gebhart/patrepeval huggingface dataset:
Engineered Glycan-Binding Proteins for Recognition of the Thomsen–Friedenreich Antigen and Structurally Related Disaccharides (2022)

Glycan-binding proteins (GBPs) are widely used reagents for basic research and clinical applications. These reagents allow for the identification and manipulation of glycan determinants without specialized equipment or time-consuming experimental methods. Existing GBPs, mainly antibodies and lectins, are limited, and discovery or creation of reagents with novel specificities is time consuming and difficult. Here, we detail the generation of GBPs from a small, hyper-thermostable DNA-binding protein by directed evolution. Yeast surface display of a variable library of rcSso7d proteins was screened to find variants with selectivity toward the cancer-associated glycan Galβ1-3GalNAcα or Thomsen-Friedenreich antigen and various relevant disaccharides. Characterization of these proteins shows them to have specificities and affinities on par with currently available lectins. The proteins can be readily functionalized with fluorophores or biotin using sortase-mediated ligation to create reagents that prove useful for glycoprotein blotting and cell staining applications. The presented methods for the development of GBPs toward specific saccharides of interest will have great impact on both biomedical and glycobiological research.
Fuzzy logic mode switching in helicopters (1993)

The application of fuzzy logic to a wide range of control problems has been gaining momentum internationally, fueled by a concentrated Japanese effort. Advanced Research & Development within the Engineering Department at Sikorsky Aircraft undertook a fuzzy logic research effort designed to evaluate how effective fuzzy logic control might be in relation to helicopter operations. The mode switching module in the advanced flight control portion of Sikorsky's motion based simulator was identified as a good candidate problem because it was simple to understand and contained imprecise (fuzzy) decision criteria. The purpose of the switching module is to aid a helicopter pilot in entering and leaving coordinated turns while in flight. The criteria that determine the transitions between modes are imprecise and depend on the varied ranges of three flight conditions (i.e., simulated parameters): Commanded Rate, Duration, and Roll Attitude. The parameters were given fuzzy ranges and used as input variables to a fuzzy rulebase containing the knowledge of mode switching. The fuzzy control program was integrated into a real time interactive helicopter simulation tool. Optimization of the heading hold and turn coordination was accomplished by interactive pilot simulation testing of the handling quality performance of the helicopter dynamic model. The fuzzy logic code satisfied all the requirements of this candidate control problem.
<title>Multifunction automated crawling system (MACS)</title> (1996)

Nondestructive evaluation instruments and sensors are becoming smaller with enhanced computer controlled capability and increasingly use commercially available hardware and software. Further, robotic instruments are being developed to serve as mobility platforms allowing automation of the inspection process. This combination of miniaturized sensing and robotics technology enables hybrid miniature technology solutions for identified aircraft inspection needs. Integration of inspection and robotics technologies is benefited by the use of a standard computing platform. JPL investigated the application of telerobotic technology to inspection of aircraft structures using capabilities that were developed for use in space exploration. A miniature crawler that can travel on the surface of aircraft using suction cups for adherence was developed and is called multifunction automated crawling systems (MACS). MACS is an operational tool that can perform rapid large area inspection of aircraft, which has a relatively large platform to carry miniature inspection instruments payload. The capability of MACS and the trend towards autonomous inspection crawlers will be reviewed and discussed in this paper.
Development and application of a simplified liquid ventilator (1995)

Liquid ventilation can be performed successfully utilizing this simple adaptation of an extracorporeal life-support circuit. This modification to an existing extracorporeal circuit may allow other centers to apply this new investigational method of ventilation in the laboratory or clinical setting.
A Family of Multiaddressable, Multicolored Photoresponsive Copolymers Prepared by Ring-Opening Metathesis Polymerization (2005)

A series of homo- and copolymers containing different photochromic dithienylethene (DTE) architectures was prepared by ring-opening metathesis polymerization (ROMP) techniques. Each DTE structure can be uniquely addressed in the two- and three-component copolymers, providing a means to generate a wide range of colors when the compounds are selectively photocyclized to their ring-closed forms. Multicomponent, multiaddressable materials of this type are beneficial for applications such as multistate photochromic recording, displays, inks, and barcodes.
Designing multi-role, collaborative Web sites with WebML: a conference management system case study (2001)

