gebhart/patrepeval huggingface dataset:
Theoretical and experimental analysis of wire segment holograms for statistical interconnect metrology (1998)

Theoretical and experimental results using computer generated wire segment holograms for statistical interconnect metrology are presented. Test structures have been constructed using a process capable of imaging 1-/spl mu/m features and consist of arrays of wire segments illuminated by a He-Ne Laser. Since the holograms are fabricated at the same time as actual wires on the wafer, the quality of the projected image correlates with the emergence of global feature patterning errors. Specifically, this paper presents data on the effect of varied exposure time on the intensity of the projected image. An initial statistical analysis indicates that the test structures are capable of detecting variations in wire geometry which are approximately 1.0% of the nominal wire width. It is anticipated that significant improvements to this level of sensitivity can be obtained by optimization of the holographic encoding process and test image selection.
Shape‐Selective Zeolites Promote Ethylene Formation from Syngas via a Ketene Intermediate (2018)

Abstract Syngas conversion by Fischer–Tropsch synthesis (FTS) is characterized by a wide distribution of hydrocarbon products ranging from one to a few carbon atoms. Reported here is that the product selectivity is effectively steered toward ethylene by employing the oxide‐zeolite (OX‐ZEO) catalyst concept with ZnCrO x ‐mordenite (MOR). The selectivity of ethylene alone reaches as high as 73 % among other hydrocarbons at a 26 % CO conversion. This selectivity is significantly higher than those obtained in any other direct syngas conversion or the multistep process methanol‐to‐olefin conversion. This highly selective pathway is realized over the catalytic sites within the 8‐membered ring (8MR) side pockets of MOR via a ketene intermediate rather than methanol in the 8MR or 12MR channels. This study provides substantive evidence for a new type of syngas chemistry with ketene as the key reaction intermediate and enables extraordinary ethylene selectivity within the OX‐ZEO catalyst framework.
A Rational Approach for Creating Peptides Mimicking Antibody Binding (2019)

This study reports a novel method to design peptides that mimic antibody binding. Using the Knob-Socket model for protein-protein interaction, the interaction surface between Cetuximab and EGFR was mapped. EGFR binding peptides were designed based on geometry and the probability of the mapped knob-sockets pairs. Designed peptides were synthesized and then characterized for binding specificity, affinity, cytotoxicity of drug-peptide conjugate and inhibition of phosphorylation. In cell culture studies, designed peptides specifically bind and internalize to EGFR overexpressing cells with three to four-fold higher uptake compared to control cells that do not overexpress EGFR. The designed peptide, Pep11, bound to EGFR with K<sub>D</sub> of 252 nM. Cytotoxicity of Monomethyl Auristatin E (MMAE)-EGFR-Pep11 peptide-drug conjugate was more than 2,000 fold higher against EGFR overexpressing cell lines A431, MDA MB 468 than control HEK 293 cells which lack EGFR overexpression. MMAE-EGFR-Pep11 conjugate also showed more than 90-fold lower cytotoxicity towards non-EGFR overexpressing HEK 293 cells when compared with cytotoxicity of MMAE itself. In conclusion, a method that can rationally design peptides using knob-socket model is presented. This method was successfully applied to create peptides based on the antigen-antibody interaction to mimic the specificity, affinity and functionality of antibody.
<title>Microlens array for staring infrared imager</title> (1991)

This paper describes the fabrication and testing of 64 X 96 arrays of microlenses used for fill-factor enhancement of uncooled infrared detector arrays. Each lenslet represents a f/0.9 Fresnel phase lens at 10 micrometers wavelength. All arrays were etched into silicon wafers as either 8-level or 16-level staircase kinoforms. When integrated with a detector array having 20 fill factor, these microlens arrays were capable of increasing the magnitude of the measured signal with f/2.2 fore-optics by 2.5-fold.
CONTINUOUS ANALYSIS OF ATMOSPHERIC AEROSOLS USING MICROCHIP ELECTROPHORESIS (2008)

