gebhart/patrepeval huggingface dataset:
Single-shot spectrally resolved interferometry for the simultaneous measurement of the thickness and surface profile of multilayer films (2021)

We present a single-shot spectrally-resolved interferometry for simultaneously measuring the film thickness and surface profile of each layer of a patterned multilayer film structure. For this purpose, we implemented an achromatic phase shifting method based on the geometric phase using the polarization characteristics of the light and obtained four phase-shifted interferograms in the spectrally-resolved fringe pattern at the same time by combining a pixelated polarizing camera with an imaging spectrometer. As a result, we could simultaneously measure the reflectance and phase of the sample over a wide wavelength range with a single measurement. To evaluate the validity of the proposed method, we measured a patterned five-layer film specimen and compared our measurement results with those from commercial instruments, an ellipsometer and a stylus profiler, respectively. We confirmed the results matched each other well.
Dynamic analysis of immune and cancer cell interactions at single cell level in microfluidic droplets (2016)

Cell-cell communication mediates immune responses to physiological stimuli at local and systemic levels. Intercellular communication occurs via a direct contact between cells as well as by secretory contact-independent mechanisms. However, there are few existing methods that allow quantitative resolution of contact-dependent and independent cellular processes in a rapid, precisely controlled, and dynamic format. This study utilizes a high-throughput microfluidic droplet array platform to analyze cell-cell interaction and effector functions at single cell level. Controlled encapsulation of distinct heterotypic cell pairs was achieved in a single-step cell loading process. Dynamic analysis of dendritic cell (DC)-T cell interactions demonstrated marked heterogeneity in the type of contact and duration. Non-stimulated DCs and T cells interacted less frequently and more transiently while antigen and chemokine-loaded DCs and T cells depicted highly stable interactions in addition to transient and sequential contact. The effector function of CD8<sup>+</sup> T cells was assessed via cytolysis of multiple myeloma cell line. Variable cell conjugation periods and killing time were detected irrespective of the activation of T cells, although activated T cells delivered significantly higher cytotoxicity. T cell alloreactivity against the target cells was partially mediated by secretion of interferon gamma, which was abrogated by the addition of a neutralizing antibody. These results suggest that the droplet array-based microfluidic platform is a powerful technique for dynamic phenotypic screening and potentially applicable for evaluation of novel cell-based immunotherapeutic agents.
Joint reconstruction of simultaneously acquired MR-PET data with multi sensor compressed sensing based on a joint sparsity constraint (2014)

State-of-the-art MR-PET scanners allow simultaneous data acquisition. However, image reconstruction is performed separately and results are only combined at the visualization stage. PET images are reconstructed using a variant of EM and MR data are reconstructed using an inverse Fourier transform or iterative algorithms for parallel imaging or compressed sensing. We propose a new iterative joint reconstruction framework based on multi-sensor compressed sensing that exploits anatomical correlations between MR and PET.

Joint reconstruction is motivated by the fact that MR and PET are based on the same anatomy. High resolution MR information can be used to enhance the PET reconstruction and MR artifacts are not present in the PET image. Therefore a dedicated reconstruction can exploit the incoherence of artifacts in the joint space. Our approach uses a nonlinear constrained optimization problem. In each iteration OSEM enforces data consistency of the current solution with measured PET rawdata. An l1-norm based joint sparsity term exploits anatomical correlations. MR data consistency is enforced with the MR forward operator, consisting of coil sensitivity modulation and a (non-uniform) Fourier transform. Data were acquired on a clinical 3T MR-PET unit (Siemens Biograph mMR). 10 mCi 18F-FDG were injected followed by a 60min list mode scan. 3D MP-RAGE was used for MR data acquisition: TR=2300ms, TE=2.98ms, TI=900ms, FA=9°, acceleration factor 2, 24 ACS lines, 256 matrix, voxel size=1×1×1mm3, 192 slices.

