gebhart/patrepeval huggingface dataset:
Single-shot angular compounded optical coherence tomography angiography by splitting full-space B-scan modulation spectrum for flow contrast enhancement (2016)

We proposed a single-shot spatial angular compounded optical coherence tomography angiography (AC-Angio-OCT) for blood flow contrast enhancement. By encoding incident angles in B-scan modulation frequencies and splitting the modulation spectrum in the spatial frequency domain, angle-resolved independent subangiograms were obtained and compounded to improve the flow contrast. A full space of the spatial frequency domain allows a wide modulation spectrum. To get access to the full space of the spatial frequency domain and avoid the complex-conjugate ambiguity of the modulation spectrum, a complex-valued OCT spectral interferogram was retrieved by removing one of the conjugate terms in the depth space. To validate the proposed concept, both flow phantom and live animal experiments were performed. The proposed AC-Angio-OCT offers a ∼50% decrease of misclassification errors, and an improved flow contrast and vessel connectivity, which contributes to the interpretation of OCT angiograms.
Quantifying substrate removal induced electrothermal degradation in AlGaN/GaN HEMTs (2017)

Strained heteroepitaxial HEMTs without the mechanical support of a substrate have been demonstrated only for small-sized AlGaN/GaN membranes, i.e., the substrate was removed from within the immediate vicinity of the transistor area [1]. Such transistors have exhibited improved breakdown voltage and frequency response. However, wafer-scale substrate removal has been considered detrimental to the heterostructure integrity [2]. In this work, by means of a wet-etch removal of the Si substrate over a large circular area (>5 mm diameter) underneath samples with conventionally-processed AlGaN/GaN HEMTs, we demonstrate HEMT operation on large-area AlGaN/GaN membranes and quantify aspects of device performance that were most affected by the substrate removal process.
Monoclonal, but not polyclonal, antibodies protect against Plasmodium yoelii sporozoites (1991)

One of the primary strategies for malaria vaccine development has been to design subunit vaccines that induce protective levels of antibodies against the circumsporozoite (CS) protein of malaria sporozoites. In the Plasmodium yoelii mouse model system such vaccines have been uniformly unsuccessful in protecting against sporozoite-induced malaria. To demonstrate that antibodies to P. yoelii CS protein could provide protection we established a passive transfer model. Passive transfer of Navy yoelii sporozoite 1 (NYS1), an IgG3 mAb against the P. yoelii CS protein, protected 100% of mice against challenge with 5000 P. yoelii sporozoites. Binding of NYS1 to sporozoites was inhibited by incubation with (QGPGAP)2, a synthetic peptide derived from the repeat region of the P. yoelii CS protein, indicating that the epitope on sporozoites recognized by this mAb was included within this peptide. The levels of antibodies to (QGPGAP)2 by ELISA, and to sporozoites by indirect fluorescent antibody test and CS precipitation reaction were similar in sera from mice that received NYS1 in passive transfer and were protected against challenge with 5000 sporozoites, and from mice that had been immunized with subunit vaccines containing (QGPGAP)2 but were not protected against challenge with 40-200 sporozoites. To determine if antibody avidity, not absolute concentration could explain the striking differences in protection, we established a thiocyanate elution assay. The results suggest that NYS1, the protective mAb, has a lower avidity for (QGPGAP)2 and for sporozoites than do the vaccine-induced antibodies. Although the results of the conventional antibody assays did not correlate with protection, sera from the protected animals inhibited sporozoite development in mouse hepatocyte cultures significantly more than did the sera from the unprotected, subunit vaccine-immunized animals, correlating with protection. The data clearly demonstrate that antibodies to the CS protein can protect against intense sporozoite infection. Improved understanding of the differences between protective mAb and nonprotective polyclonal antibodies will be important in the further development of malaria vaccines.
Protective Role of Cross-Reactive CD8 T Cells Against Dengue Virus Infection (2016)

