gebhart/patrepeval huggingface dataset:
Structure-Based Drug Design: Progress Toward the Discovery of the Elusive Bradykinin Receptor Antagonists (1995)

The de nova design of a non-peptide bradykinin receptor antagonist (or the optimization of a lead discovered by random screening) will ultimately require knowledge about the receptor topology. In the absence of an experientally-determined structure of the bradykinin-bradykinin receptor complex, we have attempted to gain insights from other sources. Specifically, we have synthesized conformationally constrained lignads, and completed extensive computer modeling and mutagenesis experiments on the bradykinin receptor. For the former, the recently reported hydroxyproline ether­ containing peptides have been useful in mapping the bradykinin receptor topology. Moreover, using systematic synthetic modifications, we have explored the relative importances of selected amide bonds 1 and side chains in second generation peptides and have made a series of and/or N-methyl 1 substitutions at positions four and five which led to the discovery of two new cyclic peptide antagonists. 1 For the latter, computational simulations led to a proposed model of bradykinin bound to its receptor which was found to be in good agreement with mutagens is results. This model led ultimately to the design and synthesis of D-Arg0-Arg 1 -(12- aminododecanoy1)2-Ser3-D-Tic4-0ic5-Arg6, a pseudo-peptide leading into a third generation of antagonists. Further improvements in tis lead structure were achieved via combinatorial non-peptide libraries.
MOESM2 of Repositioning of bromocriptine for treatment of acute myeloid leukemia (2016)

Additional file 2: Table S2. Downregulated probe set upon AML differentiation.
Semisolid solidification of high temperature superconducting oxides (2000)

Americanae nace como un proyecto conjunto que surge dentro de la Red Europea de Información y Documentación sobre América Latina (REDIAL), y que ha afrontado la Biblioteca de la Agencia Española de Cooperación Internacional para el Desarrollo (AECID). Esta nueva biblioteca virtual hace más accesibles los libros digitales de tema americanista a los investigadores y usuarios interesados de cualquier parte del mundo.
Catch and Release: Integrated System for Multiplexed Detection of Bacteria (2013)

An integrated system with automated immunomagnetic separation and processing of fluidic samples was demonstrated for multiplexed optical detection of bacterial targets. Mixtures of target-specific magnetic bead sets were processed in the NRL MagTrap with the aid of rotating magnet arrays that entrapped and moved the beads within the channel during reagent processing. Processing was performed in buffer and human serum matrixes with 10-fold dilutions in the range of 10(2)-10(6) cells/mL of target bacteria. Reversal of magnets' rotation post-processing released the beads back into the flow and moved them into the microflow cytometer for optical interrogation. Identification of the beads and the detection of PE fluorescence were performed simultaneously for multiplexed detection. Multiplexing was performed with specifically targeted bead sets to detect E. coli 0157.H7, Salmonella Common Structural Antigen, Listeria sp., and Shigella sp., dose-response curves were obtained, and limits of detection were calculated for each target in the buffer and clinical matrix. Additional tests demonstrated the potential for using the MagTrap to concentrate target from larger volumes of sample prior to the addition of assay reagents.
Synthesis and polymerization of p‐(p′‐vinylbenzoyl)‐peroxybenzoic acid tert‐butylester: A monomer containing a photodissociable radical source (1981)

Abstract In a previous report we have shown that efficiently photodecomposable, but thermally stable, peresters can be made from a compound that contains both a triplet photosensitizer functionality and a perester group. This fundamental approach has been extended to make a novel vinyl monomer containing a triplet sensitizer and a perester group. Thus, the monomer p ‐vinylbenzoyl‐ p ‐ tert ‐butyl perbenzoate (VBPE) has been synthesized and polymerized by normal procedures without loss of perester activity. The resulting polymer perester can be used as an efficient photolabile radical source by irradiating at the λ max of the benzophenone carbonyl moiety. The homopolymer (PVBPE) and copolymers with other monomers, such as styrene, could be photocrosslinked with high efficiency. Copolymers of VBPE and styrene containing low percentages of VBPE have been used to initiate graft chains of poly(methyl methacrylate) by irradiating a solution of the copolymer in methyl methacrylate at 366 nm.
Trimolecular Complex Formation of IgE, FcεRI, and a Recombinant Nonanaphylactic Single-Chain Antibody Fragment with High Affinity for IgE (2009)

