gebhart/patrepeval huggingface dataset:
Mapping of the Adrenomedullin-Binding Domains in Human Complement Factor H (2003)

Adrenomedullin (AM) is a multifunctional peptide involved in roles as varied as blood pressure regulation, growth, neurotransmission, and inflammation control, among others. We previously identified complement factor H as a serum binding protein for AM and showed that factor H regulates AM functions and vice versa. Here we searched for the specific binding sites for AM by using recombinant fragments of factor H and a non-radioactive binding assay with fluorescein-tagged AM. By this methodology, two specific binding sites for AM were found in factor H. One of them shows a high affinity for AM and is located at the carboxy terminal end of factor H, comprising short consensus repeats (SCR) 15-20. Smaller fragments of this region did not bind to AM efficiently, suggesting that the high affinity binding site of factor H requires a complex three-dimensional structure to recognize AM. Another binding site with lower affinity for AM was found in the middle of the factor H molecule, at SCR 8-11. Antibodies against factor H prevented AM binding altogether, but the main binding partner of factor H, C3b, did not, indicating that C3b and AM bind to different regions of factor H. These structure-function data support previous biochemical observations. Our understanding of the binding between AM and factor H may help in the development of new treatments for diseases in which these molecules play active roles.
[<sup>3</sup>H]WIN 35,065–2: A Ligand for Cocaine Receptors in Striatum (1990)

[3H]WIN 35,065-2 binding to striatal membranes was characterized, primarily by centrifugation assay. Like [3H]cocaine, [3H]WIN 35,065-2 binds to both high- and low-affinity sites. [3H]WIN 35,065-2, however, exhibits consistently higher affinities than [3H]cocaine. Saturation experiments indicate a low-affinity binding site with an apparent KD of approximately 160 nM and a Bmax of 135 fmol/mg of tissue. A high-affinity site has also been identified with an apparent KD of 5.6 nM and a Bmax of 5.2 fmol/mg of tissue. The specific-to-nonspecific binding ratios with [3H]WIN 35,065-2 were higher than with [3H]cocaine in both centrifugation and filtration assays. Pharmacological characterization suggests that [3H]WIN 35,065-2 binds to the dopamine transporter. Mazindol, GBR 12909, nomifensine, and (-)-cocaine are potent inhibitors of [3H]WIN 35,065-2 binding. In contrast, the norepinephrine transporter ligand desipramine is a weak inhibitor, and the serotonin transporter ligand citalopram does not inhibit binding. The effect of sodium on binding was examined under conditions in which (a) the low-affinity site was primarily (87%) occupied and (b) approximately 50% of both sites were occupied. The results indicate that both sites are sodium dependent. Injection of 6-hydroxydopamine into the striatum results in a significant loss of both high- and low-affinity sites, a finding suggesting that both sites are on dopaminergic nerve terminals. Taken together, these data are consistent with the presence of multiple cocaine binding sites associated with the dopamine transporter.
Programmable high-speed polarization multiplexed optical scanner (2003)

A fast digital-analog control polarization-based optical scanner with complete three-dimensional beam-forming programmability is described. Its features include low power consumption and large-aperture liquid-crystal-based optics, digital repeatability, and time-multiplexed accurate analog beam forming. Analog frequency and amplitude control of the nematic liquid-crystal beam-former cells permits continuous fine-scan programmability over a 0.66-mrad horizontal deflection, a 0.75 mrad vertical deflection, and an infinity-to-1.84-m focal-length longitudinal scan. First demonstrations included an 8-point volumetric scan and a 2-bit digital lens scan, both at 1310 nm, with a 35-micros random-access time.
Highly potent, chemically stable quorum sensing agonists for vibrio Cholerae (2013)

In the <i>Vibrio cholerae</i> pathogen, initiation of bacterial quorum sensing pathways serves to suppress virulence. We describe herein a potent and chemically stable small molecule agonist of <i>V. cholerae</i> quorum sensing, which was identified through rational drug design based on the native quorum sensing signal. This novel agonist may serve as a useful lead compound for the control of virulence in <i>V. cholerae</i>.
HCV NS3 protease enhances liver fibrosis via binding to and activating TGF-β type I receptor (2013)

