gebhart/patrepeval huggingface dataset:
Matching protein structures with fuzzy alignments (2003)

Unraveling functional and ancestral relationships between proteins as well as structure-prediction procedures require powerful protein-alignment methods. A structure-alignment method is presented where the problem is mapped onto a cost function containing both fuzzy (Potts) assignment variables and atomic coordinates. The cost function is minimized by using an iterative scheme, where at each step mean field theory methods at finite "temperatures" are used for determining fuzzy assignment variables followed by exact translation and rotation of atomic coordinates weighted by their corresponding fuzzy assignment variables. The approach performs very well when compared with other methods, requires modest central processing unit consumption, and is robust with respect to choice of iteration parameters for a wide range of proteins.
Implanted user interfaces (2012)

We investigate implanted user interfaces that small devices provide when implanted underneath human skin. Such devices always stay with the user, making their implanted user interfaces available at all times. We discuss four core challenges of implanted user interfaces: how to sense input through the skin, how to produce output, how to communicate amongst one another and with external infrastructure, and how to remain powered. We investigate these four challenges in a technical evaluation where we surgically implant study devices into a specimen arm. We find that traditional interfaces do work through skin. We then demonstrate how to deploy a prototype device on participants, using artificial skin to simulate implantation. We close with a discussion of medical considerations of implanted user interfaces, risks and limitations, and project into the future.
Catalytic Hydrothermal Liquefaction of Food Waste Using CeZrOx (2018)

Approximately 15 million dry tons of food waste is produced annually in the United States (USA), and 92% of this waste is disposed of in landfills where it decomposes to produce greenhouse gases and water pollution. Hydrothermal liquefaction (HTL) is an attractive technology capable of converting a broad range of organic compounds, especially those with substantial water content, into energy products. The HTL process produces a bio-oil precursor that can be further upgraded to transportation fuels and an aqueous phase containing water-soluble organic impurities. Converting small oxygenated compounds that partition into the water phase into larger, hydrophobic compounds can reduce aqueous phase remediation costs and improve energy yields. HTL was investigated at 300 °C and a reaction time of 1 h for conversion of an institutional food waste to bio-oil, using either homogeneous Na2CO3 or heterogeneous CeZrOx to promote in situ conversion of water-soluble organic compounds into less oxygenated, oil-soluble products. Results with food waste indicate that CeZrOx improves both bio-oil higher heating value (HHV) and energy recovery when compared both to non-catalytic and Na2CO3-catalyzed HTL. The aqueous phase obtained using CeZrOx as an HTL catalyst contained approximately half the total organic carbon compared to that obtained using Na2CO3—suggesting reduced water treatment costs using the heterogeneous catalyst. Experiments with model compounds indicated that the primary mechanism of action was condensation of aldehydes, a reaction which simultaneously increases molecular weight and oxygen-to-carbon ratio—consistent with the improvements in bio-oil yield and HHV observed with institutional food waste. The catalyst was stable under hydrothermal conditions (≥16 h at 300 °C) and could be reused at least three times for conversion of model aldehydes to water insoluble products. Energy and economic analysis suggested favorable performance for the heterogeneous catalyst compared either to non-catalytic HTL or Na2CO3-catalyzed HTL, especially once catalyst lifetime differences were considered. The results of this study establish the potential of heterogeneous catalysts to improve HTL economics and energetics.
At-wavelength detection of extreme ultraviolet lithography mask blank defects (1998)

We report the design and operation of an at-wavelength system for extreme ultraviolet lithography mask blank defect detection. Initial results demonstrate sensitivity to submicron size phase defects. The performance of the system is compared with the practical requirements for a mask blank inspection system in terms of the sensitivity and scanning time.
Bulk Re-registration for Proxy Mobile IPv6 (2009)

The Proxy Mobile IPv6 specification requires the Mobile Access Gateway
(MAG) to send a separate Proxy Binding Update (PBU) message to the
Local Mobility Agent (LMA) for each mobile node (MN), to renew the
MN's mobility binding, when the MNs binding lifetime is close to
expiry. This document defines a mechanism by which a MAG can update
the mobility bindings of multiple MNs attached to it with a single PBU
message to the serving LMA.
Purification and properties of glutathione peroxidase from Mucor hiemalis. (1983)

