Computer Engineering Commons^™

Gene Expression Analysis Of Embryonic Stem Cells Expressing Ve-Cadherin (Cd144) During Endothelial Differentiation, Vesna Nikolova-Krstevski, Manoj Bhasin, Hasan H. Otu, Towia A. Libermann, Peter Oettgen

Department of Electrical and Computer Engineering: Faculty Publications

Background: Endothelial differentiation occurs during normal vascular development in the developing embryo. This process is recapitulated in the adult when endothelial progenitor cells are generated in the bone marrow and can contribute to vascular repair or angiogenesis at sites of vascular injury or ischemia. The molecular mechanisms of endothelial differentiation remain incompletely understood. Novel approaches are needed to identify the factors that regulate endothelial differentiation.

Methods: Mouse embryonic stem (ES) cells were used to further define the molecular mechanisms of endothelial differentiation. By flow cytometry a population of VEGF-R2 positive cells was identified as early as 2.5 days after differentiation …

Aspects Of Producing, Directing, Conditioning, Impinging And Detecting Spectroscopic Electromagnetic Radiation From Small Spots On Samples, Martin M. Liphardt, Ping He, Blaine D. Johs, Galen L. Pfeiffers, James D. Welch, John A. Woollam

Department of Electrical and Computer Engineering: Faculty Publications

Sytems and mehtods for providing and enhancing electromagnetic radiation beam radail energy homogeneity and intensity vs. wavelength content, for reliably directing electromagnetic radiation emitted by a source thereof in a common direction, for achromatically reducing spot size on a sample (eg. liquid cavity containing lenses and low aberration 1:1 imaging systems modified to perform as spatial filters), and for directing directing different wavelengths into different detectors, in ellipsometer, polarizer or the like systems.

System And Method Ofselectively Monitoring Sample Front And Backside Reflections In Ellipsometer And The Like Systems, James D. Welch, John A. Woollam, Martin M Liphardt

Department of Electrical and Computer Engineering: Faculty Publications

A spectrophotometer, reflectometer, ellipsometer polarimeter or the like system having a detector means for independently intercepting electromagnetic radiation reflected from a sample frontside or backside, and methodology for pursuing less correlated determination of refractive index and thickness values.

Rotating Or Rotatable Compensator Systemi Providing Aberation Corrected Electromagnetic Raadation To A Spot On A Sample At Multiple Angles Of Ancidence, Martin M. Liphardt, Blaine D. Johs, Jeffrey S. Hale, Craig M. Herzinger, Steven E. Green, Ping He, John A. Woollam

Department of Electrical and Computer Engineering: Faculty Publications

The present invention relates to ellipsometer systems, and more particularly to ellipsometer systems comprising trans missive rotating or stepwise rotatable compensators for continuously or step-wise varying polarization states and further comprising transmissive multi-element lens focusing of a spectroscopic electromagnetic beam into a small, chromatically relatively undispersed area spot on a sample system. The ellipsometer system optionally is present in an environmental control chamber.

System For Sequentially Providing Aberation Corrected Electromagnetic Radation To A Spot On A Sample At Multiple Angles Of Incidence, Martin M. Liphardt, John A. Woollam,

Department of Electrical and Computer Engineering: Faculty Publications

A system for sequentially providing electromagnetic radia tion to a spot on a sample at different angles of incidence, and after reflection therefrom into a detector. The system includes a plurality of spherical mirrors, and a refractive element for correcting aberration.

Application Of Intermediate Wavelength Band Spectroscopic Ellipsometry To In-Stu. Real Time Fabrication Of Multiple Layer Alternating Hghalow Refractive Index Filters, Blaine D. Johs, Jeffery S. Hale, John A. Woollam, Craig M. Herzinger

Department of Electrical and Computer Engineering: Faculty Publications

Disclosed is application of oblique angle of incidence, reflection and/or transmission mode spectroscopic ellipsometry PSI and/or DELTA, (including combinations thereof and/or mathematical equivalents), vs. wavelength data over an intermediate wavelength band range around a pass or reject band, to monitor and/or control fabrication of multiple layer high/low refractive index band-pass, band-reject and varied attenuation vs. wavelength thin film interference filters, either alone or in combination with transmissive non-ellipsometric electromagnetic beam turning point vs. layer data obtained at an essentially normal angle of incidence.