Joint MR-PET reconstruction improves resolution in PET images when structures are aligned with MR. PET signal information cannot be improved in regions showing no distinctive MR contrast, but it is also not influenced falsely. The availability of simultaneously-acquired MR and PET data will also enable incorporation of dynamic correlations and motion correction into the joint reconstruction framework. We expect that this provides additional enhancements to the information content of multimodality studies.
Novel Gas Turbine Exhaust Temperature Measurement System (2013)

Siemens Energy, Inc. has been investigating the potential of a new approach to measuring the process gas temperature leaving the turbine of their heavy industrial gas turbine engines using an acoustic pyrometer system. This system measures the bulk temperature crossing a plane behinds the last row of turbine blades and is a non-intrusive measurement. It has the potential to replace the current intrusive multiple point measurement sensor arrays for both engine control and performance evaluation. The acoustic pyrometer is a device that measures the transit time of an acoustic pulse across the exhaust duct of the engine. An estimate of the temperature of the process fluid can be made from the transit time. Multiple passes may be made at various radial positions to improve the measurement. The gas turbine exhaust is a challenging environment for acoustic temperature measurement where there can be significant temperature stratification and high velocity. Previous applications of acoustic pyrometers to measure process gas temperature in power plants have been confined to applications such as boilers where rapid temperature changes are not expected and fluid velocity patterns are well known. The present study describes the results of acoustic pyrometer testing in an operating gas turbine engine under load using an active acoustic pyrometer system containing eight sets of transmitters and receivers, all external to the turbine exhaust flow path. This active method technology is based on the temperature dependence of the isentropic speed of sound from the simple ideal gas assumptions. Sound transmitters and receivers are mounted around the exhaust duct to measure the speed of sound. Very sophisticated topographical mapping techniques have been developed to extract temperature distribution from using any where from 2 to 8 sensors with up to 24 paths and 400 points. Cross correlation of sensor results to obtain topographical mapping of gas isotherms in a plane in full engine field tests have been conducted to prove the feasible of this technology on a gas turbine engine. The initial installation of the active acoustic pyrometer system in an engine exhaust was accomplished in 2009. All the tests indicate that the steady state measurements of the acoustic pyrometer system fall within 10C of the measured exhaust thermocouple data. An additional installation on a different model engine was subsequently made and data have been gathered and analyzed. Results of these tests are presented and future evaluation options discussed.
Study of Deposition Methods for Silicon Powder (1990)

Silicon powder tends to agglomerate at normal atmospheric conditions and is, hence, difficult to aerosolize. Several methods of aerosolizing silicon powder and finally depositing it on various substrates were investigated. This paper presents the investigated methods of aerosolization. The electrostatic spray coating used in dry paint application was found to be the most suitable. The general merits of this method and its use for silicon powder deposition to form films are discussed.
Mutational studies of yeast transcription factor IIB <i>in vivo</i> reveal a functional surface important for gene activation (1997)

Recent experiments in yeast (Saccharomyces cerevisiae) cells have identified a species-specific region of yeast transcription factor IIB (TFIIB) located at residues 144-157. According to the human TFIIB structure, this region is part of a solvent-exposed helix in the first repeat of the carboxyl-terminal core domain. In this report, we systematically analyze four positions in this region (Lys-147, Cys-149, Lys-151, and Glu-152) that together have been shown previously to be important for yeast TFIIB's function in vivo. Our experiments suggest that all of these four positions, and in particular positions 151, 149, and 152, are critical for yeast TFIIB's ability to support cell growth. In addition, we describe an intragenic suppressor screening experiment to identify mutations that reverse, or partially reverse, the temperature-sensitive phenotype of a yeast TFIIB derivative bearing amino acid changes at these four positions to human residues. The suppressor mutations reveal changes at positions 115, 117, and 182 that are located outside the species-specific region of yeast TFIIB, suggesting an extended surface available to interact with other proteins. Finally, we demonstrate that the suppressor mutations restore gene activation in vivo, further supporting the idea that one important function of yeast TFIIB in living cells is to mediate gene activation.
Advantages and Limitations of Androgen Receptor-Based Methods for Detecting Anabolic Androgenic Steroid Abuse as Performance Enhancing Drugs (2016)