Selenium-independent glutathione peroxidase was purified from a cell-free extract of Mucor hiemalis by ammoniumsulfate fractionation, column chromatographies on DEAE-Sephadex and hydroxylapatite, and gel filtration on Bio-Gel P-100. The purified enzyme was homogeneous on ultracentrifugation. The enzyme had a molecular weight of 45, 000 and an isoelectric point of 5.2. The enzyme could reduce cumenehydroperoxide and r-butyl hydroperoxide, but could not reduce hydrogen peroxide. The enzymewas highly specific for glutathione as a hydrogen donor. Mucor glutathione peroxidase was proved to be different from mammalian selenium-dependent glutathione peroxidase I and selenium-independent glutathione peroxidase II in some physicochemical and enzymatic properties.
Improved reflectance and stability of Mo-Si multilayers (2002)

Commercial EUV lithographic systems require multilayers with higher reflectance and better stability then that published to date. Interface-engineered Mo/Si multilayers with 70% reflectance at 13.5 nm wavelength (peak width of 0.545 nm) and 71% at 12.7 nm wavelength (peak width of 0.49 nm) were developed. These results were achieved with 50 bilayers. These new multilayers consist of Mo and Si layers separated by thin boron carbide layers. Depositing boron carbide on interfaces leads to reduction in silicide formation on the Mo-on-Si interfaces. Bilayer contraction is reduced by 30% implying that there is less intermixing of Mo and Si to form silicide. As a result the Mo-on-Si interfaces are sharper in interface-engineered multilayers than in standard Mo/Si multilayers. The optimum boron carbide thicknesses have been determined and appear to be different for Mo-on-Si and Si-on-Mo interfaces. The best results were obtained with 0.4 nm thick boron carbide layer on the Mo-on-Si interface and 0.25 nm thick boron carbide layer on the Si-on-Mo interface. Increase in reflectance is consistent with multilayers with sharper and smoother interfaces. A significant improvement in oxidation resistance of EUV multilayers has been achieved with ruthenium terminated Mo/Si multilayers. The best capping layer design consists of a Ru layer separated from the last Si layer by a boron carbide layer. This design achieves high reflectance and the best oxidation resistance in a water vapor (i.e. oxidation) environment. Electron beam exposures of 4.5 hours in the presence of 5x10{sup -7} torr water vapor partial pressure show no measurable reflectance loss and no increase in the oxide thickness of Ru terminated multilayers. Longer exposures in different environments are necessary to test lifetime stability of many years.
Micropole Undulators in Accelerator and Storage Ring Technology (1987)

In this paper, a general overview of the properties of micropole undulators as insertion devices for both accelerators and synchrotron storage rings is given. Comparisons with longperiod devices are drawn on the basis of a coherence length/output power parameter defined by us for the purpose of this study. It is shown that micropole insertion devices, particularly undulators, have the potential for transforming conventional accelerator and synchrotron radiation technology. Some novel physical experiments, made possible by the availability of such devices, are mentioned.
NIMG-36. EVALUATION OF [18F]DASA-23 FOR NON-INVASIVE MEASUREMENT OF ABERRANTLY EXPRESSED PYRUVATE KINASE M2 IN GLIOMA: FIRST-IN-HUMAN STUDY (2019)

Abstract OBJECTIVES We developed 1-((2-fluoro-6-(fluoro-[18F])phenyl)sulfonyl)-4-((4-methoxyphenyl)sulfonyl)piperazine ([18F]DASA-23) as a novel radiopharmaceutical to measure pyruvate kinase M2 levels by positron emission tomography (PET). PKM2 catalyzes the final step in glycolysis, the key process of tumor metabolism. PKM2 is preferentially expressed by glioblastoma (GBM) cells with minimal expression in the healthy brain, making it an important biomarker of cancer glycolytic re-programming. Here, we report the first evaluation of [18F]DASA-23 in human healthy volunteers and subjects with low-grade (LGG) and high-grade glioma (HGG). METHODS [18F]DASA-23 was synthesized under GMP conditions. Brain [18F]DASA-23 PET/MRI scans (3T) were performed in human healthy volunteers (n=5) and subjects with LGG (n=3) and HGG (n=2). The PET imaging duration was 60 min and standardized uptake value (SUV) calculations were performed on the 30–60 min summed images. The maximum SUV in the tumor (TumorSUVmax) and contralateral white matter (WMSUVmax) were calculated. RESULTS [18F]DASA-23 specific activity was 2961±873 mCi/µmol (n=10) with radiochemical purity >95%, injected mass of 1.8±0.7 mcg, and dose of 0.3±0.02 mcg per kg body weight. In healthy volunteers, [18F]DASA-23 crossed the intact blood-brain barrier and was rapidly cleared through the bladder and also showed uptake in the gallbladder, liver, and intestines over time. [18F]DASA-23 was found to be intact in plasma up to 10 min post-injection and 75% intact at 30 min post-injection. In subjects with glioma, TumorSUVmax was significantly greater in HGG (2.2±0.4, n=2) compared to LGG (0.8±0.3m n=3), p=0.02. In this early human series, the normalized ratio of TumorSUVmax/WMSUVmax was not significantly different between subjects with HGG (2.0±0.6) and LGG (1.0±0.4), p=0.1. CONCLUSION [18F]DASA-23 is a promising new imaging agent for the non-invasive delineation of LGG and HGG based on aberrantly expressed PKM2. An ongoing study is evaluating the utility of this agent in additional patients with intracranial malignancies (NCT03539731).
Functional map of arrestin binding to phosphorylated opsin, with and without agonist (2016)

