gebhart/patrepeval huggingface dataset:
Power Characterization for L1 and L5 Transmissions (2016)

This article aims to characterize the GPS L5 signal power, and how it differs from the GPS L1 C/A signal power. This was done in order to determine if the GPS L5 signal would be advantageous to use indoors. The specifications of the GPS L5 signals show a 3.6 dB increase from the specifi- cations for legacy L1 C/A signals. To verify the increased transmitted power an estimate of the satellite transmit antenna pattern was found for two of the Block IIF satellites with high enough passes over Boulder, Colorado, by subtracting the receiver antenna pattern. The L5 signal showed an average transmitted higher power of 2.7-3.1 dB which is slightly less than expected, but still close. A second experiment was set up to measure the impact of the reception antenna pattern. Four different antennas were used to collect data and compare the measured signal power to expected signal power for GPS L5. Two of the antennas show lower than expected signal powers for L5, especially for high elevation angles. As mentioned above this research effort took place in order to determine whether the GPS L5 signal would be preferable to use indoors. An assisted technique was used to detect the L1 and L5 signals inside the engineering building of University of Colorado. The results showed a mean of 3.5 dB higher power for GPS L5 compared to GPS L1 which shows that GPS L5 would be a good choice for indoor GPS applications.
Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin (2020)

Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies.
High performance 25 nm FDSOI devices with extremely thin silicon channel (2004)

We demonstrate 25 nm mid-gap metal gate fully-depleted silicon on insulator (FDSOI) devices with the highest reported drive current for a single-gate PMOS device (I/sub on/=789 /spl mu/A//spl mu/m and I/sub off/=27 nA//spl mu/m for V/sub gs/-V/sub t/=1.25 V). We observe electron and hole mobility degradation for very thin channels (/spl sim/7 nm). Devices show good hot carrier and gate dielectric reliability.
Platelet Abnormalities during Colonic Inflammation (2013)

Patients with inflammatory bowel disease are susceptible to microvascular thrombosis and thromboembolism. The increased incidence of thrombosis is accompanied by enhanced coagulation and abnormalities in platelet function. Clinical studies have revealed thrombocytosis, alterations in platelet activation, enhanced platelet-leukocyte interactions, and elevated plasma levels of prothrombotic cytokines. This study was directed toward determining whether the thrombocytosis, altered platelet functions, and enhanced platelet-leukocyte interactions observed in patients with inflammatory bowel disease can be recapitulated in the dextran sodium sulfate and T-cell transfer models of murine colonic inflammation. Flow cytometry was used to characterize platelet function in heparin-anticoagulated whole blood of control mice and in mice with colonic inflammation. Platelets were identified by characteristic light scattering and membrane expression of CD41. Thiazole orange labeling was used to differentiate between immature and mature platelets. Platelet activation was monitored using the expression of an activation epitope of GPIIb/IIIa integrin. The combination of CD41, CD45.2, Gr-1, F4/80, and isotype control antibodies was used to detect and quantify aggregates of leukocytes, neutrophils, and monocytes with platelets. Our results indicated that colonic inflammation is associated with thrombocytosis, leukocytosis, and the appearance of immature platelets. An increased number of circulating activated platelets was detected in colitic mice, along with the formation of aggregates of leukocytes (PLA), neutrophils (PNA), and monocytes (PMA) with platelets. Selectin blockade with fucoidin inhibited dextran sodium sulfate-induced PLA formation. The findings of this study indicate that many features of the altered platelet function detected in human inflammatory bowel disease can be reproduced in animal models of colonic inflammation.
Heterogeneity and Plasticity of Melanoma: Challenges of Current Therapies (2017)

