gebhart/patrepeval huggingface dataset:
Robust Wireless Fingerprinting: Generalizing Across Space and Time. (2020)

Can we distinguish between two wireless transmitters sending exactly the same message, using the same protocol? The opportunity for doing so arises due to subtle nonlinear variations across transmitters, even those made by the same manufacturer. Since these effects are difficult to model explicitly, we investigate learning device fingerprints using complex-valued deep neural networks (DNNs) that take as input the complex baseband signal at the receiver. Such fingerprints should be robust to ID spoofing, and to distribution shifts across days and locations due to clock drift and variations in the wireless channel. In this paper, we point out that, unless proactively discouraged from doing so, DNNs learn these strong confounding features rather than the subtle nonlinear characteristics that are the basis for stable signatures. Thus, a network trained on data collected during one day performs poorly on a different day, and networks allowed access to post-preamble information rely on easily-spoofed ID fields. We propose and evaluate strategies, based on augmentation and estimation, to promote generalization across realizations of these confounding factors, using data from WiFi and ADS-B protocols. We conclude that, while DNN training has the advantage of not requiring explicit signal models, significant modeling insights are required to focus the learning on the effects we wish to capture.
Development of Selective High Affinity Antagonists, Agonists, and Radioligands for the P2Y1 Receptor (2020)

The P2Y1 receptor is a member of the P2Y family of nucleotide-activated G protein-coupled receptors, and it is an important therapeutic target based on its broad tissue distribution and essential role in platelet aggregation. We have designed a set of highly selective and diverse pharmacological tools for studying the P2Y1 receptor using a rational approach to ligand design. Based on the discovery that bisphosphate analogues of the P2Y1 receptor agonist, ADP, are partial agonists/competitive antagonists of this receptor, an iterative approach was used to develop competitive antagonists with enhanced affinity and selectivity. Halogen substitutions of the 2-position of the adenine ring provided increased affinity while an N6 methyl substitution eliminated partial agonist activity. Furthermore, various replacements of the ribose ring with symmetrically branched, phosphorylated acyclic structures revealed that the ribose is not necessary for recognition at the P2Y1 receptor. Finally, replacement of the ribose ring with a five member methanocarba ring constrained in the Northern conformation conferred dramatic increases in affinity to both P2Y1 receptor antagonists as well as agonists. These combined structural modifications have resulted in a series of selective high affinity antagonists of the P2Y1 receptor, two broadly applicable radioligands, and a high affinity agonist capable of selectively activating the P2Y1 receptor in human platelets. Complementary receptor modeling and computational ligand docking have provided a putative structural framework for the drug-receptor interactions. A similar rational approach is being applied to develop selective ligands for other subtypes of P2Y receptors.
Lambertian thermal emitter based on plasmonic enhanced absorption (2016)

In this paper, a narrow band thermal emission at 10 μm is demonstrated using a one dimensional metasurface. The proposed metasurface structure provides magnetic resonance mode that enhances the phonon absorption of SiO<sub>2</sub>. The proposed metasurface thermal emitter shows a Lambertian distribution. Additionally, 5.8-folds enhancement of emissivity is achieved by optimizing the cavity thickness of the metasurfaces. This type of thermal emitter will be useful for IR sensing applications.
Nanotechnology applications to HIV vaccines and microbicides (2012)

Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) remains one of the most serious threats to global health. Today there are no HIV vaccines which can prevent HIV infection. All of the candidates being studied are in the experimental stage. Preventive vaccine candidates are being tested in HIV-negative people to see if they can prevent infection. With of the development of a safe and effective vaccine still likely to be years away, topical microbicide formulations that are applied vaginally and rectally are receiving greater interest as an effective alternative to slow down the global spread of HIV. Current microbicide trials that aim to prevent the sexual transmission of HIV are using gels, creams, rings, films and there is also work underway to explore other types of 'delivery' systems. There have been numerous reports on safety and lack of toxicity of the application of nanotechnology for targeted delivery and slow, sustained release of drugs, proteins, peptides or nucleic acids by any route to maximize effectiveness and minimize adverse effects. The application of nanotechnology for targeting drugs and macromolecules to specific tissues or cells is one of the most important areas in nanomedicine research. Thus far nanoparticles provide a strong platform to combine protein and DNA based vaccines/microbicides and will facilitate the production, preclinical evaluation and clinical testing in the future.
TERMinator: A Neural Framework for Structure-Based Protein Design using Tertiary Repeating Motifs (2022)