This report describes the design and implementation in WebML of the Conference Management System case study (CMS, from now on), proposed by the organizers of the IWWOST 2001 Workshop
Preliminary Assessment of a Concept of Looping Combustion of Carbon (2008)

A novel concept of looping combustion of carbon (CarboLoop) is presented. It is based on the feature of carbons to extensively uptake oxygen upon exposure to air at moderate temperatures. Surface oxides of carbon are eventually released as combustion products (CO, CO2) as the oxidized fuel is brought to moderate-to-high temperature in an oxygen-free atmosphere. This concept is pursued to the formulation of a preliminary scheme of a looping combustor of carbons based on a dual interconnected bed reactor system. One of the reactors is air-blown and acts as the fuel oxidizer. The second reactor, operated with partial recycle of gaseous effluents (CO2 + impurities), acts as the fuel desorber. Operating conditions of the oxidation and desorption stages may be properly tuned, leading to alternative looping strategies. The present study lays down the basic mechanistic background for analyzing the process, based on a simplified semiglobal approach to combustion and oxidation of solid carbons. The soundness of the CarboLoop concept has been verified by purposely designed experiments. The alternated oxidation/desorption stages typical of a looping combustor are simulated in a thermogravimetric analyzer. Experiments were directed to monitoring the oxidation and desorption steps under simulated looping conditions. Graphitized coke has been used as a surrogate carbon fuel. The experimental results confirm the soundness and potential of the CarboLoop concept and lay the path for its further development.
An oxygen sensitive self-decision making engineered CAR T-cell (2017)

A key to the success of chimeric antigen receptor (CAR) T-cell based therapies greatly rely on the capacity to identify and target antigens with expression restrained to tumor cells. Here we present a strategy to generate CAR T-cells that are only effective locally (tumor tissue), potentially also increasing the choice of targetable antigens. By fusing an oxygen sensitive subdomain of HIF1α to a CAR scaffold, we generated CAR T-cells that are responsive to a hypoxic environment, a hallmark of certain tumors. Along with the development of oxygen-sensitive CAR T-cells, this work also provides a basic framework to use a multi-chain CAR as a platform to create the next generation of smarter self-decision making CAR T-cells.
Incorporating query difference for learning retrieval functions in information retrieval (2006)

We discuss information retrieval methods that aim at serving a diverse stream of user queries. We propose methods that emphasize the importance of taking into consideration of query difference in learning effective retrieval functions. We formulate the problem as a multi-task learning problem using a risk minimization framework. In particular, we show how to calibrate the empirical risk to incorporate query difference in terms of introducing nuisance parameters in the statistical models, and we also propose an alternating optimization method to simultaneously learn the retrieval function and the nuisance parameters. We illustrate the effectiveness of the proposed methods using modeling data extracted from a commercial search engine.
Release system for deployable micro satellites (2017)

A novel method of releasing a deployable in the micro-satellite class is developed from concept to launch environment and separation testing. The release system is a linear Marman-style mechanism that is lightweight, has a low part count, and is relatively simple and inexpensive to fabricate and assemble. This release system was conceptualized and structurally analyzed for a deployable in the 50 to 100 kg class of satellites. An integral component of the system is the dispenser plate which is mounted to a launch vehicle and serves as a clamping interface for the deployable. The clamped, flyaway portion of the system is the base plate of the deployable. The first key feature of the release system is the pair of linear Marman-style clamps that lock the flyaway to the dispenser on two opposite edges of the mating interface. The second key feature is the bowed spring bar that is used to nearly equally distribute preload over the entire linear clamp bar. A variety of pyrotechnic or non-explosive separation nuts can be used to restrain the clamp bar and spring bar. The release system was tested prior to the end of FY16 in sine and random vibrations simulating launch environments and in pre- and post-vibration deployments. A space vehicle mass simulator was built for the test to provide realistic conditions for the release system. The objective of the test was to demonstrate the structural capability of the release system. The separation function was also tested pre- and post-vibration to validate that the system will release the deployable after launch. All development and testing of the release system were supported by APL internal R&D (IRAD) funding.
Spoiling of transverse magnetization in gradient‐echo (GRE) imaging during the approach to steady state (1996)