A Theoretical Framework For Quality-Aware Cross-Layer Optimized Wireless Multimedia Communications, Song Chi, Haohong Wang, Dalei Wu

Department of Electrical and Computer Engineering: Faculty Publications

Although cross-layer has been thought as one of themost effective and efficient ways formultimedia communications over wireless networks and a plethora of research has been done in this area, there is still lacking of a rigorous mathematical model to gain indepth understanding of cross-layer design tradeoffs, spanning from application layer to physical layer. As a result, many existing cross-layer designs enhance the performance of certain layers at the price of either introducing side effects to the overall system performance or violating the syntax and semantics of the layered network architecture. Therefore, lacking of a rigorous theoretical study makes existing cross-layer …

Use Of Ellipsometry And Surface Plasmon Resonance In Monitoring Thin Film Deposition Or Removal From A Substrate Surface, John A. Woollam, Blaine D. Johs, Thomas E. Tiwald, Martin M. Liphardt, James D. Welch

Department of Electrical and Computer Engineering: Faculty Publications

Improved methodology for monitoring deposition or removal of material to or from a process and/or Wittness substrate Which demonstrates a negative e1 at some Wave length. The method involves detection of changes in P-polarized electromagnetism ellipsometric DELTA at SPR Resonance Angle-of-lncidence (A01) to monitor deposition of and/or removal of minute amounts of materials onto, or from, said process and/or Witness substrate. The methodology can optionally monitor ellipsometric PS1, and involves simultaneously or sequentially applying non-P-polarized electromagnetism at the same angle of incidence, or electromagnetic radiation of any polarization at a different angle-of-incidence and Wavelength to the process or Witt ness …

Flying Mobile On-Board Ellipsometer, Polarimeter, Reflectometer And The Like Systems, Blaine D. Johs,, Ping He, Martin M. Liphardt, Christopher A. Goeden, John A. Woollam, James D. Welch

Department of Electrical and Computer Engineering: Faculty Publications

A substantially self-contained “on-boar ” material system investigation system functionally mounted on a three dimen sional locational system to enable positioning at desired locations on, and distances from, the surface of a large sample, including the capability to easily and conveniently change the angle-of-incidence of a beam of electromagnetic radiation onto a sample surface.

Sample Entry Purge System In Spectrophotometer, Ellipsometer, Polarimeter And The Like Systems, Steven E. Green, Ping He, Galen L. Pfeiffer, Brian D. Guenther, Gerald T. Cooney, John A. Woollam, Martin M. Liphardt, Blaine D. Johs, Craig M. Herzinger

Department of Electrical and Computer Engineering: Faculty Publications

A sample sequestering system which allows access to a subspace in a chamber encompassed generally enclosed space, for use in entering and removing a sample when the subspace is opened to atmosphere. Sufficient purge gas is flowed from withing the generally enclosed space into the subspace discourage atmospheric contaminates from entering into the space is a spectrophotometer, ellipsometer or polarimeter or the like system which operates at wavelengths, (eg. UV), which are advesely affected, (eg. absorded), by typical atmospheric contents.

System For And Method Of Investigating The Exact Same Point On A Sample Substrate With Multiple Wavelengths, Galen L. Pfeiffer, Martin M. Liphardt, Blaine D. Johs, Craig M. Herzinger, Christopher A. Goeden, Ping He, John A. Woollam, James D. Welch

Department of Electrical and Computer Engineering: Faculty Publications

Disclosed are system for and method of analyzing a sample at substantially the exact same small spot point on a sample with a plurality of wavelengths.