Atmospheric aerosols represent the most significant unknown for predicting the impact of human activity on the atmosphere. To understand their impact, we must also understand their composition. Here, we have developed a miniaturized total analysis system to collect aerosol particles and analyze their components by microchip capillary electrophoresis. The microchip reservoirs are interconnected via air ducts to compensate for a sampling-induced pressure drop. Conductivity detection is performed in a novel bubble cell zone that improves compatibility with high separation fields. The coupled system allows for semi-continuous measurements of common aerosol components with one minute time resolution.
An optical processing system using photoanisotropy in a bacteriorhodopsin film (2002)

We have successfully demonstrated a real-time, self-adaptive optical image processing system using the photoinduced dichroic characteristics of a bacteriorhodopsin film. The advantages of the system are simplicity in operation with no alignment required at the Fourier plane to perform the processing, no vibration isolation systems are required and even a coherent source is not a requirement to perform the experiment.
Sewage Sludge/Metal Sludge/Waste Oil Composites as Catalysts for Desulfurization of Digester Gas (2007)

Composite adsorbents based in mixtures of sewage sludge/metal sludge and waste oil were prepared by pyrolysis at 650 and 950 °C. The materials were characterized using adsorption of nitrogen, Fourier transform infrared (FTIR), X-ray diffraction (XRD), inductively couple plasma (ICP), scanning electron microscopy (SEM), pH measurements, and thermal analysis. As-received materials were used as adsorbents of hydrogen sulfide from digester gas. To evaluate the importance of waste oil addition, the results were compared to those obtained on sewage sludge/metal sludge composites. The results clearly showed the importance of the carbonaceous phase from the oil precursor for enhancing the catalytic properties. Besides providing porosity, necessary for a dispersion of inorganic sludge base catalyst, an addition of a carbon phase alters the surface chemistry via providing a more reducing environment during the pyrolysis and via providing the carbon for more efficient formation of such compounds as carbides. The results indicated that the adsorbents obtained at 950 °C are much more active in the process of hydrogen sulfide oxidation than those obtained at 650 °C. In the case of the high temperature of heat treatment, longer treatment is beneficial for the development of surface catalytic properties. As a result of this, the carbon phase was stabilized via increasing its degree of aromatization and it became more porous owing to the release of activation agents from the decomposition and rearrangement of an inorganic phase. In very small pores, oxygen important for oxidation can be chemisorbed.
Fabrication and Analysis of Spatially Uniform Field Electrokinetic Flow Devices:  Theory and Experiment (2005)

A uniform-field design approach can improve the performance of microanalytical, chip-based devices for a number of applications, including separations and sample preparation. The faceted prism paradigm allows the design of microfluidic devices possessing spatially uniform fields in electrokinetically driven flows. We present the first quantitative study of the velocity fields obtained using faceted interfaces between deep and shallow channel sections. Electrokinetic flows were generated in a series of wet-etch fabricated microfluidic channels. The resulting velocity fields were analyzed by particle image velocimetry and compared with simulations of the two-dimensional Laplace equation using both the designed channel geometry and the as-fabricated channel geometry. This analysis found localized differences between the designed and observed flow fields that were directly attributable to the limitations of isotropic substrate etching. Simulations using the as-fabricated channel geometry reproduced the experimental electrokinetic velocity field, quantitatively accounting for speed field variations due to the limits of the fabrication method. The electrokinetic speed fields were also compared to corresponding pressure-driven speed fields.
Studies of MEMS Acoustic Sensors as Implantable Microphones for Totally Implantable Hearing-Aid Systems (2009)