The signal evolution behaviors and corresponding image appearances for different methods of spoiling or refocusing the transverse magnetization in short TR gradient-echo imaging during the approach to steady state were investigated experimentally and using computer simulations based on the Bloch equations. Specifically, ideally spoiled, gradient-spoiled, gradient-refocused, and RF-spoiled pulse sequence configurations were studied. This study showed that, for the gradient-spoiled configuration, the signal evolution is position and phase-encoding order-dependent and, under typical imaging conditions, can deviate substantially from the ideally spoiled signal evolution at some spatial positions, resulting in intensity banding image artifacts. For the gradient-refocused configuration, the signal evolution oscillates toward the steady state and, generally, does not closely approximate that of ideal spoiling, resulting in different image contrast or image blurring. Using RF spoiling, the signal evolution closely approximates the ideally spoiled case for flip angles less than approximately 20 degrees and T2 values of less than approximately 200 ms and results in relatively artifact-free images. Also, this study showed that, for RF spoiling, an RF-pulse phase-difference increment other than 117 degrees, such as 84 degrees may be optimal for gradient-echo imaging during the approach to steady state.
In vivo nerve-specificity of rhodamines and Si-rhodamines (2020)

Accidental nerve damage or transection of vital nerve structures remains an unfortunate reality that is often associated with surgery. Despite the existence of nerve-sparing techniques, the success of such procedures is not only complicated by anatomical variance across patients but is also highly dependent on a surgeon's first-hand experience that is acquired over numerous procedures through trial and error, often with highly variable success rates. Fluorescent small molecules, such as rhodamines and fluoresceins have proven incredibly useful for biological imaging in the life sciences, and they appeared to have potential in illuminating vital nerve structures during surgical procedures. In order to make use of the current clinically relevant imaging systems and to provide surgeons with fluorescent contrast largely free from the interference of hemoglobin and water, it was first necessary to spectrally tune known fluorescent scaffolds towards near infrared (NIR) wavelengths. To determine whether the well-documented Si-substitution strategy could be applied towards developing a NIR fluorophore that retained nerve-specific properties of candidate molecules, an <i>in vivo</i> comparison was made between two compounds previously shown to highlight nervous structures - TMR and Rhodamine B - and their Si-substituted derivatives.
POLSAR data compensation for terrain azimuth slope variation (2003)

This paper addresses the problem of polarimetric SAR data correction for slope induced radar cross section variations in the azimuth direction. Most radiometric slope corrections remove slope effects in the range direction to account for local incidence angle variation. Two approaches to compensate azimuth slope effects are proposed. In the first approach, the DEM, obtained from interferometric SAR or other means is used to estimate the orientation angle, and in the second approach, the orientation angle is derived from Cloude's and Huynen's decompositions, and the peak-shift in polarization signature. Comparison on the accuracy of estimating the orientation angle with that derived from the DEM is given. NASA/JPL AIRSAR data is used for illustration.
An immobilized cell reactor with simultaneous product separation. I. Reactor design and analysis (1985)

Abstract A four‐phase reactor–separator (gas, liquid, solid, and immobilized catalyst) is proposed for fermentations characterized by a volatile product and nonvolatile substrate.In this reactor, the biological catalyst is immobilized onto a solid column packing and contacted by the liquid containing the substrate.A gas phase is also moved through the column to strip the volatile product into the gas phase. The Immobilized Cell Reactor–Separator (ICRS) consists of two basic gas–liquid flow sections: a cocurrent “enricher” followed by a countercurrent–“stripper”. In this article, an equilibrium stage model of the reactor is developed to determine the feasibility and important operational variables of such a reactor–separator. The ICRS concept is applied to the ethanol from whey lactose fermentation using some preliminary immobilized cell reactor performance data. A mathematical model for a steady‐state population based on an adsorbed monolayer of cells is also developed for the reactor. The ICRS model demonstrated that the ICRS should give a significant increase in reactor productivity as compared to an identically sized Immobilized Cell Reactor (ICR) with no separation. The gas‐phase separation of the product also allows fermentation of high inlet substrate concentrations. The model is used to determine the effects of reactor parameters on ICRS performance including temperature, pressure, gas flow rates, inlet substrate concentration, and degree of microbial product inhibition.
Design and implementation of a structured LDPC decoder on FPGA (2004)