IgE is a central molecule in allergic disease. We have isolated cDNAs coding for the heavy and light chains of a murine mAb specific to human IgE and expressed a recombinant single-chain variable fragment (ScFv) derived thereof in Escherichia coli. The purified recombinant ScFv has a molecular mass of 28 kDa as measured by mass spectrometry and shows a beta-sheet fold as determined by circular dichroism. In biosensor-based studies it was demonstrated that the ScFv rapidly and stably binds to human IgE with an affinity of K(D) of 1.52 x 10(-10) M, which is almost as high as the affinity of IgE for FcepsilonRI, and that the ScFv is able to recognize FcepsilonRI-bound IgE and to prevent IgE binding to FcepsilonRI. The ScFv reacts specifically with IgE but not with other isotypes, allows the measurement of allergen-specific IgE in serum samples, and specifically targets cells that contain FcepsilonRI- or FcepsilonRII-bound IgE or that secrete IgE. Using negative-stain electron microscopy we demonstrated the formation of bimolecular complexes consisting of two ScFv molecules and one IgE and trimolecular complexes consisting of IgE, FcepsilonRI, and ScFv in which only one ScFv is able to bind to IgE. Accordingly, we found that the ScFv does not cross-link basophil-bound IgE and hence does not induce histamine release or activation of basophils as demonstrated by FACS analysis of CD203c expression and by histamine release experiments. In vivo skin testing confirmed the lack of allergenic activity of the ScFv. The recombinant ScFv may represent a universal tool for the IgE-targeted treatment of allergies.
Ionic Liquids for the Dissolution and Regneration of Cellulose (2002)

There is an increasing willingness to develop new cellulose-based materials, particularly from homogeneous solution, due to the fact that cellulose is the earth's most abundant biorenewable resource. The opportunity to use ionic liquids as solvents for clean extraction and processing of cellulose has been investigated. Cellulose can be dissolved in a number of ionic liquids and easily regenerated by contacting with water. This allows a simple, benign system for the processing of cellulose into fibers, monoliths, and films by forming into an aqueous phase. This has potential environmental and cost advantages over current processing methodologies which make use of volatile or hazardous solvents.
The Regulator Interactions of p21 and PCNA in Human Breast Cancer (2001)

Abstract : To better understand the role of DNA replication in breast cancer, it is essential to examine the machinery that carries out the DNA synthetic process. Our laboratory has successfully purified a complex of proteins from breast cells that is fully competent to carry out T-antigen dependent, SV4O origin specific DNA replication in vitro, which we have termed the DNA synthesome. Analysis of the constituent proteins of the DNA synthesome of malignant and non-malignant breast cells by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) has uncovered a modification in an essential DNA replication protein, proliferating cell nuclear antigen (PCNA). 2D PAGE analysis revealed that PCNA of malignant breast cells resolves as two distinct species, an unmodified form and a modified form, while PCNA present in non-malignant cell resolves exclusively as one form, the modified form. PCNA functions by forming a trimeric sliding clamp that encircles the DNA and interacts with the DNA polymerases delta and epsilon. Polymerase delta carries out leading strand DNA synthesis, and although a role for polymerase E has not1 yet been ascribed, it has been hypothesized to function in DNA repair. Another protein that interacts with PCNA is p21WAFl/CIPl/SDI1. P21 is a CDK inhibitor that, when induced by p53 in response to DNA damage, binds PCNA and effectively competes away polymerase 8 leading to the efficient inhibition of DNA replication. This inhibition impedes the replication of damaged DNA and theoretically allots time for the cell to repair its damaged DNA. Therefore, any alterations of the PCNA molecule could potentially abrogate p2 1 binding leading to replication of damaged DNA and/or insufficient time for DNA repair. It is our goal to study the interaction of p2 1 with the modified and non-modified forms of PCNA and to investigate any functional consequences alterations in PCNAIp2 1 binding may have on DNA replication, DNA repair, and DNA replication fidelity.
Direct Hysteresis Heating of Catalytically Active Ni–Co Nanoparticles as Steam Reforming Catalyst (2017)