There is a need for high-quality implantable microphones for existing semiimplantable middle-ear hearing systems and cochlear prosthesis to make them totally implantable, thus overcoming discomfort, inconvenience, and social stigma. This paper summarizes and compares the results of an in-vitro study on three design approaches and the feasibility of using microelectromechanical system acoustic sensors as implantable microphones to convert the umbo vibration directly into a high-quality sound signal. The requirements of sensors were selected including the ability to withstand large body shocks or sudden changes of air pressure. Umbo vibration characteristics were extracted from literature and laboratory measurement data. A piezoelectric vibration source was built and calibrated to simulate the umbo vibration. Two laboratory models of the acoustic sensor were studied. The model-A device, using electrets-microphone as the sensor, was designed and tested in the laboratory and on temporal bones. The results verify that the laboratory measurement is consistent with the temporal bone characterization and achieves a near flat frequency response with a minimum detectable signal of a 65-dB sound-pressure-level (SPL) at 1 kHz. The model-B sensor was then designed to increase the sensitivity and provide an easy mounting on umbo. The model-B device can detect 40-dB SPL sound in the 1-2 kHz region, with 100-Hz channel bandwidth. The results of model-A and model-B displacement sensors and the acceleration sensor are summarized and compared. A preliminary design of the implantable displacement sensor for totally implantable hearing-aid systems is also presented.
Synthesis and Characterization of Magnesium Oxide Supported Catalysts with a Meso-Macropore Structure (2013)

Nanostructured magnesium oxide catalyst support materials with controlled morphology and size were synthesized from a supercritical carbon dioxide/ethanol solution via chemical reaction of soluble precursors and subsequent thermal decomposition. Leaf-like magnesium hydroxide precursors with high specific surface area were formed by a low-temperature chemical reaction at below 140 degrees C, while magnesium carbonate cubes with a very low surface area less than 3.3 m2/g were formed by temperature-induced phase transition from a loose to a dense structure during carbonation reaction at above 150 degrees C. The specific surface area has significantly increased higher than 90 m2/g due to the creation of highly porous MgO cubes with mesopore structure formed after thermal decomposition of the magnesium carbonate precursors. Ni-magnesium oxide catalysts with bimodal pore structure were finally formed by the consequence of packing heterogeneity of the porous magnesium oxides with different morphologies and sizes.
Genomic and Expression Profiling of Adrenocortical Carcinoma: Application to Diagnosis, Prognosis and Treatment (2009)

Adrenocortical carcinoma (ACC) is an aggressive endocrine tumor with a poor 5-year survival rate of 10–20%. Current therapy is often ineffective and may be associated with intolerable side effects. Although ACC is extremely rare, recent advances in genomic and expression profiling, coupled with knowledge gained from the study of the inherited syndromes that increase ACC risk, are beginning to bring together a picture of a tumor type dependent on p53, the G2/M cell cycle transition and IGF2 stimulation. Nevertheless, ACC remains a heterogeneous disease. Only recently have sufficient tumors been characterized and results published to permit an exploration of this diversity. Advances in treatment will depend on exploiting those pathways already implicated in ACC, along with those yet to be identified, and testing those treatments in better models of the disease than the three cell lines that currently exist and are widely available to the community.
Gene structure and expression of the<i>Mbol</i>restriction − modification system (1993)

The genes from Moraxella bovis encoding the MboI restriction--modification system were cloned and expressed in Escherichia coli. Three open reading frames were found in the sequence containing the genes. These genes, which we named mboA, mboB, and mboC, had the same orientation in the genome. Genes mboA and mboC encoded MboI methyltransferases (named M.MboA and M.MboC) with 294 and 273 amino acid residues, respectively. The mboB gene coded for MboI restriction endonuclease (R.MboI) with 280 amino acid residues. Recombinant E.coli-MBOI, which contained the whole MboI system, overproduced R.MboI. R.MboI activity from E.coli-MBOI was 480-fold that of M.bovis. The amino acid sequences deduced from these genes were compared with those of other restriction--modification systems. The protein sequences of the MboI system had 38-49% homology with those of the DpnII system.
A two step, three color, white-light pseudocolor encoding process (1988)

Pseudocolor encoding is a commonly used enhancement procedure for grey level images. One of the classical techniques for three color white light pseudocolor encoding was presented by Yu et al. (1984). A variation of this three color encoding method is described that uses moire fringe patterns from two encodings to carry the information previously obtained from the third encoding. Both a theoretical description and experimental results are presented.
Photocatalytic activity of quantum dot–magnetite nanocomposites to degrade organic dyes in the aqueous phase (2013)