Testosterone (T) and related androgens are performance enhancing drugs (PEDs) abused by some athletes to gain competitive advantage. To monitor unauthorized androgen abuse, doping control programs use mass spectrometry (MS) to detect androgens, synthetic anabolic-androgenic steroids (AASs) and their metabolites in an athlete's urine. AASs of unknown composition will not be detected by these procedures. Since AASs achieve their anabolic effects by activating the Androgen Receptor (AR), cell-based bioassays that measure the effect of a urine sample on AR activity are under investigation as complementary, pan-androgen detection methods. We evaluated an AR BioAssay as a monitor for androgen activity in urine pre-treated with glucuronidase, which releases T from the inactive T-glucuronide that predominates in urine. AR BioAssay activity levels were expressed as 'T-equivalent' concentrations by comparison to a T dose response curve. The T-equivalent concentrations of androgens in the urine of hypogonadal participants supplemented with T (in whom all androgenic activity should arise from T) were quantitatively identical to the T measurements conducted by MS at the UCLA Olympic Analytical Laboratory (0.96 ± 0.22). All 17 AASs studied were active in the AR BioAssay; other steroids were inactive. 12 metabolites of 10 commonly abused AASs, which are used for MS monitoring of AAS doping because of their prolonged presence in urine, had reduced or no AR BioAssay activity. Thus, the AR BioAssay can accurately and inexpensively monitor T, but its ability to monitor urinary AASs will be limited to a period immediately following doping in which the active AASs remain intact.
Antibodies Reactive with the N-Terminal Domain ofPlasmodium falciparum Serine Repeat Antigen Inhibit Cell Proliferation by Agglutinating Merozoites and Schizonts (1999)

The serine repeat antigen (SERA) is a vaccine candidate antigen ofPlasmodium falciparum. Immunization of mice withEscherichia coli-produced recombinant protein of the SERA N-terminal domain (SE47′) induced an antiserum that was inhibitory to parasite growth in vitro. Affinity-purified mouse antibodies specific to the recombinant protein inhibited parasite growth between the schizont and ring stages but not between the ring and schizont stages. When Percoll-purified schizonts were cultured with the affinity-purified SE47′-specific antibodies, schizonts and merozoites were agglutinated. Indirect-immunofluorescence assays with unfixed parasite cells showed that SE47′-specific immunoglobulin G (IgG) bound to SERA molecules on rupturing schizonts and merozoites but the IgG did not react with the schizont-infected erythrocytes (RBC). Furthermore, double-fluorescence staining against SE47′-specific IgG and anti-human RBC membrane IgG showed that the RBC membrane disappeared from SE47′-specific-IgG-bound schizonts after cultivation. These observations suggest that the SE47′-specific antibodies inhibit parasite growth by cross-linking SERA molecules that are associated with merozoites in rupturing schizonts with partly broken RBC and parasitophorous vacuole membranes, blocking merozoite release.
Ultrasonic breast imaging using a wave-equation migration method (2003)

Reflection imaging has the potential to produce higher-resolution breast images than transmission tomography; however, the current clinical reflection imaging technique yields poor-quality breast images due to speckle. We present a new ultrasonic breast imaging method for obtaining high-resolution and clear breast images using ultrasonic reflection data acquired by a new ultrasonic scanning device that provides a better illumination of targets of interest than the clinical B-scan. The new imaging method is based on the solution of the wave equation in Cartesian coordinates and is implemented using Fast Fourier Transform algorithms. We apply the new ultrasonic breast imaging method to two ultrasonic data sets obtained using an experimental ultrasound scanner recently developed by the Karmanos Cancer Institute. One data set was acquired for a "cyst" phantom using 360 transmitter positions and 321 receiver positions along a 20-cm diameter ring. Another data set was collected with 180 transmitter positions and 1601 receiver positions along a 30-cm diameter ring with the breast specimen located at the center of the ring. We report on the breast imaging results for these two data sets using the new breast imaging method. The results demonstrate that the wave-equation-based ultrasonic breast imaging has the potential to produce high-resolution breast images.
Generating Contrastive Explanations with Monotonic Attribute Functions. (2019)