We demonstrated a proof-of-concept catalytic steam reforming flow reactor system heated only by supported magnetic nickel–cobalt nanoparticles in an oscillating magnetic field. The heat transfer was facilitated by the hysteresis heating in the nickel–cobalt nanoparticles alone. This produced a sufficient power input to equilibrate the reaction at above 780 °C with more than 98% conversion of methane. The high conversion of methane indicated that Co-rich nanoparticles with a high Curie temperature provide sufficient heat to enable the endothermic reaction, with the catalytic activity facilitated by the Ni content in the nanoparticles. The magnetic hysteresis losses obtained from temperature-dependent hysteresis measurements were found to correlate well with the heat generation in the system. The direct heating of the catalytic system provides a fast heat transfer and thereby overcomes the heat-transfer limitation of the industrial-scale steam reformer. This could consequently enable a more compact steam reformer design.
Lightweight Techniques for Private Heavy Hitters (2021)

This paper presents a new protocol for solving the private heavy-hitters problem. In this problem, there are many clients and a small set of data-collection servers. Each client holds a private bitstring. The servers want to recover the set of all popular strings, without learning anything else about any client’s string. A web-browser vendor, for instance, can use our protocol to figure out which homepages are popular, without learning any user’s homepage. We also consider the simpler private subset-histogram problem, in which the servers want to count how many clients hold strings in a particular set without revealing this set to the clients.Our protocols use two data-collection servers and, in a protocol run, each client send sends only a single message to the servers. Our protocols protect client privacy against arbitrary misbehavior by one of the servers and our approach requires no public-key cryptography (except for secure channels), nor general-purpose multiparty computation. Instead, we rely on incremental distributed point functions, a new cryptographic tool that allows a client to succinctly secret-share the labels on the nodes of an exponentially large binary tree, provided that the tree has a single non-zero path. Along the way, we develop new general tools for providing malicious security in applications of distributed point functions.A limitation of our heavy-hitters protocol is that it reveals to the servers slightly more information than the set of popular strings itself. We precisely define and quantify this leakage and explain how to ameliorate its effects. In an experimental evaluation with two servers on opposite sides of the U.S., the servers can find the 200 most popular strings among a set of 400,000 client-held 256-bit strings in 54 minutes. Our protocols are highly parallelizable. We estimate that with 20 physical machines per logical server, our protocols could compute heavy hitters over ten million clients in just over one hour of computation.
Evidence for Intracellular and Extracellular Dimethylsulfoniopropionate (DMSP) Lyases and DMSP Uptake Sites in Two Species of Marine Bacteria (1997)

The kinetics of dimethylsulfoniopropionate (DMSP) uptake and dimethylsulfide (DMS) production from DMSP in two bacterial species, Alcaligenes sp. strain M3A, an isolate from estuarine surface sediments, and Pseudomonas doudoroffii, from seawater, were investigated. In Alcaligenes cells induced for DMSP lyase (DL) activity, DMS production occurred without DMSP uptake. In DL-induced suspensions of P. doudoroffii, uptake of DMSP preceded the production of DMS, indicating an intracellular location of DL; intracellular DMSP levels reached ca. 7 mM. DMSP uptake rates in noninduced cells showed saturation at three concentrations (K(inft) [transport] values, 3.4, 127, and 500 (mu)M). In DL-induced cells of P. doudoroffii, DMSP uptake rates increased ca. threefold (V(infmax), 0.022 versus 0.065 (mu)mol of DMSP taken up min(sup-1) mg of cell protein(sup-1)), suggesting that the uptake binding proteins were inducible. DMSP uptake and DL activity in P. doudoroffii were both inhibited by CN(sup-), 2,4-dinitrophenol, and membrane-impermeable thiol-binding reagents, further indicating active uptake of DMSP by cell surface components. The respiratory inhibitors had limited or no effect on DL activity by the Alcaligenes sp. Of the structural analogs of DMSP tested for their effect on DMSP metabolism, glycine betaine (GBT), but not methyl-3-mercaptopropionic acid (MMPA), inhibited DMSP uptake by P. doudoroffii, suggesting that GBT shares a binding protein with DMSP and that MMPA is taken up at a separate site. Two models of DMSP uptake, induction, and DL location found in marine bacteria are presented.
ChemInform Abstract: Efficient Monophosphorus Ligands for Palladium‐Catalyzed Miyaura Borylation. (2011)