Infection with one of the four dengue virus serotypes (DENV1-4) presumably leads to lifelong immunity against the infecting serotype but not against heterotypic reinfection, resulting in a greater risk of developing Dengue Hemorrhagic Fever/Dengue Shock Syndrome (DHF/DSS) during secondary infection. Both antibodies and T cell responses have been implicated in DHF/DSS pathogenesis. According to the T cell-based hypothesis termed "original antigenic sin," secondary DENV infection is dominated by non-protective, cross-reactive T cells that elicit an aberrant immune response. The goal of our study was to compare the roles of serotype-specific and cross-reactive T cells in protection vs. pathogenesis during DENV infection in vivo. Specifically, we utilized IFN-α/βR<sup>-/-</sup> HLA*B0702 transgenic mice in the context of peptide vaccination with relevant human CD8 T cell epitopes. IFN-α/βR<sup>-/-</sup> HLA*B0702 transgenic mice were immunized with DENV serotype 2 (DENV2)-specific epitopes or variants found in any of the other three serotypes (DENV1, DENV3 or DENV4), followed by challenge with DENV. Although cross-reactive T cell responses were lower than responses elicited by serotype-specific T cells, immunization with either serotype-specific or variant peptide epitopes enhanced viral clearance, demonstrating that both serotype-specific and cross-reactive T cells can contribute to protection in vivo against DENV infection.
Electro-optic Fabry–Perot pixels for phase-dominant spatial light modulators (1992)

A theoretical analysis of phase enhancement by resonant Fabry-Perot picture elements in III-V semiconductor spatial light modulators (SLM's) is presented. For 90% reflecting electrodes, a phase modulation of 0.7pi rad is found in transmission when the electro-optic input phase is 0.06pi rad. Implementation of this resonant phase-dominant SLM in a 1.5-microm-thick AlGaAs/GaAs multiple quantum well (MQW) structure is proposed. Field effects and carrier-induced electro-optic effects are suggested for the MQW's.
Probing the Mechanism of Improved Performance for Sodium-ion Batteries by Utilizing Three-electrode Cells: Effects of Sodium-ion Concentration in Ionic Liquid Electrolytes (2019)

We investigated the full-cell performance of sodium-ion batteries composed of a hard carbon (HC) negative electrode, a NaCrO2 positive electrode, and an ionic liquid electrolyte Na[FSA]–[C3C1pyrr][FSA] (FSA = bis(fluorosulfonyl)amide, C3C1pyrr = N-methyl-N-propylpyrrolidinium) at 333 K. Before the full-cell tests, charge–discharge tests of the Na/HC and Na/NaCrO2 half cells were conducted, from which the practical capacities were determined to be ca. 250 mAh (g-HC)−1 and ca. 115 mAh (g-NaCrO2)−1, respectively. Using these capacities, the performance of HC/NaCrO2 full cells with practical loading masses was evaluated by three-electrode cells with a sodium metal reference electrode, and the energy density was calculated to be 177 Wh (kg-(NaCrO2 + HC))−1. In particular, we focused on the effect of the sodium-ion concentration on the performance by varying the molar fraction of Na[FSA] (x(Na[FSA])) from 0.20 to 0.50. The best rate capability was obtained at a composition of x(Na[FSA]) = 0.50. The effect of the sodium-ion concentration was discussed in terms of the potential profiles of the positive and negative electrodes. The results were explained by the sodium-ion supplying capability of the electrolyte inside the electrode, where the sodium insertion reaction occurs.
Stress Physiology of Higher Plants: Cross‐Talk between Abiotic and Biotic Stress Signaling (2009)

This chapter contains sections titled: Introduction Cuticles and Stomata Hormone Signaling Governs Biotic and Abiotic Stress Responses Roles of ROS at Points of Convergence between Biotic and Abiotic Stress Response Pathways Transcription Factors Involved in the Cross-talk between Abiotic and Biotic Stress Signaling Mitogen-Activated Protein Kinase Cascade Effects of Humidity and Temperature on Biotic Stress Responses Conclusions References
A framework for automated test mocking of mobile apps (2020)