Computational protein design has the potential to deliver novel molecular structures, binders, and catalysts for myriad applications. Recent neural graph-based models that use backbone coordinate-derived features show exceptional performance on native sequence recovery tasks and are promising frameworks for design. A statistical framework for modeling protein sequence landscapes using Tertiary Motifs (TERMs), compact units of recurring structure in proteins, has also demonstrated good performance on protein design tasks. In this work, we investigate the use of TERM-derived data as features in neural protein design frameworks. Our graph-based architecture, TERMinator, incorporates TERM-based and coordinate-based information and outputs a Potts model over sequence space. TERMinator outperforms state-of-the-art models on native sequence recovery tasks, suggesting that utilizing TERM-based and coordinate-based features together is beneficial for protein design.
Tunable multiwavelength fiber laser based on nematic liquid crystal device for fiber-optic electric field sensor (2017)

We present a tunable multiwavelength fiber laser based on nematic liquid crystal device (NLC) for fiber-optic electric field sensor. The lasing multiwavelength could be tuned over 18 nm by applying electric field to the NLC device.
Immunomodulatory Activity of Monoclonal Anti-Idiotypic Antibody to Anti-Colorectal Carcinoma Antibody CO17–1A in Animals and Patients (1994)

Monoclonal anti-idiotypic antibody (Ab2) VF2 was derived from rats immunized with anti-colorectal carcinoma (anti-CRC) monoclonal antibody (Ab1) CO17-1A. In rabbits the Ab2 induced anti anti-idiotypic antibodies (Ab3) that shared idiotopes with the Ab1, bound to the same epitope on CRC cells as Ab1, and bound to the isolated CO17-1A antigen. Monoclonal Ab2 VF2 was superior to the previously described polyclonal goat Ab2 against Ab1 CO17-1A in its capacity to elicit humoral immunity in animals. Ab2 VF2 also induced a specific delayed-type hypersensitivity (DTH) response to challenge with irradiated CO17-1A antigen-positive human CRC cells in mice. Of nine CRC patients immunized with aluminum hydroxide-precipitated Ab2 VF2, six developed antibodies that bound to Ab2, but only three patients developed Ab3 that bound to idiotypic determinants on Ab2. However, the Ab3 did not bind to CO17-1A antigen-positive CRC cells. In contrast, in a previously described trial with polyclonal goat Ab2 to Ab1 CO17-1A, most of the patients developed anti-CRC antibodies. Four of the nine patients immunized with Ab2 VF2 developed DTH responses to intradermal challenge with the Ab2, and in one patient DTH was both Ab2- and antigen-specific. Peripheral blood mononu-clear cells of the four DTH-reactive patients did not proliferate in response to in vitro stimulation with either Ab2 or antigen. These studies demonstrate that the immunomodulatory activity of monoclonal Ab2 VF2 in animals is only in part predictive of its activity in patients.
Mechanical and permeability properties of biodegradable extruded starch/polycaprolactone films (1998)

Barley starch and glycerol were mixed with polycaprolactone (PCL) powder in various combinations and plasticized in a twin-screw extruder. When possible, extrudates were processed into films in a single-screw extruder and subjected to an orientation process with the aim of improving the water durability and mechanical strength of the starch films. The mechanical properties, water vapour and oxygen permeabilities, sorption isotherms and solubility of the processed films were studied. The films containing 20% or more PCL achieved a tensile strength of 20 MPa or higher. Orientation of the film still further improved the tensile strength, and also the water vapour and oxygen barrier properties. With PCL contents of 0–20% the starch/PCL films proved to be excellent oxygen barriers. Increase in PCL content beyond this impaired the oxygen barrier properties, whilst improving the water barrier properties. Copyright © 1998 John Wiley & Sons, Ltd.
Purification of the glucocorticoid receptor-mineralocorticoid receptor modulator-2 from rabbit liver. (1995)