The heterogeneity and plasticity of aggressive melanoma presents for­midable challenges in the design of current therapies. Plasticity is defined as the phenotype of cancer cells expressing properties normally related to stem cells, including the expression of genes associated with multiple cellular phenotypes and appearing as undifferentiated, embryonic-like cells. The multipotent pheno­type of these tumor cells, expressing vascular, embryonic, and cancer stem cell (CSC) capabilities, offers new insights into their functional adaptation and resis­tance to current therapies. This chapter highlights major advances in research that (i) help clarify the underlying challenges associated with angiogenesis inhibitor therapy; (ii) discuss important implications of the discovery of reactivation of the normally dormant Nodal embryonic signaling pathway that underlies the CSC phenotype, unregulated tumor growth and metastasis, and resistance to current therapies; and (iii) demonstrate the advantage of using combinatorial strategies to effectively target heterogeneous melanoma subpopulations to eliminate relapse and disease progression.
Commentary Novel biomarkers in critical care: utility or futility? (2007)

One of the holy grails of modern medicine, across a range of clinical sub-specialties, is establishing highly sensitive and specific biomarkers for various diseases. Significant success has been achieved in some of these clinical areas, most notably identifying high-sensitivity C-reactive peptide, troponin I/T and brain natriuretic peptide as significant prognosticators for both the acute outcome and the development of cardiovascular pathology. However, it is highly debatable whether this translates to complex, multi-system pathophysiological insults. Is critical care immune from the application of these novel biomarkers, given the numerous confounding factors interfering with their interpretation? In the previous issue of Critical Care [1], Fellahi and colleagues, in a large observational study, describe troponin-I release in three cohorts of cardiac surgical patients undergoing bypass grafts, valve replacement(s) or both. They report that patients undergoing both valve and bypass graft procedures sustained more cardiac damage, but the troponin-threshold for clinically significant events was higher in these patients. There are no cardiac tissue samples or serial echocardiographic data to provide histopathological and/or physiologic corroboration of these findings. On face value these results are perhaps not surprising, given that intuitively greater cardiac tissue damage, longer bypass time and hence a larger inflammatory stimulus would be predicted for patients undergoing valvular replacement alone or the dual procedure. Nevertheless, these are valuable data in that they illustrate some of the complexities surrounding troponin, a justifiably established star of the new biomarker age, in the sphere of critical care. The limitations of troponin, including the lack of universal measurement standards and its interpretation in the critically ill patient have been discussed in detail in this journal recently [2]. A key issue surrounding the utility of troponin remains the mechanism(s) of myocardial injury in both the cardiac surgical and critically ill patient
Proteomic and Transcriptomic Analysis of Neural Cell Fate in Developing Xenopus Embryos (2021)

The progeny of the D1 blastomere in the 8‐cell X. laevis embryo make major contributions to the central nervous system, brain, and retina of the adult animal. The lineage of this cell was tracked at the protein and mRNA levels at seven developmental time points up to the mid‐neurula stage. In addition, descendant cells from an excised D1 blastomere were analyzed at the same developmental stages. Transcriptomic analysis reveals that at early neurulation, the progeny tissue has committed to the expected neural fate, whereas the explant tissue has begun to differentiate into non‐neural ectoderm/epidermis. Bioinformatics analysis indicates that Notch signaling through the Jagged 1 (Jag1), Jagged 2 (Jag2), and Delta‐like 1 (Dll1) ligands is critical for determining the neural fate of the D1 progeny in the intact embryo. This study has also revealed a considerable amount of regulation at the level of translation. Notable examples include REST and Churchill. While the mRNA encoding these proteins is found in D1 progeny of the intact embryo and the explant tissue, REST protein, a repressor of neural gene expression, was only detected in explant tissue. Conversely, Churchill protein, involved in neural induction, was only detected in D1 progeny from the intact embryo. Continued bioinformatics analysis of the data generated by the strategy used here has three specific aims: 1. Identification of other intercellular signaling pathways that determine the neural fate of D1 progeny; 2. Identification of novel gene products that direct neurogenesis; 3. Identification of translational regulators (RNA binding proteins and miRNAs) of neural‐specific transcripts.
Terahertz Waveguides for Next Generation Communication Network (2021)

