gebhart/patrepeval huggingface dataset:
Discrimination of 5‘-GGGG-3‘, 5‘-GCGC-3‘, and 5‘-GGCC-3‘ Sequences in the Minor Groove of DNA by Eight-Ring Hairpin Polyamides (1997)

Eight-ring hairpin polyamides which differ only by the linear arrangement of pyrrole (Py) and imidazole (Im) amino acids were designed for recognition of six base pair DNA sequences containing four contiguous G,C base pairs. The respective DNA binding properties of three polyamides, ImImPyPy-γ-ImImPyPy-β-Dp, ImPyImPy-γ-ImPyImPy-β-Dp, and ImImImIm-γ-PyPyPyPy-β-Dp, were analyzed by footprinting and affinity cleavage on a DNA fragment containing the respective match sites 5‘-TGGCCA-3‘, 5‘-TGCGCA-3‘, and 5‘-TGGGGA-3‘. Quantitative footprint titrations demonstrate that ImImPyPy-γ-ImImPyPy-β-Dp binds the designed match site 5‘-TGGCCA-3‘ with an equilibrium association constant of Ka = 1 × 1010 M-1 and >250-fold specificity versus the mismatch sequences, 5‘-TGCGCA-3‘ and 5‘-TGGGGA-3‘. The polyamides ImPyImPy-γ-ImPyImPy-β-Dp and ImImImIm-γ-PyPyPyPy-β-Dp recognize their respective 5‘-TGCGCA-3‘ and 5‘-TGGGGA-3‘ match sites with reduced affinity relative to ImImPyPy-γ-ImImPyPy-β-Dp, but again with high specificity with regard to mismatch sites. These results expand the DNA sequence repertoire targeted by pyrrole-imidazole polyamides and identify sequence composition effects which will guide further second-generation polyamide design for DNA recognition.
<title>Raman detection of carotenoid pigments in the human retina</title> (2001)

We have used resonant Raman scattering as a novel, non- invasive, in-vivo optical technique to measure the concentration of macular carotenoid pigments in the living human retina of young and elderly adults. Using a backscattering geometry and resonant molecular excitation in the visible, we measure the Raman peaks originating from the single- and double-bond stretch vibrations of the (pi) - electron conjugated molecule's carbon backbone. The Raman signals scale linearly with carotenoid content while the required laser excitation is well below safety limits for macular exposure. Measured macular pigment levels decline significantly with increasing age. The Raman technique is objective and quantitative and may lead to a new method for rapid screening of carotenoid pigment levels in large populations at risk for vision loss from age-related macular degeneration, the leading cause of blindness in the elderly in the United States.
Disparate Mutations Confer Therapeutic Gain of Hsp104 Function (2015)

Hsp104, a protein disaggregase from yeast, can be engineered and potentiated to counter TDP-43, FUS, or α-synuclein misfolding and toxicity implicated in neurodegenerative disease. Here, we reveal that extraordinarily disparate mutations potentiate Hsp104. Remarkably, diverse single missense mutations at 20 different positions interspersed throughout the middle domain (MD) and small domain of nucleotide-binding domain 1 (NBD1) confer a therapeutic gain of Hsp104 function. Moreover, potentiation emerges from deletion of MD helix 3 or 4 or via synergistic missense mutations in the MD distal loop and helix 4. We define the most critical aspect of Hsp104 potentiation as enhanced disaggregase activity in the absence of Hsp70 and Hsp40. We suggest that potentiation likely stems from a loss of a fragilely constrained autoinhibited state that enables precise spatiotemporal regulation of disaggregase activity.
Totally synthetic steroid heterocycles. Part 1. Synthesis of intermediate precursors of 16-oxa- and 16-thia-D-homoestrogens (1978)