Modulators-1 and -2 are endogenous low-mol-wt regulators of glucocorticoid and mineralocorticoid receptors and protein kinase C. Structural analysis of apparently purified modulators suggested that these molecules were novel ether aminophosphoglycerides. Subsequent X-ray crystallography and NMR spectroscopy indicated that the ultra-large scale modulator preparations were contaminated with glutamate and aspartate, although these amino acids lacked modulator activity. In this article, we describe the purification of modulator-2 from rabbit liver cytosol and the separation of this phosphoglyceride from these amino acids. This purification was similar to the ultra-large scale version (Bodine, P.V. and Litwack, G. [1990] J. Biol. Chem. 265, 9544-9554), but involved the chromatography of trypsinized rabbit liver cytosol on the 7-L bed volume Sephadex G-15 gel-filtration column. As before, two peaks of modulator activity (modulator-1 and -2), as well as a DNA-binding inhibitor (peak-3), eluted from the gel-filtration column. The resulting modulator-2 pool was incubated with glutamate decarboxylase and treated batch-wise with Dowex-50W cation-exchange resin and Chelex-100 resin. This enzyme/resin-treated modulator-2 preparation was then chromatographed on a Dowex-1 anion-exchange column. Finally, modulator-2 was purified by preparative silica TLC. This last purification step resulted in the separation of modulator-2 from glutamate, aspartate, and gamma-aminobutyrate. In summary, rabbit liver cytosol appears to be a reasonable source of modulator-2. In addition, treatment of the preparation with glutamate decarboxylase seems to facilitate the subsequent separation of modulator-2 from the contaminating amino acids.
Aggregatibacter actinomycetemcomitans serotypes associate with periodontal and coronary artery disease status (2018)

Aggregatibacter actinomycetemcomitans serotypes "b" and "c" associate with both periodontal and CAD status. Detectable serotypes associate with the quantity and the serology of the bacterium emphasizing both local and systemic effect of the A. actinomycetemcomitans serotypes.
Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions (2018)

Abstract Immunofluorescence (IF) imaging using antibodies to visualize specific biomolecules is a widely used technique in both biological and clinical laboratories. Standard IF imaging methods using primary antibodies followed by secondary antibodies have low multiplexing capability due to limited availability of primary antibodies raised in different animal species. Here, we used a DNA-based signal amplification method, Hybridization Chain Reaction (HCR), to replace secondary antibodies to achieve multiplexed imaging using primary antibodies of the same species with superior signal intensity. To enable imaging with DNA-conjugated antibodies, we developed a new antibody staining protocol to minimize nonspecific binding of antibodies caused by conjugated DNA oligonucleotides. We also expanded the HCR hairpin pool from previously published 5 to 13 for highly multiplexed in situ imaging. We finally demonstrated multiplexed in situ protein imaging using the technique in both cultured cells and mouse retina sections.
On binary constructions of quantum codes (1999)

We improve estimates on the parameters of quantum codes obtained by Steane's (see ibid., vol.45, no.7, p.2492-5, 1999) construction from binary codes. This yields several new families of quantum codes.
Historical Growth of Ultrasound Elastography and Directions for the Future (2018)

This chapter examines how the field of ultrasound elastography has grown over time. It analyses the publication record using PubMed for the field and focuses at different distinctions and trends. The chapter offers a perspective on future investigations that could be pursued for the use of acoustic radiation force (ARF) for ultrasound elastographic applications. It demonstrates the various techniques employed in the field of elastography and elasticity imaging as a whole. Analysis of the underlying fine structure of the "ultrasound elastography" histogram allows one to see the dynamics of relative contributions of various modalities. In most of the ARF-based imaging modalities, the ARF is dependent on an absorbing or attenuating tissue. Unfocused beams and focused beams were used in subsequent implementations of a method called comb-push ultrasound shear elastography, which uses the simultaneous production of many shear waves and then uses directional filtering and correlation-based techniques to measure shear wave velocity.
Implantation and Early Embryonic Development: Implications for Pregnancy (2007)