The terahertz frequency band (0.1–10 THz) is a promising candidate to meet the high bandwidth demand set by the next generation of wireless communications systems. So far, most of the THz communication prototypes have been demonstrated for free-space wireless environments. Although wireless systems present many advantages such as convenience for mobile end-users and easier upgrades, many challenges remain. Notably, wireless links are prone to high alignment errors due to the highly directional nature of the THz beam. In turn, this requires complex beamsteering algorithms for reliable communication. This situation is even worse for non-line-of-sight links in indoor communications, for example. In this context, THz waveguides can be an additional tool in the design of future THz networks. They can offer reliable coupling to the receiver and transmitter by enclosing the THz radiation in a highly controlled propagation medium. They can span complex geometrical paths in both static and dynamic operations. Advanced THz waveguides can be used for real-time signal processing as an alternative to all-electronic solutions. In this chapter, we cover the most recent advances of THz waveguides applied to THz communications. We start by proposing several applications where THz waveguides/devices can be beneficial. Then, we present the inherent challenges related to the design of THz waveguides for communications. We then cover various types of THz waveguides developed in recent years. Finally, we show all-waveguide designs of passive/active components such as dispersion compensators, couplers, splitters, and add-drop multiplexers for signal processing.
Characterization of Host-Cell Line Specific Glycosylation Profiles of Early Transmitted/Founder HIV-1 gp120 Envelope Proteins (2013)

Glycosylation plays an essential role in regulating protein function by modulating biological, structural, and therapeutic properties. However, due to its inherent heterogeneity and diversity, the comprehensive analysis of protein glycosylation remains a challenge. As part of our continuing effort in the analysis of glycosylation profiles of recombinant HIV-1 envelope-based immunogens, we evaluated and compared the host-cell specific glycosylation pattern of recombinant HIV-1 surface glycoprotein, gp120, derived from clade C transmitted/founder virus 1086.C expressed in Chinese hamster ovary (CHO) and human embryonic kidney containing T antigen (293T) cell lines. We used an integrated glycopeptide-based mass mapping workflow that includes a partial deglycosylation step described in our previous study with the inclusion of a fragmentation technique, electron transfer dissociation (ETD), to complement collision-induced dissociation. The inclusion of ETD facilitated the analysis by providing additional validation for glycopeptide identification and expanding the identified glycopeptides to include coverage of O-linked glycosylation. The site-specific glycosylation analysis shows that the transmitted/founder 1086.C gp120 expressed in CHO and 293T displayed distinct similarities and differences. For N-linked glycosylation, two sites (N386 and N392) in the V4 region were populated with high mannose glycans in the CHO cell-derived 1086.C gp120, while these sites had a mixture of high mannose and processed glycans in the 293T cell-derived 1086.C gp120. Compositional analysis of O-linked glycans revealed that 293T cell-derived 1086.C gp120 consisted of core 1, 2, and 4 type O-linked glycans, while CHO cell-derived 1086.C exclusively consisted of core 1 type O-linked glycans. Overall, glycosylation site occupancy of the CHO and 293T cell-derived 1086.C gp120 showed a high degree of similarity except for one site at N88 in the C1 region. This site was partially occupied in 293T-gp120 but fully occupied in CHO-gp120. Site-specific glycopeptide analysis of transmitted/founder 1086.C gp120 expressed in CHO cells revealed the presence of phosphorylated glycans, while 293T cell-produced 1086.C gp120 glycans were not phosphorylated. While the influence of phosphorylated glycans on immunogenicity is unclear, distinguishing host-cell specific variations in glycosylation profiles provide insights into the similarity (or difference) in recombinant vaccine products. While these differences had minimal effect on envelope antigenicity, they may be important in considering immunogenicity and functional capacities of recombinant envelope proteins produced in different expression systems.
Agrobacterium rhizogenes-mediated transformation of a dioecious plant model Silene latifolia (2018)