The total synthesis of 16-oxa- and 16-thia-D-homoestrogen derivatives is described. A straightforward synthesis of 16-thia- and 16-oxa-3-methoxy-D-homoestra-1,3,5(10),8,14-pentaen-17a-one (8a and b) and their 6-didehydro derivatives (24a and b) is achieved by condensation of 2-methyl-5-thia- and 5-oxacyclohexane-1,3-dione (1a and b) with 6-methoxy-1,2,3,4-tetrahydronaphthylidene-ethylisothiuronium acetate (5). The ethyl homologues (9a and b) are also prepared using the corresponding diones (2a and b). An alternative route to the estrapentaene (8a) starting with Michael addition of 6-m-methoxyphenylhex-1-en-3-one (25) to the dione (1a) also produces 3-methoxy-9,10-seco-16-thia-D-homoestra-1,3,5(10),8(14)-tetraene-9,17a-dione (29).
Waveguide‐integrated superconducting nanowire single‐photon detectors (2017)

Abstract Integration of superconducting nanowire single‐photon detectors with nanophotonic waveguides is a key technological step that enables a broad range of classical and quantum technologies on chip‐scale platforms. The excellent detection efficiency, timing and noise performance of these detectors have sparked growing interest over the last decade and have found use in diverse applications. Almost 10 years after the first waveguide‐coupled superconducting detectors were proposed, here, we review the performance metrics of these devices, compare both superconducting and dielectric waveguide material systems and present prominent emerging applications.
Semiautomatic Optimization of External Beam Radiation Treatment Planning (1974)

In this method, the operator/therapist is enabled to assign dosage constraints directly to points in the patient's cross section rather than field strengths as in the programmed console. Linear programming then solves for field strengths, optimizing for uniformity within the constraints imposed by the operator, and aiding also in the selection of wedges and beam directions. The iterative nature of the interaction between operator and machine is stressed. Two examples of treatment plans are simulated through the system. Computer calculation of field strengths combined with rapid interaction allows the therapist to examine more variations of beam directions than otherwise currently feasible.
Demonstration of a laser-based ultrasonic inspection system for industrial applications (1996)

Summary form only given. We have fabricated an automated, computer-controlled prototype laser-based ultrasound system, enabling inspection of real-world workpieces, including weld-joint dimensioning of rough-cut components using neural network classification, detection of inclusions in aluminum billets, hardness, and remote temperature and thickness measurements. Our system, called Compensated Laser Ultrasonic Evaluation, or CLUE, employs various forms of all-optical wavefront compensation, including nonlinear optical phase conjugation and nonsteady-state photoinduced emf.
Antitumor efficacy of D2C7-(scdsFv)-PE38KDEL, a novel immunotoxin targeting EGFRwt and EGFRvIII, by convection-enhanced delivery in orthotopic brain tumor mouse models (2013)

Meeting abstracts The epidermal growth factor receptor (EGFR) gene is most frequently amplified and overexpressed, along with its truncated mutant, EGFRvIII, in glioblastomas. We tested the antitumor efficacy of the recombinant immunotoxin, D2C7-(scdsFv)-PE38KDEL (D2C7-IT), which is reactive with a
Electrochemical Filter Design for the Removal of CO Contaminant in Reformate Hydrogen (2009)

Carbon monoxide contamination in reformate hydrogen decreases the performance of the proton exchange membrane (PEM) fuel cells significantly through anode poisoning. The cost, in terms of parasitic power losses and reactor volume for decreasing the CO concentration to a tolerable level, can be high. Here, we demonstrate a PEM-based twin-cell electrochemical filter that offers the possibility of a compact and efficient device to reduce the CO concentration to 10 ppm or lower. The potential and flow are switched between the two filter cells so that alternative CO adsorption and oxidation occur in each cell, while providing a continuous flow of H2 to a fuel cell. The effects of filter switching time and applied potential on CO concentration of gas exiting the filter are presented for a 1,000 ppm CO in nitrogen anode stream and a 4% H2/N2 cathode stream flowing at 100 and 40 cc/min, respectively.
Achieving Ultralow Wear with Stable Nanocrystalline Metals (2018)