Viruses sometimes mimic host proteins and hijack the host cell machinery. Hepatitis C virus (HCV) causes liver fibrosis, a process largely mediated by the overexpression of transforming growth factor (TGF)-β and collagen, although the precise underlying mechanism is unknown. Here, we report that HCV non-structural protein 3 (NS3) protease affects the antigenicity and bioactivity of TGF-β2 in (CAGA)9-Luc CCL64 cells and in human hepatic cell lines via binding to TGF-β type I receptor (TβRI). Tumor necrosis factor (TNF)-α facilitates this mechanism by increasing the colocalization of TβRI with NS3 protease on the surface of HCV-infected cells. An anti-NS3 antibody against computationally predicted binding sites for TβRI blocked the TGF-β mimetic activities of NS3 in vitro and attenuated liver fibrosis in HCV-infected chimeric mice. These data suggest that HCV NS3 protease mimics TGF-β2 and functions, at least in part, via directly binding to and activating TβRI, thereby enhancing liver fibrosis.
Free-space micromachined optical crossconnects: routes to enhanced port-count and reduced loss (2003)

We investigate fundamental loss mechanisms in free-space micromachined optical crossconnects due to diffraction, aperturing, and mirror-curvature, and identify means of combating them. The effects are shown experimentally to permit 16/spl times/16 crossconnects with 2.9 dB of loss. Theory suggests a route to 1024-port multistage switches with 6 dB of loss.
Automatic Intelligent Data Analysis (2009)

This chapter introduces a new way of using soft constraints for selecting data analysis methods that match certain user requirements. It presents a software platform for automatic data analysis that uses a fuzzy knowledge base for automatically selecting and executing data analysis methods. In order to support business users in running data analysis projects the analytical process must be automated as much as possible. The authors argue that previous approaches based on the formalisation of analytical processes were less successful because selecting and running analytical methods is very much an experience-led heuristic process. The authors show that a system based on a fuzzy knowledge base that stores heuristic expert knowledge about data analysis can successfully lead to automatic intelligent data analysis.
Comparison of optical performances of alternative grazing incidence collector designs for EUV lithography (2007)

Two designs of grazing incidence collectors for EUV lithography are described as alternative solutions to the type I Wolter configuration. The main purposes of the designs are the improvement of collection efficiency and the increase in the flexibility with which the design can be adapted and adjusted to the boundary specifications set by the source and the illuminator. With reference to a specific scenario, examples of these designs and their performances are presented, discussed, and compared to what can be achieved with a Wolter collector. In this scenario, one of the designs offers the possibility to achieve large collection efficiency with a limited number of mirrors as opposed to the Wolter case where high values of the collection efficiency are possible provided the number of mirrors is increased.
Photophysical Properties and Singlet Oxygen Generation Efficiencies of Water‐Soluble Fullerene Nanoparticles (2014)

As various fullerene derivatives have been developed, it is necessary to explore their photophysical properties for potential use in photoelectronics and medicine. Here, we address the photophysical properties of newly synthesized water-soluble fullerene-based nanoparticles and polyhydroxylated fullerene as a representative water-soluble fullerene derivative. They show broad emission band arising from a wide-range of excitation energies. It is attributed to the optical transitions from disorder-induced states, which decay in the nanosecond time range. We determine the kinetic properties of the singlet oxygen ((1)O2) luminescence generated by the fullerene nanoparticles and polyhydroxylated fullerene to consider the potential as photodynamic agents. Triplet state decay of the nanoparticles was longer than (1)O2 lifetime in water. Singlet oxygen quantum yield of a series of the fullerene nanoparticles is comparably higher ranging from 0.15 to 0.2 than that of polyhydroxylated fullerene, which is about 0.06.
Large-area high-resolution lithography and photoablation systems for microelectronics and optoelectronics fabrication (2002)

An important requirement in the production of numerous microelectronic, optoelectronic, and microsystem devices is lithographic patterning on a large area with high image resolution and precise layer-to-layer alignment. Whereas for production of semiconductor devices advances have been steadily made in steppers and other conventional lithography systems, the lithography requirements for the fabrication of large-format products, such as displays, multilayer circuits, and flexible electronics, are distinctly different, rendering various conventional lithography tools inadequate. These requirements and distinctions of large-area lithography are discussed. In the last several years, we have developed a new class of projection lithography systems that provide both high-resolution imaging and very large exposure area capability with high-precision alignment. The systems, using excimer laser sources, function as dual-mode, high-throughput production tools, capable of patterning in photoresists as well as photoablation in polymers, making them attractive for production of numerous large-format products, with feature sizes ranging from 15 /spl mu/m to below 1 /spl mu/m and substrate sizes ranging from 150 /spl times/ 150 mm to 610 /spl times/ 915 mm. We review the new lithography system technology, several completed systems, and demonstrated results.
<title>Applications of shape memory alloys: advantages, disadvantages, and limitations</title> (2001)