We present a design framework for the implementation for a Low-Density Parity-Check (LDPC) decoders. We employed a scalable decoding architecture for a certain class of structured LDPC codes.
Operation of universal gates in a solid-state quantum computer based on clean Josephson junctions between<b><i>d</i></b>-wave superconductors (2000)

The operation of a solid-state superconducting quantum computer based on clean Josephson junctions between two d-wave superconductors is considered. We show that freezing of passive qubits can be achieved using a dynamic global refocusing technique. Further, we demonstrate that a universal set of gates can be realized on this system, thereby proving its universality.
Abstract 1889: Synthesis of substituted tetrahydroisoquinoline chromone-2-carboxamidesas anti-breast cancer agents (2022)

Abstract According to World Health Organization, breast cancer is second leading cause of mortality among women, accounting for 12% of all new annual cancer cases worldwide. In 2021, the American Cancer Society (ACS) reported that there will be 281,550 new cases of breast cancer in U.S. and about 43,600 women will be expected to die from the disease. Unfortunately, the recovery rate from advanced breast cancer by current available drug treatment is unacceptably low. Hence, there is an urgent need to develop more effective and less toxic small drug molecules with a unique mechanism of action. Chromones are benzannulated oxygen containing heterocyclic compounds that are widely distributed in nature and have a gamma-pyrone ring. Natural and synthetic molecules having chromone scaffold displayed interesting pharmacological activities such as anti-cancer, anti-HIV, antiviral and anti-inflammatory activities with low toxicity. In continuation of our current research work, we report the synthesis of substituted tetrahydroisoquinoline chromone carboxamides. Modifications of the chromone scaffold at pyrone ring by attaching substituted tetrahdyrosioquinolines were carried out to prepare compounds with a potential of acting as anti-breast cancer agents. The starting material, substituted chromone-2-carbonyl chloride was obtained by the acylation reaction of corresponding carboxylic acids using phosphorous pentachloride in dry cyclohexane. An equimolar amount of acyl chloride was slowly added to a stirred solution of corresponding substituted N-aminoisoquinoline in dry THF, in the presence of triethyl amine and refluxed at 70 degrees C that led to the formation of the ylides. The ylides were reduced using sodium borohydride to yield the desired substituted tetrahydroisoquinoline chromone-2-carboxamides in moderate to good yields. The synthesized compounds were characterized by NMR, IR, and elemental analysis. These compounds were evaluated for their cytotoxic effects on MBA-MB-231 ER-ve breast cancer cell lines using a Synergy HTX multi-mode reader (Bio-Tek, Winooski, VT, USA) with excitation/emission wavelength settings at 550/580. Compound N-(3,4-dihydroisoquinolin-2-(1H0-yl)-6-methyl-4-oxo-4H-1-benzopyran-2-carboxmaide showed the most potent cytotoxicity with an IC50 value 0.82 microgram/mL on MDA-MB-231 cell line. This research was supported by the National Institute on Minority Health and Health Disparities of the National Institutes of Health under the Award Number U54 MD007582. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Citation Format: Kinfe Ken Redda, Madhavi Gangapuram, Elizabeth Mazzio, Ramesh Badisa, Suresh Eyunni, Karam F. A. Soliman. Synthesis of substituted tetrahydroisoquinoline chromone-2-carboxamidesas anti-breast cancer agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1889.
Preparation and Characterization of Molecularly Imprinted Polymeric Nanoparticles for Atrial Natriuretic Peptide (ANP) (2011)