Recent work suggests that thermally stable nanocrystallinity in metals is achievable in several binary alloys by modifying grain boundary energies via solute segregation. The remarkable thermal stability of these alloys has been demonstrated in recent reports, with many alloys exhibiting negligible grain growth during prolonged exposure to near-melting temperatures. Pt-Au, a proposed stable alloy consisting of two noble metals, is shown to exhibit extraordinary resistance to wear. Ultralow wear rates, less than a monolayer of material removed per sliding pass, are measured for Pt-Au thin films at a maximum Hertz contact stress of up to 1.1 GPa. This is the first instance of an all-metallic material exhibiting a specific wear rate on the order of 10<sup>-9</sup> mm<sup>3</sup> N<sup>-1</sup> m<sup>-1</sup> , comparable to diamond-like carbon (DLC) and sapphire. Remarkably, the wear rate of sapphire and silicon nitride probes used in wear experiments are either higher or comparable to that of the Pt-Au alloy, despite the substantially higher hardness of the ceramic probe materials. High-resolution microscopy shows negligible surface microstructural evolution in the wear tracks after 100k sliding passes. Mitigation of fatigue-driven delamination enables a transition to wear by atomic attrition, a regime previously limited to highly wear-resistant materials such as DLC.
Abstract 15969: A Novel Proteomic Predictor of Cholesterol Efflux Capacity Demonstrates Inverse Association With Cardiovascular Disease (2018)

Introduction: Cholesterol efflux capacity (CEC) is a cell-based measure of HDL function. Low CEC has been shown to be associated with cardiovascular disease. However, cell-based CEC assay is comple...
Low-jitter laser-triggered vacuum switch using a composite target (1988)

A laser-triggered high-voltage vacuum switch with a composite KCl/Ti target pellet is described. The switch triggers reliably for 532-nm laser input energies of 20 mu J corresponding to a peak irradiance of 1 MW/cm/sup 2/. Jitter times of less than +or-15 ns and delay times of less than 100 ns are observed. Several experiments were performed to explore the operation of the switch. It was found that the amount of energy needed to trigger the switch and the jitter time was strongly dependent on the position of the pellet relative to the cathode. It is noted that the mechanism responsible for the operation of the switch is not completely understood.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<title>DNA sequencing by single molecule detection of labeled nucleotides sequentially cleaved from a single strand of DNA</title> (1993)

We are developing a laser-based technique for the rapid sequencing of large DNA fragments (several kb in size) at a rate of 100 to 1000 bases per second. Our approach relies on fluorescent labeling of the bases in a single fragment of DNA, attachment of this labeled DNA fragment to a support, movement of the supported DNA into a flowing sample stream, sequential cleavage of the end nucleotide from the DNA fragment with an exonuclease, and detection of the individual fluorescently labeled bases by laser-induced fluorescence.
Tracking of cyclic motion with phase‐contrast cine MR velocity data (1995)

A method of computing trajectories of objects by using velocity data, particularly as acquired with phase-contrast magnetic resonance (MR) imaging, is presented. Starting from a specified location at one time point, the method recursively estimates the trajectory. The effects of measurement noise and eddy current-induced velocity offsets are analyzed. When the motion is periodic, trajectories can be computed by integrating in both the forward and backward temporal directions, and a linear combination of these trajectories minimizes the effect of velocity offsets and maximizes the precision of the combined trajectory. For representative acquisition parameters and signal-to-noise ratios, the limitations due to measurement noise are acceptable. In a phantom with reciprocal rotation, the measured and true trajectories agreed to within 3.3%. Sample trajectory estimates of human myocardial regions are encouraging.
Reflection support for adaptive distributed applications (1999)

The DART (Distributed Adaptive Run-Time) project is developing an adaptive software environment for general-purpose distributed applications. The goal of the project is to provide a software run-time system that allows application authors to quickly develop distributed software, such as network or World Wide Web software, without having to deal with the details of the distribution technology. DART compile-time and run-time components configure the application execution environments depending on hints provided with the application. An essential feature of the run-time component is its ability to reconfigure, or adapt itself, both to the application requirements and to the system and networking environment. To achieve both distribution and adaptation, we use meta-level object programming techniques and run-time monitoring.
Minimal Solvers for Monocular Rolling Shutter Compensation Under Ackermann Motion (2018)