Explaining decisions of deep neural networks is a hot research topic with applications in medical imaging, video surveillance, and self driving cars. Many methods have been proposed in literature to explain these decisions by identifying relevance of different pixels, limiting the types of explanations possible. In this paper, we propose a method that can generate contrastive explanations for such data where we not only highlight aspects that are in themselves sufficient to justify the classification by the deep model, but also new aspects which if added will change the classification. In order to move beyond the limitations of previous explanations, our key contribution is how we define addition for such rich data in a formal yet humanly interpretable way that leads to meaningful results. This was one of the open questions laid out in in Dhurandhar this http URL. (2018) [6], which proposed a general framework for creating (local) contrastive explanations for deep models, but is limited to simple use cases such as black/white images. We showcase the efficacy of our approach on three diverse image data sets (faces, skin lesions, and fashion apparel) in creating intuitive explanations that are also quantitatively superior compared with other state-of-the-art interpretability methods. A thorough user study with 200 individuals asks how well the various methods are understood by humans and demonstrates which aspects of contrastive explanations are most desirable.
Pre-TCRα supports CD3-dependent reactivation and expansion of TCRα-deficient primary human T-cells (2014)

Chimeric antigen receptor technology offers a highly effective means for increasing the anti-tumor effects of autologous adoptive T-cell immunotherapy, and could be made widely available if adapted to the use of allogeneic T-cells. Although gene-editing technology can be used to remove the alloreactive potential of third party T-cells through destruction of either the α or β T-cell receptor (TCR) subunit genes, this approach results in the associated loss of surface expression of the CD3 complex. This is nonetheless problematic as it results in the lack of an important trophic signal normally mediated by the CD3 complex at the cell surface, potentially compromising T-cell survival in vivo, and eliminating the potential to expand TCR-knockout cells using stimulatory anti-CD3 antibodies. Here, we show that pre-TCRα, a TCRα surrogate that pairs with TCRβ chains to signal proper TCRβ folding during T-cell development, can be expressed in TCRα knockout mature T-cells to support CD3 expression at the cell surface. Cells expressing pre-TCR/CD3 complexes can be activated and expanded using standard CD3/CD28 T-cell activation protocols. Thus, heterologous expression of pre-TCRα represents a promising technology for use in the manufacturing of TCR-deficient T-cells for adoptive immunotherapy applications.
CMOS imager based on single photon avalanche diodes (2005)

In this paper we report on a 32/spl times/32 optical imager based on single photon avalanche diodes integrated in CMOS technology. The maximum measured dynamic range is 120dB and the minimum noise equivalent intensity is 1.3 /spl times/ 10/sup -3/ lx. The minimum integration time per pixel is 4 /spl mu/s. The output of each pixel is digital, thereby requiring no complex read-out circuitry, no amplification, no sample and hold, and no ADC.
Analyzing Strongly Nonlinear Multitone Circuits by Multi-Time Methods (1998)

Harmonic balance and traditional time-domain simulation techniques are limited in their applicability when strong nonlinearities and multi-tone signals are both present. In this paper, new simulation algorithms are described and used to analyse strongly nonlinear microwave circuits with multi-tone excitations. The techniques are based on representing multi-tone waveforms as functions of several "time" variables, and solving a partial differential form of the circuit equations using time-domain methods. The methods scale linearly with increasing circuit size, regardless of the number of nonlinearities. A switching mixer is analyzed using the new methods. Speedups of over two orders of magnitude over traditional techniques are obtained. Moreover, the multi-time representations obtained from the new methods provide intuitive and powerful visualisations of the operation of the circuit.
Hybrid planar and optical fiber waveguides integrated with epsilon-near-zero materials (2021)