Mobile apps interact with their environment extensively, and these interactions can complicate testing activities because test cases may need a complete environment to be executed. Interactions with the environment can also introduce test flakiness, for instance when the environment behaves in non-deterministic ways. For these reasons, it is common to create test mocks that can eliminate the need for (part of) the environment to be present during testing. Manual mock creation, however, can be extremely time consuming and error-prone. Moreover, the generated mocks can typically only be used in the context of the specific tests for which they were created. To address these issues, we propose MOKA, a general framework for collecting and generating reusable test mocks in an automated way. MOKA leverages the ability to observe a large number of interactions between an application and its environment and uses an iterative approach to generate two possible, alternative types of mocks with different reusability characteristics: advanced mocks generated through program synthesis (ideally) and basic record-replay-based mocks (as a fallback solution). In this paper, we describe the new ideas behind MOKA, its main characteristics, a preliminary empirical study, and a set of possible applications that could benefit from our framework.
Controlled and tunable biomimetic apatite mineralization of synthetic hydrogels (2016)

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A robust real-time speckle tracking algorithm for ultrasonic elasticity imaging (2009)

In this study, we report a robust speckle tracking algorithm specifically designed for quasi-static ultrasound-based elasticity imaging. The proposed algorithm is a novel combination of our regularized speckle tracking algorithm and a competitive (i.e. quality-based) seeding strategy proposed by Chen et al. Through processing of in vivo breast and thyroid tissue data, our findings demonstrated that the new algorithm provides more consistent displacement estimates than our previous real-time algorithm for in vivo clinical data. Our preliminary results support that this novel algorithm might potentially make ultrasound-based elasticity imaging more easy to use by providing high quality strain imaging data in real-time.
The protein kinase CK2 is involved in regulation of circadian rhythms in <i>Arabidopsis</i> (1999)

A wide range of processes in plants, including expression of certain genes, is regulated by endogenous circadian rhythms. The circadian clock-associated 1 (CCA1) and the late elongated hypocotyl (LHY) proteins have been shown to be closely associated with clock function in Arabidopsis thaliana. The protein kinase CK2 can interact with and phosphorylate CCA1, but its role in the regulation of the circadian clock remains unknown. Here we show that plants overexpressing CKB3, a regulatory subunit of CK2, display increased CK2 activity and shorter periods of rhythmic expression of CCA1 and LHY. CK2 is also able to interact with and phosphorylate LHY in vitro. Additionally, overexpression of CKB3 shortened the periods of four known circadian clock-controlled genes with different phase angles, demonstrating that many clock outputs are affected. This overexpression also reduced phytochrome induction of an Lhcb gene. Finally, we found that the photoperiodic flowering response, which is influenced by circadian rhythms, was diminished in the transgenic lines, and that the plants flowered earlier on both long-day and short-day photoperiods. These data demonstrate that CK2 is involved in regulation of the circadian clock in Arabidopsis.
Clustered Backface CUlling (1998)

Abstract This paper presents a simple, practical, and effective backface-culling technique for clusters of polygons, as well as a method for generating efficient clusters from a set of triangle strips. The cluster-backface test is directly derived from the traditional single-polygon test, and has about the same complexity. Memory requirements are 40 bytes per test. Cluster-backface tests may be arranged hierarchically, and frontface tests added for symmetry. Experiments show graphics performance improvements of up to 50 percent in terms of the number of effective polygons rendered per second.
Modeling of filamentary resistive memory by concentric cylinders with variable conductivity (2014)

We demonstrate a method for modeling memristors (resistive random access memories) where the filament is composed of a set of nanoscale or sub-nanoscale concentric cylinders, each having its own conductivity. This approach allows for the inclusion of multiple state variables, which, we show experimentally, can be used to control electrical behavior. The simulations accurately reproduce the current-voltage hysteresis loop as well as these more complex experimental behaviors resulting from intricate switching histories. The simulations can be both static and dynamic, and are based upon physical design parameters, so optimized values from simulation can be easily linked to device design.
Melting Curve Analysis of SNPs (McSNP <sup>®</sup> ): A Gel-Free and Inexpensive Approach for SNP Genotyping (2001)