System For And Method Of Investigating The Exact Same Point On A Sample Substrate With Multiple Wavelengths, Galen L. Pfeiffer, Martin M. Liphardt, Blaine D. Johs, Craig M. Herzinger, Christopher A. Goeden, Ping He, John A. Woollam, James D. Welch

Department of Electrical and Computer Engineering: Faculty Publications

Disclosed are system for and method of analyzing a sample at Substantially the exact same Small spot point on a sample with a plurality of wavelengths.

United States Patent Application Publication: System And Method For Sequence Distance Measure For Phylogenetic Tree Construction, K. Sayood, Hasan H. Otu, Steven H. Hinrichs

Department of Electrical and Computer Engineering: Faculty Publications

The present invention permits identification of biological materials following recovery of DNA using standard techniques by comparing a mathematical characterization of the unknown sequence with the mathematical characterization of DNA sequences of known genera and species. The clinical identification of infectious organisms is required for accurate diagnosis and selection of antimicrobial therapeutics. The invention allows an ab initio approach with the potential for rapid identification of biological materials of unknown origin. The approach provides for identification and classification of emergent or new organisms without previous phenotypic identification. The technique may also be used in monitoring situations where the need exists …

C-Fos As A Proapoptotic Agent In Trail-Induced Apoptosis In Prostate Cancer Cells, Xiaoping Zhang, Liang Zhang, Hongmei Yang, Xu Huang, Hasan H. Otu, Towia A. Libermann, William C. Dewolf, Roya Khosravi-Far, Aria F. Olumi

Department of Electrical and Computer Engineering: Faculty Publications

Tumor necrosis factor–related apoptosis-inducing ligand (TRAIL)/Apo-2L promotes apoptosis in cancer cells while sparing normal cells. Although many cancers are sensitive to TRAIL-induced apoptosis, some evade the proapoptotic effects of TRAIL. Therefore, differentiating molecular mechanisms that distinguish between TRAIL-sensitive and TRAIL-resistant tumors are essential for effective cancer therapies. Here, we show that c-Fos functions as a proapoptotic agent by repressing the antiapoptotic molecule c-FLIP(L). c-Fos binds the c-FLIP(L) promoter, represses its transcriptional activity, and reduces c-FLIP(L) mRNA and protein levels. Therefore, c-Fos is a key regulator of c-FLIP(L), and activation of c-Fos determines whether a cancer cell will undergo cell death …

Serum Proteome Profiling Detects Myelodysplastic Syndromes And Identifies Cxc Chemokine Ligands 4 And 7 As Markers For Advanced Disease, Manuel Aivado, Dimitrios Spentzos, Ulrich Germing, Gil Alterovitz, Xiao-Ying Meng, Franck Grall, Aristoteles A. N. Giagounidis, Giannoula Klement, Ulrich Steidl, Hasan H. Otu, Akos Czibere, Wolf C. Prall, Christof Iking-Konert, Michelle Shayne, Marco F. Ramoni, Norbert Gattermann, Rainer Haas, Constantine S. Mitsiades, Eric T. Fung, Towia A. Libermann

Department of Electrical and Computer Engineering: Faculty Publications

Myelodysplastic syndromes (MDS) are among the most frequent hematologic malignancies. Patients have a short survival and often progress to acute myeloid leukemia. The diagnosis of MDS can be difficult; there is a paucity of molecular markers, and the pathophysiology is largely unknown. Therefore, we conducted a multicenter study investigating whether serum proteome profiling may serve as a noninvasive platform to discover novel molecular markers for MDS. We generated serum proteome profiles from 218 individuals by MS and identified a profile that distinguishes MDS from non-MDS cytopenias in a learning sample set. This profile was validated by testing its ability to …

Spectrophotometer, Ellipsometer, Polarmeter And The Like Systems, John A. Woollam, Steven E. Green, Ping He, Blaine D. Johs, Craig M. Herzinger, Galen L. Pfeiffer, Brian D. Guenther, Martin M. Liphardt

Department of Electrical and Computer Engineering: Faculty Publications

Disclosed are improvements in ellipsometer and the like systems capable of operating in the Vacuum-Ultra-Violet (VUV) to Near Infrared (NIR) wavelength range, and methodology of use.