Modern automotive vehicles are often equipped with a budget commercial rolling shutter camera. These devices often produce distorted images due to the inter-row delay of the camera while capturing the image. Recent methods for monocular rolling shutter motion compensation utilize blur kernel and the straightness property of line segments. However, these methods are limited to handling rotational motion and also are not fast enough to operate in real time. In this paper, we propose a minimal solver for the rolling shutter motion compensation which assumes known vertical direction of the camera. Thanks to the Ackermann motion model of vehicles which consists of only two motion parameters, and two parameters for the simplified depth assumption that lead to a 4-line algorithm. The proposed minimal solver estimates the rolling shutter camera motion efficiently and accurately. The extensive experiments on real and simulated datasets demonstrate the benefits of our approach in terms of qualitative and quantitative results.
Next-generation, high-efficiency III-V multijunction solar cells (2002)

Next-generation solar cell approaches such as AlGaInP/GaAs/GaInNAs/Ge 4-junction cells, lattice-mismatched GaInP/GaInAs/Ge, concentrator cells, and improved 3-junction device structures hold the promise of greater efficiency than even today's highly successful multijunction cells. Wide-bandgap tunnel junctions, improved heterointerfaces, and other device structure improvements have resulted in several record-efficiency GaInP/GaAs/Ge cell results. Triple-junction (3J) cells grown in this work have demonstrated 29.3% efficiency for space (AMO, 1 sun). Space concentrator 3J cells have efficiency up to 30.0% at low concentration (AMO, 7.6 suns), and terrestrial concentrator cells grown at Spectrolab and processed at NREL have reached 32.3% (AM1.5D, 440 suns).
In vivo assessment of corneal mechanical response to heartbeat measured by heartbeat OCE (2021)

Corneal biomechanical properties can provide important information to measure tissue health. Elastography provides a useful tool to measure the biomechanical properties of tissues in vivo, but typically relies on measuring a response to external excitation. Passive elastography is a method to assess mechanical response to physiological pressures, which can be useful in the field of ophthalmology. In this work, we utilize our technique, Hb-OCE, to measure the mechanical properties of cornea in vivo. Furthermore, we were able to successfully distinguish stiffness in an untreated and crosslinked cornea using this technique, demonstrating its effectiveness as a tool for measuring corneal biomechanics.
A multi-interval Chebyshev collocation method for efficient high-accuracy RF circuit simulation (2000)

Most RF circuit analysis tools use either shooting-Newton or harmonic balance methods. Neither can efficiently achieve high accuracy on strongly nonlinear circuits possessing waveforms with rapid transitions. We present a multi-interval-Chebyshev (MIC) method that discretizes the circuit equations by dividing the simulation domain into a set of intervals whose size is adaptively chosen and using Chebyshev polynomials to represent the solution in each interval. The MIC method has excellent stability properties, is as effective at solving nonlinear problems as shooting techniques, can achieve high resolution on a wide variety of circuits, and in conjunction with an appropriate preconditioner can be combined with matrix-implicit Krylov-subspace solvers to analyze large circuits with moderate computational cost.
Performance comparison between compressed sensing and statistical iterative reconstruction algorithms (2009)

Of all available reconstruction methods, statistical iterative reconstruction algorithms appear particularly promising since they provide accurate physical noise modeling. The newly developed compressed sensing (CS) algorithm has shown the potential to accurately reconstruct images from highly undersampled data. In x-ray CT reconstructions, the CS algorithm can be implemented in the statistical reconstruction framework. In this study, we compared the performance of two standard statistical reconstruction algorithms (penalized weighted least square and q-GGMRF) to the CS algorithm. In assessing the image quality using these non-linear reconstructions it is critical to utilize realistic background anatomy as the reconstruction results are object dependent. A cadaver head was scanned on a Varian Trilogy system at different dose levels. A quality factor which accounts for the noise performance and the spatial resolution was introduced to objectively evaluate the performance of the algorithm under two conditions: 1) constant undersampling factor comparing different algorithms at different dose levels and 2) varying undersampling factors and dose levels for the CS algorithm. To facilitate this comparison the original CS method was also formulated in the framework of the statistical image reconstruction algorithm. This is also a novel aspect of this work. Important conclusions of the measurements are that: for realistic anatomy over 100 projections are needed to avoid streak artifacts even with CS reconstruction, regardless of the algorithm employed it is beneficial to distribute the total dose to many views as long as each view remains quantum noise limited, and the CS method is not appropriate for low dose levels because while it can mitigate streaking artifacts the images being to exhibit a patchy behavior.
A tetravalent virus-like particle vaccine designed to display domain III of dengue envelope proteins induces multi-serotype neutralizing antibodies in mice and macaques which confer protection against antibody dependent enhancement in AG129 mice (2018)