Implantation represents the limiting step in governing reproductive outcomes. The process is driven by both embryo and endometrium alike. Minute perturbations in this orchestration lay foundation for pregnancy-associated complications that may manifest throughout the gestational course. Furthermore, placental function dictates many aspects of fetal development inclusive of preeclampsia and intrauterine growth restriction (IUGR). Novel techniques such as Multigate Spectral Doppler Analysis (MSDA) may allow for early detection and diagnosis of potentially deleterious fetal outcomes.
Transport and Dispersion of Nanoparticles in Periodic Nanopost Arrays (2014)

Nanoparticles transported through highly confined porous media exhibit faster breakthrough than small molecule tracers. Despite important technological applications in advanced materials, human health, energy, and environment, the microscale mechanisms leading to early breakthrough have not been identified. Here, we measure dispersion of nanoparticles at the single-particle scale in regular arrays of nanoposts and show that for highly confined flows of dilute suspensions of nanoparticles the longitudinal and transverse velocities exhibit distinct scaling behaviors. The distributions of transverse particle velocities become narrower and more non-Gaussian when the particles are strongly confined. As a result, the transverse dispersion of highly confined nanoparticles at low Péclet numbers is significantly less important than longitudinal dispersion, leading to early breakthrough. This finding suggests a fundamental mechanism by which to control dispersion and thereby improve efficacy of nanoparticles applied for advanced polymer nanocomposites, drug delivery, hydrocarbon production, and environmental remediation.
Effects of Antihypertensive Drug Classes on Regression of Connective Tissue Components of Hypertension (1991)

Summary: Hypertension leads to structural and functional adaptations which, although initially protective for the cardiovascular system, ultimately work to sustain and reinforce the hypertensive state. Although blood pressure (BP) may be effectively lowered by a variety of treatments, it is becoming clear that these structural adaptations, and the risks and consequences of hypertension, may persist long after BP has been restored to normal levels. Cardiovascular tissues appear to be highly sensitive to increased BP, responding quickly with large and proportional increases in collagen and elastin. The sensitivity of this response to increased pressure, together with the slow turnover of these connective tissue proteins, suggests a mechanism by which transient or intermittent episodes of hypertension may lead to cumulative and persistent structural changes in cardiovascular tissues. With some exceptions, studies directly investigating the reversibility of these connective tissue changes have generally confirmed that increased cardiovascular collagen and elastin persist for long periods of time after BP lowering, independent of the treatment method used to achieve that lowering. Because maintenance of elevated levels of collagen and elastin is principally caused by the slow turnover of the proteins rather than by their continued production, rapid and effective reversal of cardiovascular connective tissue changes may require the development of pharmacological agents that promote or accelerate the turnover of these proteins.
A Correspondence Between Random Neural Networks and Statistical Field Theory (2017)

A number of recent papers have provided evidence that practical design questions about neural networks may be tackled theoretically by studying the behavior of random networks. However, until now the tools available for analyzing random neural networks have been relatively ad-hoc. In this work, we show that the distribution of pre-activations in random neural networks can be exactly mapped onto lattice models in statistical physics. We argue that several previous investigations of stochastic networks actually studied a particular factorial approximation to the full lattice model. For random linear networks and random rectified linear networks we show that the corresponding lattice models in the wide network limit may be systematically approximated by a Gaussian distribution with covariance between the layers of the network. In each case, the approximate distribution can be diagonalized by Fourier transformation. We show that this approximation accurately describes the results of numerical simulations of wide random neural networks. Finally, we demonstrate that in each case the large scale behavior of the random networks can be approximated by an effective field theory.
Pronounced effect of particle size on selectivity observed for carbon monoxide hydrogenation over ruthenium–alumina catalysts (1986)