Arrestins desensitize G protein-coupled receptors (GPCRs) and act as mediators of signalling. Here we investigated the interactions of arrestin-1 with two functionally distinct forms of the dim-light photoreceptor rhodopsin. Using unbiased scanning mutagenesis we probed the individual contribution of each arrestin residue to the interaction with the phosphorylated apo-receptor (Ops-P) and the agonist-bound form (Meta II-P). Disruption of the polar core or displacement of the C-tail strengthened binding to both receptor forms. In contrast, mutations of phosphate-binding residues (phosphosensors) suggest the phosphorylated receptor C-terminus binds arrestin differently for Meta II-P and Ops-P. Likewise, mutations within the inter-domain interface, variations in the receptor-binding loops and the C-edge of arrestin reveal different binding modes. In summary, our results indicate that arrestin-1 binding to Meta II-P and Ops-P is similarly dependent on arrestin activation, although the complexes formed with these two receptor forms are structurally distinct.
Bean Yellow Dwarf Virus replicons for high‐level transgene expression in transgenic plants and cell cultures (2005)

A novel stable transgenic plant expression system was developed using elements of the replication machinery of Bean Yellow Dwarf Virus (BeYDV). The system contains two transgenes: 1) The BeYDV replicon vector with an expression cassette flanked by cis-acting DNA elements of BeYDV, and 2) The viral replication initiator protein (Rep) controlled by an alcohol-inducible promoter. When Rep expression was triggered by treatment with ethanol, it induced release of the BeYDV replicon from stably integrated T-DNA and episomal replication to high copy number. Replicon amplification resulted in substantially increased transgene mRNA levels (up to 80-fold) and translation products (up to 10-fold) after induction of Rep expression by ethanol treatment in tobacco NT1 cells and leaves of whole potato plants. Thus, the BeYDV stable transformant replicon system is a powerful tool for plant-based production of recombinant proteins.
Practical Detection of Trojan Neural Networks: Data-Limited and Data-Free Cases (2020)

When the training data are maliciously tampered, the predictions of the acquired deep neural network (DNN) can be manipulated by an adversary known as the Trojan attack (or poisoning backdoor attack). The lack of robustness of DNNs against Trojan attacks could significantly harm real-life machine learning (ML) systems in downstream applications, therefore posing widespread concern to their trustworthiness. In this paper, we study the problem of the Trojan network (TrojanNet) detection in the data-scarce regime, where only the weights of a trained DNN are accessed by the detector. We first propose a data-limited TrojanNet detector (TND), when only a few data samples are available for TrojanNet detection. We show that an effective data-limited TND can be established by exploring connections between Trojan attack and prediction-evasion adversarial attacks including per-sample attack as well as all-sample universal attack. In addition, we propose a data-free TND, which can detect a TrojanNet without accessing any data samples. We show that such a TND can be built by leveraging the internal response of hidden neurons, which exhibits the Trojan behavior even at random noise inputs. The effectiveness of our proposals is evaluated by extensive experiments under different model architectures and datasets including CIFAR-10, GTSRB, and ImageNet.
Selective Removal of Cesium from Simulated High-level Liquid Wastes by Insoluble Ferrocyanides. (1997)