Titanium-nickel (TiNi) based shape memory alloys (SMAs) are used in a wide range of applications. They are especially practical as thin film actuators because of the large work output per unit of actuator mass and ability for rapid thermal cycling due to large surface to volume ratio. Sputter deposited thin TiNi film has been developed for use in miniature actuators for microvalves, microrelays, optical switches and also for building small implantable medical devices. Chemical composition of the deposited SMA must be held within close limits and for the film to have shape memory properties a crystallization anneal is required. To avoid flaws in film quality the surface on which SMA is deposited has to meet certain criteria. Basic MEMS processes (photolithography and chemical etching) are used for device fabrication. Although TiNi is resistant to most chemicals, some acids used in MEMS can damage it. Thus, selection of processes and reagents compatible with TiNi requires care and experimentation. This paper discusses some applications of SMA thin films along with experience gained in bringing device s to production readiness. It illustrates simple design rules for incorporating shape memory microactuators in MEMS devices and describes some of the pitfalls to be avoided.
Spot weld analysis with 2D ultrasonic Arrays (2004)

This paper describes a threefold method of testing the performance of an array-based ultrasonic tool for nondestructive testing of spot welds. The tool is described in its capabilities, use, and advantages over existing counterparts. Performance testing for and the results from carrying out the testing are described. The three performance testing methods include 1) the use of calibrated samples, 2) comparisons with actual spot-welds, and 3) a performance evaluation of the embedded fitting software. The test of the fitting software was carried out by a comparison of results with reference fits supplied by the National Institute of Standards and Technology.
Studies on antifungal agents. 17. Effects of the C-5-substitution on the in vitro activity of novel 3,5-substituted isoxazolidines. (1988)

A number of novel 5-(substituted thiomethyl)-3-phenyl-3-(1H-imidazol-1-ylmethyl)-2- methylisoxazolidine derivatives were prepared and evaluated in vitro for antifungal activity in solid agar cultures against Trichophyton rubrum, Aspergillus fumigatus and Candida albicans. The effect of the 5-(substituted thiomethyl) group on the degree and scope of activity was studied and compared to that of the corresponding 5-phenoxymethyl and 5-[(substituted phenyl)thio(or amino)methyl] derivatives.
Floating body effects in partially-depleted SOI CMOS circuits (1996)

This paper presents a detailed study on the impact of floating body in partially-depleted (PD) SOI MOSFET on various digital VLSI CMOS circuit families. The parasitic bipolar effect resulting from the floating body is shown to degrade the circuit noise margin and stability in general. In certain dynamic circuits and wide multiplexers, the parasitic bipolar effect is shown to cause logic state error if not properly accounted for.
<title>New shape representation and similarity measure for efficient shape indexing</title> (2001)

Efficient search and retrieval of similar shapes in large databases stipulates two hardly compatible demands to the shape representations. On one hand, shape similarity conveys similarity of spatial relations of the shape parts. Thus, the representation should embed a kind of graph description of the shape, and allow estimation of the (inexact) correspondence between these descriptions. On the other hand, the representation should enable fast retrieval in large databases. Current shape indexing solutions do not comply well to these stipulations simultaneously. The G-graphs have been introduced as shape descriptors conveying structural and quantitative shape information. In the current work we define a representation of the G-graphs by strings consisting of the symbols from a four-letter alphabet such that two G-graphs are isomorphic as G-graphs if and only if their string representations are identical. This allows us to represent shapes by vectors consisting of strings and to introduce a shape representation satisfying both above demands. Experimental results are presented.
Single-polarization fiber (1983)

We report the first optical fiber which guides only one polarization. This fiber polarizer utilizes high birefringence to split the two polarizations of the fundamental mode and a cladding structure which attenuates one polarization by tunneling. The fiber is one of a class of recently proposed single-polarization fibers1-3 as opposed to earlier fiber polarizers which require polishing a section of fiber followed by metal coating4 or matching to a birefringent crystal.5
Fermentation conditions affecting the bacterial growth and exopolysaccharide production by Streptococcus thermophilus ST 111 in milk-based medium (2004)

The use of an appropriate milk-based medium and a combined model of temperature and pH can be of practical importance for the production of yoghurt or other fermented milks as well as for process optimization of the large-scale production of starter strains to be used for their EPS production.
Receptor for acidic fibroblast growth factor is related to the tyrosine kinase encoded by the fms-like gene (FLG). (1989)

We have previously isolated a human gene from an endothelial cell cDNA library encoding a putative tyrosine kinase; we have designated this gene the fms-like gene (FLG). To analyze the gene product(s) of FLG, we have generated rabbit polyclonal antibodies directed against a synthetic peptide from FLG and used it to immunoprecipitate biosynthetically labeled FLG protein from a variety of human cell lines. These antibodies specifically recognized glycoprotein(s) of 100, 120, and 135 kDa with protein cores of 90 and 110 kDa. Acidic fibroblast growth factor (aFGF) stimulated tyrosine kinase activity of FLG in vitro and in living cells, suggesting that FLG encodes the membrane receptor for aFGF. Further supporting evidence came from cross-linking experiments on intact cells with the covalent cross-linking agent disuccinimidyl suberate and 125I-labeled aFGF as a specific probe. The cross-linked 125I-labeled aFGF-aFGF receptor complex was specifically immunoprecipitated with FLG antipeptide antibodies. It appears, therefore, that the receptor(s) for aFGF is related to the FLG gene product.
Optimizing debt collections using constrained reinforcement learning (2010)