High-throughput methods for assaying DNA variation require two important steps: (i) discriminating the variation and (ii) detecting the signal. In this report, we describe a novel SNP genotyping method that we refer to as melting curve analysis of SNPs (McSNP). McSNP combines a classic approach for discriminating alleles, restriction enzyme digestion, with a more recent method for detecting DNA fragments, melting curve analysis. Melting curve analysis is performed by slowly heating DNA fragments in the presence of the dsDNA-specific fluorescent dye SYBR Green I. As the sample is heated, fluorescence rapidly decreases when the melting temperature of a particular fragment is reached. We show that it is possible to determine the composition of simple mixtures of DNA fragments, such as those that result from restriction enzyme digestions of short PCR products. McSNP is well suited for high-throughput genotyping because 96 samples can be analyzed and automatically scored in 20 min. Our results clearly demonstrate that McSNP is a simple, inexpensive, and accurate means of genotyping SNP variation.
Mesenchymal Stem Cells for Bone Gene Therapy and Tissue Engineering (2002)

Mesenchymal Stem Cells (MSCs) are adult stem cells that constitute a variety of adult tissues. MSCs maintain self-renewal ability with the ability to give rise to different mesenchymal cells, and are therefore responsible in part, for the regenerative capacity of mesenchymal tissues. MSCs throughout a variety of species were found to be able to differentiate to several mesenchymal tissues including: bone, cartilage, stroma, adipose, connective tissue, muscle and tendon. MSCs are relatively easily isolated from the bone marrow and expanded in vitro. It was found that MSCs play an important role in bone physiology and hematopoiesis, and in part participate in the pathophysiology related to bone diseases, mainly osteoporosis. MSCs were widely used in experimental studies in vivo, and were shown to form mesenchymal tissues. These discovered features have made MSCs good candidates for the development of various therapeutic modalities aimed to regenerate mesenchymal tissues, mainly bone. The more important approaches currently utilizing MSCs are gene therapy and tissue engineering. Both exploit the current knowledge in molecular biology and biomaterial science in order to direct MSCs to differentiate in vivo to desired lineages and tissues. Better understanding of the molecular mechanism directing the differentiation of MSCs, will eventually allow us to properly manipulate MSCs both in vivo and ex vivo to allow the regeneration of complex tissues and organs.
Centrin Gene Disruption Impairs Stage-specific Basal Body Duplication and Cell Cycle Progression in Leishmania (2004)

Centrin is a calcium-binding cytoskeletal protein involved in the duplication of centrosomes in higher eukaryotes. To explore the role of centrin in the protozoan parasite Leishmania, we created Leishmania deficient in the centrin gene (LdCEN). Remarkably, centrin null mutants (LdCEN(-/-)) showed selective growth arrest as axenic amastigotes but not as promastigotes. Flow cytometry analysis confirmed that the mutant axenic amastigotes have a cell cycle arrest at the G(2)/M stage. The axenic amastigotes also showed failure of basal body duplication and failure of cytokinesis resulting in multinucleated "large" cells. Increased terminal deoxy uridine triphosphate nick end labeling positivity was observed in centrin mutant axenic amastigotes compared with wild type cells, suggesting the activation of a programmed cell death pathway. Growth of LdCEN(-/-) amastigotes in infected macrophages in vitro was inhibited and also resulted in large multinucleated parasites. Normal basal body duplication and cell division in the LdCEN knockout promastigote is unique and surprising. Further, this is the first report where disruption of a centrin gene displays stage-specific/cell type-specific failure in cell division in a eukaryote. The centrin null mutant defective in amastigote growth could be useful as a vaccine candidate against leishmaniasis.
Obligatory role for GPER in cardiovascular aging and disease (2016)