Natriuretic peptide receptor A (NPRA), the receptor for the cardiac hormone atrial natriuretic peptide (ANP), is expressed abundantly on cancer cells and disruption of ANP-NPRA signaling inhibits tumor burden and metastasis. Since antagonists of NPRA signaling have not provided reproducible results, we reasoned that a synthetic neutralizing antibody to ANP, which has high selectivity and affinity for ANP, could be used to regulate ANP levels and attenuate NPRA signaling. In this study, we prepared molecularly imprinted polymer nanoparticles (MIPNPs) for ANP using a short peptide of ANP as the template and determined their binding affinity and selectivity. The MIPNPs were prepared by precipitation polymerization using NH<sub>2</sub>-SLRRSS-CONH<sub>2</sub>, which is a short peptide from ANP as template, methacrylic acid (MAA) and N-isopropylacrylamide (NIPAm) as functional monomers, bis-acrylamide (BIS) as crosslinker. The average diameter of MIPNPs and non-imprinted nanoparticles (NIPNPs) in water is 215.8 ±4.6 nm and 197.7±3.1 nm respectively. The binding isotherm analysis showed that MIPNPs have a much higher binding affinity for template peptide and ANP than NIPNPs. Scatchard analysis gave an equilibrium dissociation constant, K<sub>d</sub> of 7.3 μM with a binding capacity 106.7 μmol/g for template peptide and K<sub>d</sub> of 7.9 μM with a binding capacity of 36.0 μmol/g for ANP. Measurements of binding kinetics revealed that MIPNPs reach protein adsorption equilibrium in 30 min. MIPNPs found to have high specificity for ANP with little affinity for BSA or scrambled ANP peptide. MIPNPs also recognized and adsorbed ANP in cell culture media spiked with ANP and human plasma. Taken together, these results indicate that MIPNPs have high affinity and selectivity for ANP and can be used as a synthetic antibody for modulating ANP-NPRA signaling in cancers.
Authenticall: efficient identity and content authentication for phone calls (2017)

Phones are used to confirm some of our most sensitive transactions. From coordination between energy providers in the power grid to corroboration of high-value transfers with a financial institution, we rely on telephony to serve as a trustworthy communications path. However, such trust is not well placed given the widespread understanding of telephony's inability to provide end-to-end authentication between callers. In this paper, we address this problem through the AuthentiCall system. AuthentiCall not only cryptographically authenticates both parties on the call, but also provides strong guarantees of the integrity of conversations made over traditional phone networks. We achieve these ends through the use of formally verified protocols that bind low-bitrate data channels to heterogeneous audio channels. Unlike previous efforts, we demonstrate that AuthentiCall can be used to provide strong authentication before calls are answered, allowing users to ignore calls claiming a particular Caller ID that are unable or unwilling to provide proof of that assertion. Moreover, we detect 99% of tampered call audio with negligible false positives and only a worst-case 1.4 second call establishment overhead. In so doing, we argue that strong and efficient end-to-end authentication for phone networks is approaching a practical reality.
CW Direct Detection Lidar with a Large Dynamic Range of Wind Speed Sensing in a Remote and Spatially Confined Volume (2021)

A novel continuous-wave (CW) direct detection lidar (DDL) is demonstrated to be capable of wind speed measurement 40 m away with an update rate of 4 Hz using a fiber-based scanning Fabry–Perot interferometer as an optical frequency discriminator. The proposed CW DDL has a large dynamic wind speed range with no sign ambiguity and its sensitivity is assessed by comparing its performance with that of a CW coherent detection lidar (CDL) in a side-by-side wind measurement. A theoretical model of the spatial weighting function of the fiber-based CW DDL is also presented and validated experimentally. This work shows that the CW DDL has a spatially confined measurement volume with a Lorentzian axial profile similar to that of a CW CDL. The proposed DDL has potential use in various applications in which requirements such as high-speed wind sensing and directional discrimination are not met by state-of-the-art Doppler wind lidar systems.