Directing the immune response to a non-immunodominant but functionally relevant serotype-specific dengue epitope of the four DENV serotypes, displayed on a VLP platform, can help minimize the risk of inducing disease-enhancing antibodies while eliciting effective tetravalent seroconversion. DSV4 has a significant potential to emerge as a safe, efficacious and inexpensive subunit dengue vaccine candidate.
Unique rearrangement of ergocalciferol side chain in vitro: production of a biologically highly active homologue of 1,25-dihydroxyvitamin D3 (1986)

In vitro incubation of 24-epi-25-hydroxyvitamin D2 with chicken kidney homogenate produced several compounds, one of which had an affinity equal to that of 1,25-dihydroxyvitamin D2 for the chick intestinal receptor. The affinity of 24-epi-1,25-dihydroxyvitamin D2 for the same receptor was found to be half that of 1,25-dihydroxyvitamin D2. The unknown compound was produced only when homogenate was prepared from pooled kidneys taken from both vitamin D deficient and replete chickens. The compound has been tentatively identified as 1,25-dihydroxy-22-dehydro-26-homovitamin D3 by ultraviolet absorption spectrophotometry and mass spectrometry. Chemical synthesis of 1,25-dihydroxy-22-dehydro-26-homovitamin D3 provided additional evidence for the structure. Administration of this 26-homologue of 1,25-dihydroxyvitamin D3 at the dose level of 650 pmol/rat stimulated bone calcium mobilization in the hypocalcemic rat equal to that of 1,25-dihydroxyvitamin D3. Thus, this paper demonstrates unique methyl migration on the side chain of 24-epi-1,25-dihydroxyvitamin D3 to form a more biologically potent analogue.
A 12.5-MHz Bandwidth 77-dB SNDR SAR-Assisted Noise Shaping Pipeline ADC (2019)

This article presents a successive approximation register (SAR)-assisted noise-shaping (NS) pipeline architecture which breaks the speed bottleneck of the existing SAR or SAR-assisted-type NS analog-to-digital converters (ADCs). Rather than only for residue amplification and pipeline operation, the multiplying digital-to-analog converter (MDAC) is also reused as unity buffer and analog adder to realize the NS with error feedback (EF) structure in this design. While incorporating the proposed alternative loading capacitor (ALC) technique, an ideal first-order noise transfer function (NTF) is realized without additional feedback phase and only with a small analog circuit overhead. Unlike other NS SAR ADCs that involved amplification, the inter-stage gain attenuates the noise from the second-stage comparator, thus leading to both high speed and resolution. Fabricated in a 65-nm CMOS process, the prototype achieves a signal-to-noise-and-distortion ratio (SNDR) of 77.1 dB over 12.5-MHz bandwidth (BW) with only over-sampling ratio (OSR) of 8. Under a 1.2-V supply voltage, the ADC consumes 4.5 mW and exhibits a Scherier figure of merit (FoM) of 171.5 dB.
A Simple Modification to Increase Stability of a Linear Flashlamp-Pumped Dye Laser (1982)

It was determined by FitzPatrick and Piepmeier that the beam from a CMX-4 dye laser (Chromatix, Sunnyvale, CA) was most reproducible when the dye temperature was from 0.5°C cooler than the ellipsoidal cavity water to 2.0°C warmer. The CMX-4 is factory designed for tap water cooling, through heat exchangers, of two separate closed fluid loops. One loop contains deionized water used to cool the laser flashtube, the other loop contains the laser dye. To maintain the proper temperature relationship, the aforementioned authors used two regulated heating/cooling systems, one on each closed loop. We have found that rerouting the deionized water leaving the flashtube cavity of the laser through the dye-loop exchanger, in lieu of tap water, maintains the desired temperature relationship without the need of any special heating/cooling systems.