Silene latifolia serves as a model species to study dioecy, the evolution of sex chromosomes, dosage compensation and sex-determination systems in plants. Currently, no protocol for genetic transformation is available for this species, mainly because S. latifolia is considered recalcitrant to in vitro regeneration and infection with Agrobacterium tumefaciens. Using cytokinins and their synthetic derivatives, we markedly improved the efficiency of regeneration. Several agrobacterial strains were tested for their ability to deliver DNA into S. latifolia tissues leading to transient and stable expression of the GUS reporter. The use of Agrobacterium rhizogenes strains resulted in the highest transformation efficiency (up to 4.7% of stable transformants) in hairy root cultures. Phenotypic and genotypic analyses of the T1 generation suggested that the majority of transformation events contain a small number of independent T-DNA insertions and the transgenes are transmitted to the progeny in a Mendelian pattern of inheritance. In short, we report an efficient and reproducible protocol for leaf disc transformation and subsequent plant regeneration in S. latifolia, based on the unique combination of infection with A. rhizogenes and plant regeneration from hairy root cultures using synthetic cytokinins. A protocol for the transient transformation of S.latifolia protoplasts was also developed and applied to demonstrate the possibility of targeted mutagenesis of the sex linked gene SlAP3 by TALENs and CRISPR/Cas9.
Real-time compression and streaming of 4D performances (2018)

We introduce a realtime compression architecture for 4D performance capture that is two orders of magnitude faster than current state-of-the-art techniques, yet achieves comparable visual quality and bitrate. We note how much of the algorithmic complexity in traditional 4D compression arises from the necessity to encode geometry using an explicit model (i.e. a triangle mesh). In contrast, we propose an encoder that leverages an implicit representation (namely a Signed Distance Function) to represent the observed geometry, as well as its changes through time. We demonstrate how SDFs, when defined over a small local region (i.e. a block), admit a low-dimensional embedding due to the innate geometric redundancies in their representation. We then propose an optimization that takes a Truncated SDF (i.e. a TSDF), such as those found in most rigid/non-rigid reconstruction pipelines, and efficiently projects each TSDF block onto the SDF latent space. This results in a collection of low entropy tuples that can be effectively quantized and symbolically encoded. On the decoder side, to avoid the typical artifacts of block-based coding, we also propose a variational optimization that compensates for quantization residuals in order to penalize unsightly discontinuities in the decompressed signal. This optimization is expressed in the SDF latent embedding, and hence can also be performed efficiently. We demonstrate our compression/decompression architecture by realizing, to the best of our knowledge, the first system for streaming a real-time captured 4D performance on consumer-level networks.
Fundamental Considerations in One and Two-Dimensional Chromatography for Improved Chemometric Analysis (2017)

Thesis (Ph.D.)--University of Washington, 2017-06
Reflectance model for diffraction (2012)

We present a novel method of simulating wave effects in graphics using ray-based renderers with a new function: the Wave BSDF (Bidirectional Scattering Distribution Function). Reflections from neighboring surface patches represented by local BSDFs are mutually independent. However, in many surfaces with wavelength-scale microstructures, interference and diffraction requires a joint analysis of reflected wavefronts from neighboring patches. We demonstrate a simple method to compute the BSDF for the entire microstructure, which can be used independently for each patch. This allows us to use traditional ray-based rendering pipelines to synthesize wave effects. We exploit the Wigner Distribution Function (WDF) to create transmissive, reflective, and emissive BSDFs for various diffraction phenomena in a physically accurate way. In contrast to previous methods for computing interference, we circumvent the need to explicitly keep track of the phase of the wave by using BSDFs that include positive as well as negative coefficients. We describe and compare the theory in relation to well-understood concepts in rendering and demonstrate a straightforward implementation. In conjunction with standard raytracers, such as PBRT, we demonstrate wave effects for a range of scenarios such as multibounce diffraction materials, holograms, and reflection of high-frequency surfaces.
Influence of massively parallel e-beam direct-write pixel size on electron proximity correction (2011)