Pharmacological activation of the heptahelical G protein-coupled estrogen receptor (GPER) by selective ligands counteracts multiple aspects of cardiovascular disease. We thus expected that genetic deletion or pharmacological inhibition of GPER would further aggravate such disease states, particularly with age. To the contrary, we found that genetic ablation of Gper in mice prevented cardiovascular pathologies associated with aging by reducing superoxide (⋅O<sub>2</sub><sup>-</sup>) formation by NADPH oxidase (Nox) specifically through reducing the expression of the Nox isoform Nox1 Blocking GPER activity pharmacologically with G36, a synthetic, small-molecule, GPER-selective blocker (GRB), decreased Nox1 abundance and ⋅O<sub>2</sub><sup>-</sup> production to basal amounts in cells exposed to angiotensin II and in mice chronically infused with angiotensin II, reducing arterial hypertension. Thus, this study revealed a role for GPER activity in regulating Nox1 abundance and associated ⋅O<sub>2</sub><sup>-</sup>-mediated structural and functional damage that contributes to disease pathology. Our results indicated that GRBs represent a new class of drugs that can reduce Nox abundance and activity and could be used for the treatment of chronic disease processes involving excessive ⋅O<sub>2</sub><sup>-</sup> formation, including arterial hypertension and heart failure.
Vapor phase nitration of benzene using mesoporous MoO3/SiO2 solid acid catalyst (2006)

Nitration of benzene has been carried out in the vapor phase, using dilute nitric acid as the nitrating agent, over mesoporous MoO3/SiO2 solid acid catalyst with more than 90% benzene conversion and 99.9% selectivity for mononitrobenzene. A series of MoO3/SiO2 catalysts with varying MoO3 loadings (1–30 mol%) were prepared using a sol–gel technique and characterized using X-ray diffraction analysis (XRD), BET specific surface area analysis, temperature-programmed desorption (TPD) of ammonia, and FTIR spectroscopic analysis of adsorbed pyridine. XRD analysis revealed the amorphous nature of the catalyst for 1 and 10 mol% MoO3 loading, and the formation of a crystalline α-MoO3 phase on the amorphous silica support at higher MoO3 loading. The BET surface area for pure silica support was 606 m2 g−1 and the pore size distribution in the range 40–80 Å, showing the mesoporous nature of amorphous silica. The BET surface area decreased to 583 m2 g−1 with incorporation of 1% MoO3 and further decreased to 180 m2 g−1 with increasing MoO3 loading up to 20%. Above 10% MoO3 loading, formation of crystalline MoO3 clusters on amorphous silica was observed. Ammonia-TPD showed a drastic increase in acid strength after addition of 1% MoO3 compared to pure silica support and the acid strength increased with increasing MoO3 content. Among the series of catalysts prepared, MoO3/SiO2 containing 20 mol% MoO3 was found to be the most active catalyst for benzene nitration, without showing any deactivation after more than 1000 h, showing a very high potential for commercialization.
<title>Two-color infrared thermometer for low-temperature measurement using a hollow glass optical fiber</title> (1997)

A low-temperature fiber optic two-color infrared thermometer has been developed. Radiation from a target is collected via a single 700 micrometer-bore hollow glass optical fiber coated with a metallic/dielectric layer on the inner surface, simultaneously split into two paths and modulated by a gold-coated reflective chopper, and focused onto two thermoelectrically cooled mid-infrared HgCdZnTe photoconductors by 128.8 mm-radius gold-coated spherical mirrors. The photoconductors have spectral bandpasses of 2 - 6 micrometer and 2 - 12 micrometer, respectively. The modulated detector signals are recovered using lock-in amplification. The two signals are calibrated using a blackbody (emissivity equal to 1) of known temperature, and exponential fits are applied to the two resulting voltage versus temperature curves. Using the two calibration equations, a computer algorithm calculates the temperature and emissivity of a target in real time, taking into account reflection of the background radiation field from the target surface.
cellTK: Automated Layout for Asynchronous Circuits with Nonstandard Cells (2013)

Asynchronous circuits are an attractive option to overcome many challenges currently faced by chip designers, such as increased process variation. However, the lack of CAD tools to generate asynchronous circuits limits the adoption of this promising technology. In this absence of CAD tools, the most time consuming part of chip design is the back-end (physical design) effort. We propose a complete design infrastructure to physically implement an asynchronous digital net list with orders of magnitude time savings over expert human effort. The core of this flow is the ability to generate customized logic that is compatible with available ASIC flows. We evaluate our flow against several asynchronous circuit benchmarks for which full custom physical implementations exist. Compared to hand-optimized custom designs, our flow produces layout that has, on average, a 51% area overhead, with a 12% increase in energy and a 9% increase in delay.