Human Transcriptome Corresponding To Human Oocytes And Use Of Said Genes Or The Corresponding Polypeptides To Trans-Differentiate Somatic Cells, Jose Bernardo Cibelli, Arif Murat Kocabas, Bing Lim, Hasan H. Otu

Department of Electrical and Computer Engineering: Faculty Publications

The identification of 101 genes upregulated or differentially expressed by mature human oocytes is provided herein. These genes and the corresponding gene products will facilitate a greater understanding of oogenesis, folliculogenesis, fertilization, and embryonic development. In addition these genes and the corresponding gene products can be used to effect dedifferentiation and/or transdifferentiation of desired somatic cells. The resultant dedifferentiated cells and somatic cells derived therefrom can be used in cell therapies such as in the treatment of cancer, autoimmunity, and other diseases wherein specific types of cells such as hematopoietic cells may be depleted because of the underlying disease or …

On-Off Frequency-Shift Keying For Wideband Fading Channels, Mustafa Cenk Gursoy, H. Vincent Poor, Sergio Verdu

Department of Electrical and Computer Engineering: Faculty Publications

M-ary on-off frequency-shift keying (OOFSK) is a digital modulation format in which M-ary FSK signaling is overlaid on on/off keying. This paper investigates the potential of this modulation format in the context of wideband fading channels. First, it is assumed that the receiver uses energy detection for the reception of OOFSK signals. Capacity expressions are obtained for the cases in which the receiver has perfect and imperfect fading side information. Power efficiency is investigated when the transmitter is subject to a peak-to-average power ratio (PAR) limitation or a peak power limitation. It is shown that under a PAR limitation, it …

The Transcriptome Of Human Oocytes, Arif Murat Kocabas, Javier Crosby, Pablo J. Ross, Hasan H. Otu, Zeki Beyhan, Handan Can, Wai-Leong Tam, Guilherme J. M. Rosa, Robert G. Halgren, Bing Lim, Emilio Fernandez, Jose Bernardo Cibelli

Department of Electrical and Computer Engineering: Faculty Publications

The identification of genes and deduced pathways from the mature human oocyte can help us better understand oogenesis, folliculogenesis, fertilization, and embryonic development. Human metaphase II oocytes were used within minutes after removal from the ovary, and its transcriptome was compared with a reference sample consisting of a mixture of total RNA from 10 different normal human tissues not including the ovary. RNA amplification was performed by using a unique protocol. Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays were used for hybridizations. Compared with reference samples, there were 5,331 transcripts significantly up-regulated and 7,074 transcripts significantly down-regulated in the …

Energy-Constrained Quality Optimization For Secure Image Transmission In Wireless Sensor Networks, Wei Wang, Dongming Peng, Honggang Wang, Hamid Sharif, Hsiao-Hwa Chen

Department of Electrical and Computer Engineering: Faculty Publications

Resource allocation for multimedia selective encryption and energy efficient transmission has not been fully investigated in literature for wireless sensor networks (WSNs). In this article, we propose a new cross-layer approach to optimize selectively encrypted image transmission quality in WSNs with strict energy constraint. A new selective image encryption approach favorable for unequal error protection (UEP) is proposed, which reduces encryption overhead considerably by controlling the structure of image bitstreams. Also, a novel cross-layer UEP scheme based on cipher-plain-text diversity is studied. In this UEP scheme, resources are unequally and optimally allocated in the encrypted bitstream structure, including data position …

Applicationofspectroscopic Ellipsometry To In-Stu. Real-Time Fabrication Of Multiple Layer Alternating High/Low Refractive Index Filters, Blaine D. Johs, Jeffery S. Hale, John A. Woollam, Craig M. Herzinger

Department of Electrical and Computer Engineering: Faculty Publications

Disclosed is application of oblique angle of incidence, reflection and/or transmission mode spectroscopic ellipsometry PSI and/or DELTA, (including combinations thereof and/or mathematical equivalents), vs. wavelength data to monitor and/or control fabrication of multiple layer high/low refractive index band-pass, band-reject and varied attenuation vs. wavelength filters, either alone or in combination with transmissive non-ellipsometric electromagnetic beam turning point vs. layer data obtained at an essentially normal angle of incidence.