Quantum dots of Cd(Se,S) and fluorescent magnetic nanocomposites (Cd(Se,S)–magnetite) were used as photocatalytic agents in the photodegradation of methylene blue (MB) under UV irradiation at pH 6.5. Quantum dots and magnetic nanocomposites were characterized by X-ray diffraction (XRD), UV-Vis, photoluminescence and Fourier Transform Infrared (FT-IR) spectroscopy. The photo-induced degradation of MB was monitored using High Performance Liquid Chromatography (HPLC) at 660 nm and titanium dioxide (anatase and aeroxide P25 forms) was used as the photocatalyst standard. A degradation of 99.1% and 90.0% of MB was achieved in the presence of 160 mg L−1-quantum dots and the magnetic nanocomposite, respectively, after 4.5 hours of UV-irradiation. Instead, 45.9% and 100% of MB degradation was achieved using 160 mg L−1 of TiO2 anatase and aeroxide P25, respectively. The degradation products were studied by mass spectrometry (MS) and the results evidenced the formation of azure B, A, C and phenothiazine. The reuse of the magnetic nanocomposites (i.e., after one photo-degradation cycle) allowed a maximum photo-degradation capacity of 65%. The results suggested that the nanocomposite has 10% less photodegradation capacity than the widely used catalytic agents such as TiO2 aeroxide P25.
Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry (2019)

Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent acquisition (DDA) and increased throughput over targeted methods. Therefore, here we introduce DIA to QCLMS by extending a widely used DIA software, Spectronaut, to also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS<sup>3</sup>) was used to evaluate this workflow. Out of the 414 identified unique residue pairs, 292 (70%) were quantifiable across triplicates with a coefficient of variation (CV) of 10%, with manual correction of peak selection and boundaries for PSMs in the lower quartile of individual CV values. This compares favorably to DDA where we quantified cross-links across triplicates with a CV of 66%, for a single protein. We found DIA-QCLMS to be capable of detecting changing abundances of cross-linked peptides in complex mixtures, despite the ratio compression encountered when increasing sample complexity through the addition of <i>E. coli</i> cell lysate as matrix. In conclusion, the DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS.
Differentiation of Feline Immunodeficiency Virus Vaccination, Infection, or Vaccination and Infection in Cats (2008)

With the exception of viral isolation, the discriminant ELISA is the most reliable assay for diagnosis of FIV. A practical strategy for the diagnosis of FIV infection would be to use existing commercial FIV antibody assays as screening tests. Negative results with commercial assays are highly reliable predictors for lack of infection. Positive results can be confirmed with the discriminant ELISA. If the discriminant ELISA is negative, the cat is probably vaccinated against FIV but not infected. Positive results are likely to represent infection.
Ultralong Dephasing Times in Solid-State Spin Ensembles via Quantum Control (2018)

Quantum spin dephasing is caused by inhomogeneous coupling to the environment, with resulting limits to the measurement time and precision of spin-based sensors. The effects of spin dephasing can be especially pernicious for dense ensembles of electronic spins in the solid-state, such as for nitrogen-vacancy (NV) color centers in diamond. We report the use of two complementary techniques, spin bath control and double quantum coherence, to enhance the inhomogeneous spin dephasing time ($T_2^*$) for NV ensembles by more than an order of magnitude. In combination, these quantum control techniques (i) eliminate the effects of the dominant NV spin ensemble dephasing mechanisms, including crystal strain gradients and dipolar interactions with paramagnetic bath spins, and (ii) increase the effective NV gyromagnetic ratio by a factor of two. Applied independently, spin bath control and double quantum coherence elucidate the sources of spin dephasing over a wide range of NV and spin bath concentrations. These results demonstrate the longest reported $T_2^*$ in a solid-state electronic spin ensemble at room temperature, and outline a path towards NV-diamond magnetometers with broadband femtotesla sensitivity.
Development of a prototype lignin concentration sensor (1993)