The size of Ru crystallites affected markedly the selectivity for CO hydrogenation in contrast to previous reports; small particles (10 Å) produced significant proportions of higher hydrocarbons and large single crystallites (110 Å) gave mainly methane.
Discontinuous Computation Offloading for Energy-Efficient Mobile Edge Computing (2021)

We propose a novel strategy for energy-efficient dynamic computation offloading, in the context of edge-computing-aided beyond 5G networks. The goal is to minimize the energy consumption of the overall system, comprising multiple User Equipment (UE), an access point (AP), and an edge server (ES), under constraints on the end-to-end service delay and the packet error rate performance over the wireless interface. To reduce the energy consumption, we exploit low-power sleep operation modes for the users, the AP and the ES, shifting the edge computing paradigm from an <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">always on</i> to an <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">always available</i> architecture, capable of guaranteeing an on-demand target service quality with the minimum energy consumption. To this aim, we propose an online algorithm for dynamic and optimal orchestration of radio and computational resources called <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Discontinuous Computation Offloading (DisCO)</i> . In such a framework, end-to-end delay constraints translate into constraints on overall queueing delays, including both the communication and the computation phases of the offloading service. DisCO hinges on Lyapunov stochastic optimization, does not require any prior knowledge on the statistics of the offloading traffic or the radio channels, and satisfies the long-term performance constraints imposed by the users. Several numerical results illustrate the advantages of the proposed method.
Tailored Design of Protein Nanoparticle Scaffolds for Multivalent Presentation of Viral Glycoprotein Antigens (2020)

Abstract The adaptive immune system is highly sensitive to arrayed antigens, and multivalent display of viral glycoproteins on symmetric scaffolds has been found to substantially increase the elicitation of antigen-specific antibodies. Motivated by the considerable promise of this strategy for next-generation anti-viral vaccines, we set out to design new self-assembling protein nanoparticles with geometries specifically tailored to scaffold ectodomains of different viral glycoproteins. We first designed and characterized homo-trimers from designed repeat proteins with N-terminal helices positioned to match the C termini of several viral glycoprotein trimers. Oligomers found to experimentally adopt the designed configuration were then used to generate nanoparticles with tetrahedral, octahedral, or icosahedral symmetry. Examples of all three target symmetries were experimentally validated by cryo-electron microscopy and several were assessed for their ability to display viral glycoproteins via genetic fusion. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles display conformationally intact native-like HIV-1 Env, influenza hemagglutinin, and prefusion RSV F trimers in the predicted geometries. This work demonstrates that novel nanoparticle immunogens can be designed from the bottom up with atomic-level accuracy and provides a general strategy for precisely controlling epitope presentation and accessibility.
Elevated serum levels of soluble tumour necrosis factor receptors (sTNF-R) in patients with HIV infection (1992)

Serum levels of the soluble form of tumour necrosis factor receptor type II (p75) (sTNF-R) were determined in HIV-infected individuals and risk groups and were then correlated with the course of infection and prognosis. sTNF-R levels were determined by an ELISA with MoAbs and polyclonal antibodies to urine-derived sTNF-R proteins. The mean +/- s.e. levels of sTNF-R in the sera of 49 HIV+ male homosexuals, 34 HIV- male homosexuals and 44 matched controls were 6.1 +/- 0.3 ng/ml, 4.4 +/- 0.3 ng/ml and 3.4 +/- 0.2 ng/ml, respectively. All these values were significantly different between each of the groups (P less than 0.001-0.05). Sequential studies of sTNF-R revealed higher levels following seroconversion in 5/8 individuals, remained persistently high during the asymptomatic phase of the infection and became even more elevated in some ARC and AIDS patients. At the same time TNF-alpha was undetectable in sera obtained from HIV+ male homosexuals and from healthy controls. This was independent of stage of HIV infection, serum sTNF-R level and type of ELISA kit used. These findings suggest that TNF-alpha/TNF-R system is turned on before and during HIV infection and raise the possibility that sTNF-R, the natural inhibitor of TNF, may be of importance in determining the course and probably prognosis of the disease.