System And Method Enabling Simultaneous Investigation Of Sample With Two Beams Of Electromagnetic Radiation, John A. Woollam, Galen L. Pfeiffer, Daniel W. Thompson, Blaine D. Johs, Craig M. Herzinger

Department of Electrical and Computer Engineering: Faculty Publications

Disclosed are system and method for a characterizing system consisting of a fluid sample on a two-sided stage, utilizing data obtained by applying, from both sides thereof, beams of electromagnetic radiation to a fluid coated surface in a containing cell volume. The beams can have the same or different wavelength content and/or polarization state and can be applied at the same or different magnitude angles-of-incidence, and a third typically unpolarized beam can be applied at a normal angle-of-incidence.

System And Method Enabling Simultaneous Investigation Of Sample With Two Beams Of Electromagnetic Radation, John A. Woollam, Galen L. Pfeiffer, Daniel W. Thompson, Blaine D. Johs, Craig M. Herzinger

Department of Electrical and Computer Engineering: Faculty Publications

Disclosed are System and method for characterizing a System consisting of a fluid Sample on a two sided Stage, utilizing data obtained by applying, from both sides thereof, beams of electromagnetic radiation to a fluid coated Surface in a containing cell Volume. The beams can have the same or different wavelength content and/or polarization State, and can be applied at the same or different magnitude angles-of-incidence, and a third typically unpolarized beam can be applied at a normal angle-of-incidence.

Multi-Aoi-System For Easy Changing Angles Of Incidence In Ellipsometer, Polarimeter And Reflectometer Systems, Blaine D. Johs, Ping He, Martin M. Liphardt, Christopher A. Goeden, John A. Woollam, James D. Welch

Department of Electrical and Computer Engineering: Faculty Publications

Disclosed is a system for enabling easy sequential setting of different Angles-of-Incidence of a beam of electromagnetic radiation to a surface of a sample system, and to regression based methodology for evaluating and compensating the effects of the presence of electromagnetic beam intercepting angle-of-incidence changing systems, including where desired, parameterization of calibration parameters.

Preconditioning Of Primary Human Endothelial Cells With Inflammatory Mediators Alters The “Set Point” Of The Cell, Youichiro Wada, Hasan H. Otu, Shengqian Wu, Md. Ruhul Abid, Hitomi Okada, Towia Libermann, Tatsuhiko Kodama, Shu-Ching Shih, Takashi Minami, William C. Aird

Department of Electrical and Computer Engineering: Faculty Publications

Endothelial cells are highly sensitive to changes in the extracellular milieu. Sepsis results in activation of inflammatory and coagulation pathways. We hypothesized that sepsis-associated mediators may alter the response capacity (so-called “set point”) of endothelial cells. Human umbilical vein endothelial cells (HUVEC) were preincubated in the presence or absence of tumor necrosis factor (TNF)-α, lipopolysaccharide (LPS), hypoxia, hyperthermia, and/or high glucose; treated with or without thrombin for 4 h; and then processed for RNase protection assays of selected activation markers. Priming with TNF-α and LPS significantly inhibited thrombin-mediated induction of vascular cell adhesion molecule-1, intercellular adhesion molecule-1, tissue factor, and …

Observations Of The Small-Scale Variability Of Precipitation Using An Imaging Radar, Robert D. Palmer, Boon Leng Cheong, Michael Hoffman, Stephen J. Frasier, F.J. Lopez-Dekker