Abstract Sterically hindered aryl bromides and chlorides are converted with very low catalyst loadings using the new monophosphorus ligand (Ia) and Bedford′s Pd precursor (II).
Symposium 8: Monte Carlo simulations (2000)

Many heterogeneous catalysts of industrial use consist of metals and promoters supported by porous alumina of very high specific surface. In order to optimize the catalyst, it is of great practical importance to know the space distribution of active elements inside the matrix. Electron Probe Micro Analysis (EPMA) is a particularly useful technique for studying local variations of composition. Although the concentrations of metals in our catalysts are usually less than 2 % in weight, experimental EPMA measurements clearly reveal that the intensity of X-rays (A1 Koc and O Ka) emitted from porous alumina is less than the intensity from compact mono-crystalline alumina (sapphire). Moreover, the loss of X-rays depends on the particular line being measured, the accelerating voltage, the measurement time, the embedding medium, the preparation of the sample, etc. Consequently, when traditional EPMA quantitative procedures are employed, they yield unrealistically low concentrations of metals. Some authors [1,2] have suggested that the Xray signal loss might be a consequence of charge trapping in the insulating material. On the other hand, measured x-ray intensities also depend on the porosity of the sample, which indicates that the signal loss may be partially due to the porous structure of the material.
The Effect of Vibration on the Shipment of Palletized Products (1995)

&lt;div class="htmlview paragraph"&gt;Today's competitive food and produce markets require better understanding of the design of packaged, palletized products in order to minimize product damage during shipping, maintain quality, control costs, and address promotional and environmental concerns. To further define important design parameters, the effects of shipment vibration on palletized products were measured. The premise of this study was that the natural frequencies of the palletized product should be different from those of the vehicle in order to decrease resonant behavior that may lead to packaging failure. The study was conducted in two stages. First, the natural frequencies of the product itself were examined, then the natural frequencies of fully loaded truck trailers were investigated. A description of analytical and experimental methods for evaluating packaging design and suggestions for ways to avoid resonant excitation are presented.&lt;/div&gt;
A port expander using protocol-independent link-aggregation technologies for large-scale data-center networks (2014)

A port expander using protocol-independent linkaggregation technologies for distributed large-scale data-center networks was proposed and evaluated. These technologies can accommodate multiple link-layer protocols with various data rates to form distributed large-scale data centers. They also reduce processing latency of data-center networks, compared with conventional data center networks (which require multi-stage frame processing). A prototype port expander implementing the proposed technologies on field-programmable gate arrays (FPGAs) was constructed and experimentally evaluated. The implementation rate for each FPGA is 80% maximum. The prototype port expander can aggregate three kinds of different low-speed physical links (i.e., 10GbE, 40GbE, and 100GbE). This implementation demonstrates the feasibility of the proposed protocol-independent link-aggregation technologies for large-scale data center networks.
A Survey of Routing Attacks and Security Measures in Mobile Ad-Hoc\n Networks (2011)

Mobile ad hoc networks (MANETs) are a set of mobile nodes which are\nself-configuring and connected by wireless links automatically as per the\ndefined routing protocol. The absence of a central management agency or a fixed\ninfrastructure is a key feature of MANETs. These nodes communicate with each\nother by interchange of packets, which for those nodes not in wireless range\ngoes hop by hop. Due to lack of a defined central authority, securitizing the\nrouting process becomes a challenging task thereby leaving MANETs vulnerable to\nattacks, which results in deterioration in the performance characteristics as\nwell as raises a serious question mark about the reliability of such networks.\nIn this paper we have attempted to present an overview of the routing\nprotocols, the known routing attacks and the proposed countermeasures to these\nattacks in various works.\n
Novel Bidirectional Multicore EDFA Based on Twin Turbo Cladding Pumping Using Bidirectional Pumping and Recycling (2022)