Massively E-beam maskless lithography (MEBML2) is one of the potential solutions for 32-nm half-pitch and beyond. In the past, its relatively low throughput restricted EBDW development to mostly mask making, small volume wafer production and prototyping. Recently the production worthy ML2 approaches, &gt;10,000 e-beams writing in parallel, have been proposed by MAPPER, KLA and IMS. These approaches use raster scan in pattern writing. Hence the bitmap is certainly the final data format. The bitmap format used to have huge data volume with fine pixel size to maintain the CD accuracy after electron proximity correction (EPC). Data handling becomes necessary, especially on data transmission rate. The aggregated data transmission rate would be up to 1963 Tera bits per second (bps) for a 10 WPH tool using 1-nm pixel size and 1-bit gray level. It needs 19,630 fibers each transmitting 10 Gbps. The data rate per beam would be &gt;20 Gbps in 10,000-beam MEBML2. Hence data reduction using bigger pixel size to achieve sub-nm EPC accuracy is crucial for reducing the fiber number to the beam number. In this paper, the writing-error-enhanced-factor to quantitatively characterize the impact of CD accuracy by various total blur in resist is reported; and we propose the vernier pattern to verify sub-nm CD accuracy and the in-house dithering raster method to achieve sub-0.2-nm CD accuracy using multiple-nm pixel sizes, which could reduce the need of the aggregated data rate to 11%, 33%, 44% and 79% of 1963 Tbps on 22-nm, 16-nm, 11-nm, 8-nm node respectively.
Epitaxial Transitions among FCC, HCP, BCC, and Cylinder Phases in a Block Copolymer Solution (2004)

A single concentration solution (36 vol %) of a symmetric polystyrene-block-polyisoprene, total molecular weight 30 000, in the styrene-selective solvent diethyl phthalate shows a remarkably rich sequence of thermotropic order−order transitions (OOT). A combination of small-angle X-ray scattering measurements both under quiescent conditions and after shear orientation, supplemented with rheology and static birefringence, indicates the following phase sequence. At room temperature the solution adopts a close-packed lattice of spherical micelles, corresponding to a mixture of face-centered-cubic (fcc) and hexagonally close-packed (hcp) phases. At approximately 60 °C the solution undergoes a “partial” OOT, in that the fcc portion transforms to body-centered-cubic (bcc), whereas the hcp domains persist. At approximately 82 °C the hcp/bcc mixture transforms to hexagonally packed cylinders, and finally the cylinder phase undergoes the order−disorder transition at 113 °C. Through the use of two different shear cells, scattering patterns along both shear gradient and vorticity axes were obtained. These data confirmed that all three OOTs (fcc to bcc, bcc to cylinder, and hcp to cylinder) are epitaxial. The first two follow the pathways previously established, whereas the hcp to cylinder is described for the first time in block copolymers. Among the other novel features of this system are the proximity to a triple line (coexistence of hcp, bcc, and cylinders) at 82 °C.
Energy harvesting flexible regenerative power source for wearable devices (2016)

We present the design, development and testing of an electronics module to harvest, regulate and store vibrational energy. The module includes a flexible rechargeable battery to store the harvested vibrational energy generated from normal human physical motion. The proposed regenerative power source is examined by integrating with a Galvanic Skin Response (GSR) sensor suitable for continuous long term measurement of stress and fatigue levels of personnel working in physically demanding and extreme work conditions.
Behavior of surface plasmon resonance at a left-handed material nano slab (2006)

In this paper we investigate the change of surface plasma (SP) resonance of a left-handed material (LHM) nano-slab. The intrinsic parameters of the LHM slab are suitable chose so that it has both negative permittivity and permeability in a frequency range of visible light. We calculate the attenuated total reflection (ATR) spectra of the LHM slab by use of the transfer matrix method. The spectra of different cases with various slab thickness and surrounding dielectrics of the LHM slab have been studied. The variations of SP resonance wavenumber and the corresponding resonance strength are discussed from the results of calculated ATR spectra.