Click to increase image sizeClick to decrease image sizeKEYWORDS: cesium 137cesium ionshigh-level liquid wastesinsoluble ferrocyanidesion exchangeinorganic ion exchangersdistribution coefficientconcentration dependenceseparation factoruptakezeolites
New CFOA-based floating lossless negative immittance function emulators (2015)

This paper presents a new topology for emulating floating lossless negative immittance functions. The proposed circuit uses three current-feedback operational-amplifiers (CFOAs), and three passive elements. The functionality of the proposed circuit is verified using the Advanced Design System (ADS) software and the AD844 CFOA. The simulation results obtained from a floating negative lossless inductance emulator are in excellent agreement with the theoretical calculations.
Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development (2021)

Aptamers are short oligonucleotides isolated in vitro from randomized libraries that can bind to specific molecules with high affinity, and offer a number of advantages relative to antibodies as biorecognition elements in biosensors. However, it remains difficult and labor-intensive to develop aptamer-based sensors for small-molecule detection. Here, we review the challenges and advances in the isolation and characterization of small-molecule-binding DNA aptamers and their use in sensors. First, we discuss in vitro methodologies for the isolation of aptamers, and provide guidance on selecting the appropriate strategy for generating aptamers with optimal binding properties for a given application. We next examine techniques for characterizing aptamer-target binding and structure. Afterwards, we discuss various small-molecule sensing platforms based on original or engineered aptamers, and their detection applications. Finally, we conclude with a general workflow to develop aptamer-based small-molecule sensors for real-world applications.
Tryptophan and Indole Analog Mediated Plastid Transformation (2014)

A nonantibiotic/herbicide-resistance selection system for plastid transformation is described here in technical detail. This system is based on the feedback-insensitive anthranilate synthase (AS) α-subunit gene of tobacco (ASA2) as a selective marker and tryptophan (Trp) or indole analogs as selection agents. AS catalyzes the first reaction in the Trp biosynthetic pathway, naturally compartmentalized in the plastids, by converting chorismate to anthranilate and is subjected to feedback inhibition by Trp. In addition to Trp, various Trp analogs and indole compounds that can be converted to Trp analogs can also inhibit AS activity and therefore are toxic to cells. When cells are made to express the feedback-insensitive ASA2, they acquire resistance to these analogs and can be selected for during transformation process. We have demonstrated the feasibility of this selection system in tobacco (Nicotiana tabacum L. cv. Petit Havana). ASA2-expressing transplastomic plants were obtained on medium supplemented with either 7-methyl-DL-tryptophan (7-MT) or 4-methylindole (4-MI). These plants show normal phenotype and fertility and transmit the resistance to the selection agents strictly maternally.
Effect of a magnetic field on a vibrating reed with anisotropic susceptibility (1994)

A magnetic field may alter the flexural resonant frequencies of a vibrating reed that possesses an anisotropic magnetic susceptibility. The phenomenon's magnitude is a function of the field strength, the length of the reed, the radius of gyration of the reed's cross section, the Young's modulus of the material, the vibrational mode observed, the magnetic susceptibility tensor, and the field's orientation relative to the principal susceptibility directions and the reed's plane of vibration. This effect can allow a direct and extremely sensitive measure of magnetic anisostropy of nonferromagnetic materials.
Self-assembling nanoparticles into holographic nanopatterns (2004)

We demonstrate a method to self-assemble metal nanoparticles into two-dimensional lattices. Monodisperse cobalt nanoparticles were synthesized within inverse micelles of polystyrene-block-poly(2-vinylpyridine) copolymer in toluene. A periodic hole pattern of photoresist (PR) was fabricated on a GaAs substrate by holographic lithography. The nanoparticles as prepared above were self-assembled onto the PR nanopatterns by dip or spin casting. They were selectively positioned in the holes due to the capillary forces related to the pattern geometry. Our study reveals that self-assembled nanoparticles in two-dimensional lattices can be obtained with a controllable number of particles per lattice point.
Novel Biobased Polymers for Coating Applications (2016)

This chapter contains sections titled: Introduction Polymers Based on Plant Oils Polymers Based on Cardanol Polymers Based on Eugenol Conclusion Acknowledgments Disclaimer
Secure ADS-B design & evaluation (2015)