In this talk, I will present our recent development on the “Meta”-optical fiber integrated with optical plasmonic nanocircuits and epsilon-near-zero (ENZ) materials. I will present the integrated plasmonic network (e.g. directional coupler and resonator) powered by the core mode of optical fiber. I will also discuss the first experimental demonstration of optically confined ENZ resonance excitation in an optical fiber waveguide uniformly coated with AZO nanolayer. The integration of plasmonic/ENZ nanocircuits and optical fiber will open the path to revolutionary ultracompact in-fiber optical devices for optical communication, imaging, sensing/laser applications. The authors acknowledge the supports partially by the Air Force Office of Scientific Research (AFOSR, Award number: FA9550-19-1-0274) and Defense Advanced Research Projects Agency (grant number N66001-17-1-4047).
Angiotensin Converting Enzyme Inhibitors: Animal Experiments Suggest a New Pharmacological Treatment for Alcohol Abuse in Humans (1988)

The prevalence of heavy alcohol consumption is a major problem of increasing proportions throughout the world. Although alcohol sensitizing drugs and more recently serotonin uptake inhibitors are drug interventions with some following, their long term beneficial consequences have yet to be demonstrated. In recent years, we have demonstrated that manipulating activity in the renin-angiotensin system will dramatically alter voluntary alcohol consumption in rats. Based on these findings, the present study evaluated the ability of a class of drugs known as the angiotensin converting enzyme inhibitors to reduce voluntary alcohol drinking in laboratory animals. These drugs prevent the conversion of angiotensin I to angiotensin II. They have been licensed for use in Europe and North America and are indicated in the treatment of hypertension. Our experiments showed that both captopril (Capoten, Squibb) and enalapril (Vasotec, Merck Sharpe & Dohme) can reduce alcohol drinking in both normotensive and hypertensive animals regardless of whether the pattern of intake is in a bout or of a less exaggerated nature. Furthermore, this change in alcohol intake can occur without concomitant changes in blood pressure, plasma renin activity, overall fluid balance, or the distribution and metabolism of alcohol. Taken together these findings suggest that the angiotensin converting enzyme inhibitors should be evaluated in a clinical setting for they may prove to be a useful new treatment or treatment adjunct for alcohol abuse in humans.
Supramolecular complexes as photoinitiated electron collectors: applications in solar hydrogen production (2006)

The conversion of light energy into chemical energy is a focus of much research. Solar energy is of sufficient energy to drive water splitting to generate hydrogen and oxygen. The splitting of water involves multi-electron reactions and the breaking and formation of chemical bonds. Light driven water splitting has therefore proven elusive. Supramolecular complexes that contain ruthenium or osmium polyazine units can efficiently absorb visible light and generate charge transfer excited states. While many supramolecular complexes can absorb solar light efficiently, few are able to convert this energy into chemical energy via the conversion of a readily available chemical feedstock into a fuel. One process that is proposed as applicable for light to energy conversion is photoinitiated electron collection. Photoinitiated electron collection is a multi-step process whereby light energy is used to collect reducing equivalents. The collection of reducing equivalents is an essential step in the use of light energy to drive multi-electron reactions such as water splitting. The development of mixed-metal complexes as photoinitiated electron collectors is described, including the factors impacting device function. The use of Rh based electron collectors allows for the reducing equivalents generated by photoinitiated electron collection to be transferred to substrates, such as the reduction of water to produce hydrogen.
Distributed on-fiber thin film heaters for Bragg gratings with adjustable chirp (1999)

This letter describes a fiber Bragg grating device that has tunable chirp. It relies on a distributed on-fiber resistive heater that consists of a thin metal film deposited onto the outer surface of a bare fiber; the thickness of this film varies continuously with position along the fiber. The physics of heat flow and diffusion in these structures leads to temperature gradients that follow, to a remarkably good approximation, the local resistance of the tapered metal film. This temperature distribution produces a chirp with a geometry that is defined by the thickness profile of the film and at a rate that can be adjusted by changing the current. Finite element modeling illuminates aspects of the flow of heat in these structures, and optical measurements demonstrate important characteristics of the devices.