchese, G. Tremberger, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, M. Huerta, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970R (2008) https://doi.org/10.1117/12.794414

KEYWORDS: Fractal analysis, Photosynthesis, Proteins, Organisms, Calibration, Carbon, Satellite imaging, Satellites, Bioinformatics, Cadmium sulfide

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Proceedings Article | 28 August 2008 Paper

DNA sequence-based comparative studies between non-extremophile and extremophile organisms with implications in exobiology

Todd Holden, P. Marchese, G. Tremberger, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970Q (2008) https://doi.org/10.1117/12.801269

KEYWORDS: Fractal analysis, Organisms, Monte Carlo methods, Statistical analysis, Proteins, Image information entropy, Resistance, Biological research, Information science, Genetics

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Proceedings Article | 28 August 2008 Paper

Nucleotide fluctuation of RecA repair gene in Siberian permafrost Psychrobacter cryohalolentis K5

George Tremberger, T. Holden, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, P. Marchese, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970U (2008) https://doi.org/10.1117/12.794390

KEYWORDS: Fractal analysis, Image information entropy, Astrobiology, Calibration, Proteins, Genetics, Chemical analysis, Microorganisms, Thermodynamics, Biology

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Proceedings Article | 28 August 2008 Paper

Methanosarcina acetivorans 16S rRNA and transcription factor nucleotide fluctuation with implications in exobiology and pathology

Todd Holden, G. Tremberger, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, P. Marchese, O. Hiciano, H. Yao, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970V (2008) https://doi.org/10.1117/12.794398

KEYWORDS: Fractal analysis, Mars, Pathology, Chemical analysis, Proteins, Biological research, Environmental sensing, Bioinformatics, Calibration, Astrobiology

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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.

Proceedings Article | 30 October 2007 Paper

Intensity fluctuation analysis of cell scattering/imaging with clinical application

Raji Subramaniam, R. Sullivan, P. Schneider, T. Holden, G. Tremberger, E. Cheung, A. Flamholz, D. Lieberman, T. Cheung, F. Garcia, N. Bewry, N. Pennie

Proceedings Volume 6796, 67960N (2007) https://doi.org/10.1117/12.778063

KEYWORDS: Fractal analysis, Breast, Biological research, Video, Speckle pattern, Mammography, Magnetic resonance imaging, Microscopes, Speckle, Microscopy

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Proceedings Article | 15 October 2007 Paper

Imaging through diffusive layers using speckle pattern fractal analysis and application to embedded object detection in tissues

George Tremberger, A. Flamholz, E. Cheung, R. Sullivan, R. Subramaniam, P. Schneider, G. Brathwaite, J. Boteju, P. Marchese, D. Lieberman, T. Cheung, Todd Holden

Proceedings Volume 6771, 677117 (2007) https://doi.org/10.1117/12.732302

KEYWORDS: Fractal analysis, Speckle pattern, Speckle, Tissues, Computer simulations, Mammography, Binary data, Absorption, Glasses, Architectural distortion

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Proceedings Article | 19 September 2007 Paper

Fractal analysis of noise buried time series signals with applications to exoplanet spectroscopy and bio-data

George Tremberger, T. Holden, E. Cheung, A. Flamholz, P. Marchese, H. Yao, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 6693, 66931D (2007) https://doi.org/10.1117/12.732987

KEYWORDS: Fractal analysis, Interference (communication), Exoplanets, Signal detection, Stars, Spectroscopy, Computer simulations, Calibration, Detection and tracking algorithms, Genetics

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Proceedings Article | 23 October 2006 Paper

The statistical and fractal properties of surface reflectivity of raw chicken tissue with application to public health safety

Raji Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, E. Cheung, G. Tremberger, P. Wong, D. Lieberman, T. Cheung, F. Garcia, N. Bewry, A. Yee

Proceedings Volume 6381, 63810H (2006) https://doi.org/10.1117/12.686285

KEYWORDS: Fractal analysis, Natural surfaces, Tissues, Breast, Reflectivity, Cameras, Microscopes, Yeast, Safety, Calibration

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Proceedings Article | 17 October 2006 Paper

Optical speckle angular correlation and fractal property of a composite of cancer/normal cell layers with application for laboratory monitoring of drug efficacy

Regina Sullivan, R. Subramaniam, P. Schneider, A. Flamholz, G. Tremberger, E. Cheung, S. Rotenberg, P. Wong, D. Lieberman, T. Cheung, Rafael Perez

Proceedings Volume 6386, 63860B (2006) https://doi.org/10.1117/12.686241

KEYWORDS: Fractal analysis, Speckle, Breast, Mammography, Cancer, Microscopes, Composites, Speckle pattern, Diffusion, Calibration

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Proceedings Article | 1 March 2006 Paper

Fractal analysis of yeast cell optical speckle

A. Flamholz, P. Schneider, R. Subramaniam, P. Wong, D. Lieberman, T. Cheung, J. Burgos, K. Leon, J. Romero

Proceedings Volume 6084, 60840R (2006) https://doi.org/10.1117/12.646399

KEYWORDS: Fractal analysis, Yeast, Speckle, Diffusion, Refractive index, Image resolution, Calibration, Endoscopes, Absorption, Geometrical optics

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Proceedings Article | 9 December 2004 Paper

Examination of yeast cell parameters using light diffusion

Patricia Schneider, Alex Flamholz, Peter Wong, David Lieberman, Tak Cheung, Harriet Itoka, Troy Minott, Janie Quizhpi, Jacquelin Rodriguez

Proceedings Volume 5578, (2004) https://doi.org/10.1117/12.567406

KEYWORDS: Yeast, Speckle, Fractal analysis, Diffusion, Mie scattering, Refractive index, Scattering, Microscopy, Light scattering, Diamond

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Proceedings Article | 19 November 2004 Paper

Optical diffusion property of chicken tissue

Patricia Schneider, Alex Flamholz, Peter Wong, David Lieberman, Tak Cheung, Harriet Itoka, Troy Minott, Janie Quizhpi, Jacquelin Rodriguez

Proceedings Volume 5587, (2004) https://doi.org/10.1117/12.571661

KEYWORDS: Refractive index, Tissues, Correlation function, Tissue optics, Diffusion, Fourier transforms, Proteins, Breast, Calibration, Water

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Proceedings Article | 2 August 2004 Paper

Speckle intensity correlation and optical diffusion profile in biological media

Alex Flamholz, Patricia Schneider, Peter Wong, David Lieberman, Tak Cheung, Harriet Itoka, Troy Minott, Janie Quizhpi, Jacquelin Rodriguez

Proceedings Volume 5531, (2004) https://doi.org/10.1117/12.558071

KEYWORDS: Refractive index, Correlation function, Yeast, Speckle, Proteins, Diffusion, Water, Fourier transforms, Calibration, Sensors

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Showing 5 of 27 publications

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