Automatic Dependent Surveillance Broadcast (ADSB) is a newer air traffic surveillance protocol that is expected to strengthen and replace current RADAR-based surveillance systems, which has brought worldwide attention. However, its nature of clear text broadcast introduces many vulnerabilities to the system. We proposed a solution that uses keyed-hash message authentication code (HMAC) to address the authenticity and integrity deficiencies of ADS-B protocol Previously. In this paper we extend it by improving the HMAC computation procedure at the transmitter and the HMAC verification procedure at the receiver. In addition, this new approach is also evaluated under some types of attacks, comparing its performance against unmodified ADS-B transmissions.
Quantitation of Non-Inhibitory Anti-Factor VIII Antibodies in human Plasma (2008)

Abstract Hemophilia A is a clinically heterogeneous bleeding disorder characterized by the absence of functional factor VIII (FVIII). The most severe complication from exposure to exogenous factor VIII therapy is the development of alloantibodies that neutralize the effect of the therapeutic agent. The standard method for quantitation of FVIII inhibitors in human plasma is by the Nijmegen method, a modification of the Bethesda assay. Our objective was to develop a sensitive and specific fluorescence based immunoassay for the quantitation of anti-FVIII antibodies (FVIIIAb) in human plasma. An affinity purified human anti-FVIIIAb isolated from a hemophilia A patient was used as a calibrator, with a detectability limit of 40±1.5pM. The calibrator and the human plasma anti-FVIIIAb were captured on recombinant FVIII coupled microspheres and probed with mouse anti-human Ig conjugated to R-Phycoerythrin. Citrated human plasma samples from 150 healthy donors and 39 inhibitor-negative hemophilia A subjects were studied and compared to 4 inhibitor-positive hemophilia A plasma samples with inhibitor titers of 1BU (94.6±0.08nM), 11BU (214.3±7.1nM), 106BU (2209.4±84.9nM) and 140BU (2417.7±3.8nM) as measured by the Nijmegen method. Among the 150 normal control plasmas, 4 subjects (3%) were determined as positive (anti-FVIIIAb ≥ 40pM) with concentrations in the range of 0.6nM to 1.9nM, well below that of 1BU (94.6±0.08nM) inhibitor-positive sample. Anti-FVIIIAb was also evaluated in seven commercial inhibitor-free plasma samples reported to contain &lt;1% FVIII activity. Two of the seven plasmas were found to contain anti-FVIIIAb with concentrations of 112.9±1.9nM and 71.1±8.5nM. The concentration of the antibody in both samples was within the range of the measured molar concentration of an inhibitor-positive 1BU titer plasma sample. Thirty two inhibitor-negative hemophilia A subjects were also quantitated for anti-FVIIIAb. Eleven of the 32 samples tested positive for anti-FVIIIAb with molar concentrations in the range of 0.6–20nM. The overall prevalence of the non-inhibitory anti-FVIIIAbs in hemophilia A subjects evaluated by our immunoassay (n=39) is approximately 33% relative to healthy donor population in which 3% were determined as positive (≥40pM) for FVIIIAb.
Measurement of Amphotericin B concentration by Resonant Raman Spectroscopy – a novel technique that may be useful for non-invasive monitoring (2006)

We wished to determine whether Resonant Raman Spectroscopy (RRS) could be used to measure Amphotericin B (AmB) at therapeutic and subtherapeutic concentrations in a model system mimicking the anterior chamber of the eye. The goal was to develop a technique for non-invasive measurement of AmB levels in the aqueous humor (AH) of the eye. A krypton-ion laser source (406.7 nm) was used for excitation and Resonant Raman Spectra were captured with a confocal system in an anterior chamber (AC) model. These spectra were used to develop a correlation curve for prediction of AmB levels. Subsequently, one rabbit was evaluated with this system after 5 days of intravenous AmB administration (1 mg/kg/day) and AmB concentrations measured by RRS were compared to those measured by high-performance liquid chromatography (HPLC). AmB exhibited a unique spectral peak at 1557 cm(-1). Integrated area of this peak linearly correlated with AmB concentration in our model AC. When integrated peak area from multiple in vivo measurements in one animal at steady-state was plotted on this correlation curve, we were able to predict AmB levels. These closely approximated those measured by HPLC. These measurements were not significantly affected by photobleaching or depth profile at acquisition. RRS at 406.7 nm is a method that may be useful for non-invasive monitoring of intraocular AmB levels. This instrument can help physicians decide when repeat, invasive delivery of this drug is warranted based on measurement of actual drug levels in the AH. Also, there is the potential to measure the ocular concentrations of other pharmaceutical agents with similar instruments.