The US Department of Energy, Office of Industrial Technologies, is sponsoring a research and development program for the development of a real-time, in-situ sensor to measure the concentration of lignin in wood pulp. The program is composed of phase I showing feasibility which is now complete, phase II for development and testing of a Field Prototype, in progress, Phase III commercialization. Phase I work (funded entirely by B&W) demonstrated a correlation between the fluorescence intensity and lignin concentration (as measured by TAPPI procedure, T 236 hm-85 Kappa Number of Pulp) for undiluted wood pulp samples. In Phase II, a laboratory test program directed at characterizing the fluorescence of wood pulp has been conducted as a prelude to the design of a prototype sensor. The current report summarizes the testing completed in Phase I and documents the Phase II laboratory testing completed through December 1991. Future Phase II efforts include additional laboratory testing, design and fabrication of a prototype sensor, and field testing of the prototype sensor. Phase III of the program will concentrate on the incorporation of the sensor into a control system and commercialization of the sensor.
Performance metrics of an optical spectral imaging system for intra-operative assessment of breast tumor margins (2010)

As many as 20-70% of patients undergoing breast conserving surgery require repeat surgeries due to a close or positive surgical margin diagnosed post-operatively [1]. Currently there are no widely accepted tools for intra-operative margin assessment which is a significant unmet clinical need. Our group has developed a first-generation optical visible spectral imaging platform to image the molecular composition of breast tumor margins and has tested it clinically in 48 patients in a previously published study [2]. The goal of this paper is to report on the performance metrics of the system and compare it to clinical criteria for intra-operative tumor margin assessment. The system was found to have an average signal to noise ratio (SNR) >100 and <15% error in the extraction of optical properties indicating that there is sufficient SNR to leverage the differences in optical properties between negative and close/positive margins. The probe had a sensing depth of 0.5-2.2 mm over the wavelength range of 450-600 nm which is consistent with the pathologic criterion for clear margins of 0-2 mm. There was <1% cross-talk between adjacent channels of the multi-channel probe which shows that multiple sites can be measured simultaneously with negligible cross-talk between adjacent sites. Lastly, the system and measurement procedure were found to be reproducible when evaluated with repeated measures, with a low coefficient of variation (<0.11). The only aspect of the system not optimized for intra-operative use was the imaging time. The manuscript includes a discussion of how the speed of the system can be improved to work within the time constraints of an intra-operative setting.
Gelation of Regenerated Fibroin Solution (2008)

Silk fibroin is a high molecular weight multiblock ampiphillic protein known for its ability to form high strength fibers. It is also biocompatible; silk sutures have been traditionally used for many centuries. Recently, there has been much interest in making silk hydrogels for applications ranging from tissue engineering to controlled delivery. Fibroin gels can be formed from aqueous solutions by changing one or more state variables such as pH, temperature and ionic strength. In this work we present our investigations on the gelation of aqueous fibroin solutions derived from Bombyx Mori silk using light scattering, confocal microscopy and rheological techniques.
Outlier detection by active learning (2006)

Most existing approaches to outlier detection are based on density estimation methods. There are two notable issues with these methods: one is the lack of explanation for outlier flagging decisions, and the other is the relatively high computational requirement. In this paper, we present a novel approach to outlier detection based on classification, in an attempt to address both of these issues. Our approach isbased on two key ideas. First, we present a simple reduction of outlier detection to classification, via a procedure that involves applying classification to a labeled data set containing artificially generated examples that play the role of potential outliers. Once the task has been reduced to classification, we then invoke a selective sampling mechanism based on active learning to the reduced classification problem. We empirically evaluate the proposed approach using a number of data sets, and find that our method is superior to other methods based on the same reduction to classification, but using standard classification methods. We also show that it is competitive to the state-of-the-art outlier detection methods in the literature based on density estimation, while significantly improving the computational complexity and explanatory power.