By designing a multicore EDFA symmetrically between input and output bi-directional cladding pumping has been successfully demonstrated. 1.9 dB gain improvement compared with the conventional forward pumping was clarified due to the bi-directional pumping
Multi-heterodyne Characterization of Multi-Gigahertz Spaced Optical Frequency Comb Sources (2010)

Mixing products between frequency combs with detuned repetition rates are used to characterize multi-gigahertz spaced optical frequency combs generated from mode-locked semiconductor lasers. Time domain RF waveform measurements show effective sampling of the optical waveform.
Endothelial gaps and adherent leukocytes in allergen-induced early- and late-phase plasma leakage in rat airways. (1998)

Exposure of sensitized individuals to antigen can induce allergic responses in the respiratory tract, manifested by early and late phases of vasodilatation, plasma leakage, leukocyte influx, and bronchoconstriction. Similar responses can occur in the skin, eye, and gastrointestinal tract. The early-phase response involves mast cell mediators and the late-phase response is leukocyte dependent, but the mechanism of leakage is not understood. We sought to identify the leaky blood vessels, to determine whether these vessels contained endothelial gaps, and to analyze the relationship of the gaps to adherent leukocytes, using biotinylated lectins or silver nitrate to stain the cells in situ and Monastral blue as a tracer to quantify plasma leakage. Most of the leakage occurred in postcapillary venules (< 40-microns diameter), whereas most of the leukocyte migration (predominantly neutrophils) occurred in collecting venules. Capillaries and arterioles did not leak. Endothelial gaps were found in the leaky venules, both by silver nitrate staining and by scanning electron microscopy, and 94% of the gaps were distinct from sites of leukocyte adhesion or migration. We conclude that endothelial gaps contribute to both early and late phases of plasma leakage induced by antigen, but most leakage occurs upstream to sites of leukocyte adhesion.
Leaky DNN: Stealing Deep-Learning Model Secret with GPU Context-Switching Side-Channel (2020)

Machine learning has been attracting strong interests in recent years. Numerous companies have invested great efforts and resources to develop customized deep-learning models, which are their key intellectual properties. In this work, we investigate to what extent the secret of deep-learning models can be inferred by attackers. In particular, we focus on the scenario that a model developer and an adversary share the same GPU when training a Deep Neural Network (DNN) model. We exploit the GPU side-channel based on context-switching penalties. This side-channel allows us to extract the fine-grained structural secret of a DNN model, including its layer composition and hyper-parameters. Leveraging this side-channel, we developed an attack prototype named MosConS, which applies LSTM-based inference models to identify the structural secret. Our evaluation of MosConS shows the structural information can be accurately recovered. Therefore, we believe new defense mechanisms should be developed to protect training against the GPU side-channel.
Determinants and consequences of heart rate and stroke volume response to exercise in patients with heart failure and preserved ejection fraction (2021)

The haemodynamic response to exercise was very heterogeneous among patients with HFpEF, with chronotropic incompetence observed in up to 56%, and 28% had impaired increase in SVI. This suggests that haemodynamic exercise testing may be useful to identify which HFpEF patients may benefit from interventions targeting stroke volume and chronotropic response.
Effect of Somatostatin on Insulin‐Induced hypoglycemia in Man (1982)

In order to study the interaction of insulin and somatostatin on glucose regulation in the posthypoglycemic phase of a somatostatin infusion we have applied a bolus of i.v. insulin to healthy subjects receiving a continuous infusion of somatostatin. Glucose, insulin and counterregulatory hormones were determined. Somatostatin suppressed the growth hormone and glucagon responses to hypoglycemia but did not augment the hypoglycemic action of insulin. In contrast, the K-value for the decrease in blood glucose was significantly lower in the presence of somatostatin. Thus, the interaction of insulin and somatostatin on glucose metabolism is complex and time-dependent. While the peptide potentiates the action of insulin during the first hour of somatostatin infusion, it counteracts if after two hours. As somatostatin has currently been introduced in the therapy of upper gastrointestinal bleedings, these effects of the peptide must be taken into consideration.