Department of Electrical and Computer Engineering: Faculty Publications

For many years, spatial and temporal inhomogeneities in precipitation fields have been studied using scanning radars, cloud radars, and disdrometers, for example. Each measurement technique has its own advantages and disadvantages. Conventional profiling radars point vertically and collect data while the atmosphere advects across the field of view. Invoking Taylor’s frozen turbulence hypothesis, it is possible to construct time-history data, which are used to study the structure and dynamics of the atmosphere. In the present work, coherent radar imaging is used to estimate the true three-dimensional structure of the atmosphere within the field of view of the radar. The 915-MHz …

Editorial, Robert W. Stewart, Michael W. Hoffman, Stephan Weiss

Department of Electrical and Computer Engineering: Faculty Publications

In the past years, digital signal processing (DSP) algorithms and architectures for baseband communication systems have fuelled the delivery of applications such as 3G mobile communications and wireless LAN to mass markets. This was made possible by a tremendous growth in the performance of computational devices such as digital signal processors and FPGAs, as well as an increase in sampling rates of conversion devices to potentially several 100 MHz. While the development of both computational devices and ADCs/DACs continues, thus permitting DSP to be applied at IF sampling rates and possibly beyond, the opportunities for further enhancing radio devices by …

Comparison Of Antenna Array Systems Using Ofdm For Software Radio Via The Sibic Model, Khoi D. Le, Michael W. Hoffman, Robert D. Palmer

Department of Electrical and Computer Engineering: Faculty Publications

This paper investigates the performance of two candidates for software radio WLAN, reconfigurable OFDM modulation and antenna diversity, in an indoor environment. The scenario considered is a 20m × 10m × 3m room with two base units and one mobile unit. The two base units use omnidirectional antennas to transmit and the mobile unit uses either a single antenna with equalizer, a fixed beamformer with equalizer, or an adaptive beamformer with equalizer to receive. The modulation constellation of the data is QPSK and 16-QAM. The response of the channel at the mobile unit is simulated using a three-dimensional indoor WLAN …

A Novel Role For Gadd45Β As A Mediator Of Mmp-13 Gene Expression During Chondrocyte Terminal Differentiation, Kosei Ijiri, Luiz F. Zerbini, Haibing Peng, Ricardo G. Correa, Binfeng Lu, Nicole Walsh, Yani Zhao, Noboru Taniguchi, Xu-Ling Huang, Hasan H. Otu, Hong Wang, Jian Fei Wang, Setsuro Komiya, Patricia Ducy, Mahboob U. Rahman, Richard A. Flavell, Ellen M. Gravallese, Peter Oettgen, Towia A. Libermann, Mary B. Goldring

Department of Electrical and Computer Engineering: Faculty Publications

The growth arrest and DNA damage-inducible 45β (GADD45β) gene product has been implicated in the stress response, cell cycle arrest, and apoptosis. Here we demonstrated the unexpected expression of GADD45β in the embryonic growth plate and uncovered its novel role as an essential mediator of matrix metalloproteinase-13 (MMP-13) expression during terminal chondrocyte differentiation. We identified GADD45β as a prominent early response gene induced by bone morphogenetic protein-2 (BMP-2) through a Smad1/Runx2-dependent pathway. Because this pathway is involved in skeletal development, we examined mouse embryonic growth plates, and we observed expression of Gadd45β mRNA coincident with Runx2 protein …

Range Imaging Observations Of Pmse Using The Eiscat Vhf Radar: Phase Calibration And First Results, J. R. Fernandez, R. D. Palmer, P. B. Chilson, I. Haggstrom, M. T. Rietveld

Department of Electrical and Computer Engineering: Faculty Publications

A novel phase calibration technique for use with the multiple-frequency Range IMaging (RIM) technique is introduced based on genetic algorithms. The method is used on data collected with the European Incoherent SCATter (EISCAT) VHF radar during a 2002 experiment with the goal of characterizing the vertical structure of Polar Mesosphere Summer Echoes (PMSE) over northern Norway. For typical Doppler measurements, the initial phases of the transmitter and receiver are not required to be the same. The EISCAT receiver systems exploit this fact, allowing a multistatic configuration. However, the RIM method relies on the small phase differences between closely spaced frequencies. …