The problem of optimally managing the collections process by taxation authorities is one of prime importance, not only for the revenue it brings but also as a means to administer a fair taxing system. The analogous problem of debt collections management in the private sector, such as banks and credit card companies, is also increasingly gaining attention. With the recent successes in the applications of data analytics and optimization to various business areas, the question arises to what extent such collections processes can be improved by use of leading edge data modeling and optimization techniques. In this paper, we propose and develop a novel approach to this problem based on the framework of constrained Markov Decision Process (MDP), and report on our experience in an actual deployment of a tax collections optimization system at New York State Department of Taxation and Finance (NYS DTF).
Double solvent extraction of organic constituents from tar sands. [light naphtha/methanol solvent system] (1977)

Extraction of hydrocarbons from tar sands with a light naphtha/methanol solvent system results in rapid decrepitation of the tar-sand aggregate and separation of organic matter into three phases. Distribution of the extracted and non-extracted organic material is among the phases. The most desirable, non-polar organic materials are recovered from the light naphtha phase; more polar soluble constituents are recovered from the methanol phase; and less desirable asphaltenes separate as a precipitate.
Toward smart utilization of two X-ray images for 2-D/3-D registration applied to abdominal aortic aneurysm interventions (2011)

Minimally invasive abdominal aortic aneurysm (AAA) stenting can be greatly facilitated by overlaying the pre-operative 3-D model of the abdominal aorta onto the intra-operative 2-D X-ray images. Accurate 2-D/3-D registration in 3-D space makes the 2-D/3-D overlay robust to the change of C-Arm angulations. Typically at least two X-ray images showing the abdominal aorta from different angles are needed for an accurate registration of the aorta in 3-D. This requires two or multiple contrast agent injections into the aorta which on the other hand needs to be minimized for patient's safety. In this paper, a novel 2-D/3-D registration technique is proposed for using only one image with contrast injection in the abdominal aorta and one native image showing the spine to achieve accurate registration of the abdominal aorta in 3-D. The proposed method utilizes the two X-ray images in an integrated but differentiable way in order to best utilize the complementary information provided by the two types of images. A hierarchical registration scheme is deployed by a sensible partition of the registration parameter space based on the image acquisition protocol and the patient's motion constraint. The proposed method was validated using both synthetic and clinical datasets, and achieved significantly improved accuracy and robustness compared to the conventional methods.
Cloning of the Murine Counterpart of the Tumor-Associated Antigen H-L6: Epitope Mapping of the Human and Murine L6 Antigens (1995)

The murine monoclonal antibody (mAb) L6 was raised against human lung carcinoma cells and found to recognize an antigen which is highly expressed on lung, breast, colon, and ovarian carcinomas. Promising results in phase 1 clinical studies with this antibody or its chimerized counterpart suggest the antigen recognized by mAb L6 (H-L6) is an attractive target for monoclonal antibody-based cancer therapy. Further development of L6 as an anti-tumor-targeting agent would benefit from the development of a murine model. However, initial attempts to develop such a model were hampered by our inability to generate antibodies against the murine homologue of the L6 antigen, M-L6. Here we describe the preparation of the mAb 12A8, which was raised against murine thymic epithelial cells, the tissue distribution of the murine antigen recognized by 12A8, the cloning of a cDNA encoding the 12A8 target antigen, and the demonstration that this antigen is M-L6. Using H-L6/M-L6 chimeric proteins, we show that the region of the M-L6 protein recognized by mAb 12A8 corresponds to the region of H-L6 recognized by mAb L6. There are five amino acid differences in the regions of the H-L6 and M-L6 proteins recognized by L6 and 12A8, respectively. We further mapped the protein epitope recognized by L6 by individually exchanging each of these residues in H-L6 with the corresponding residue found in M-L6. Substitution of the single H-L6 residue Leu122 with Ser resulted in the H-L6 mutant HL6-L122S which failed to bind L6. The HL6-L122S mutant also failed to bind 12A8.(ABSTRACT TRUNCATED AT 250 WORDS)
Reversible optical waveguide sensor for ammonia vapors (1983)

A small glass capillary tube was fitted with a light-emitting diode and a phototransistor detector to form a multiple-reflecting optical waveguide device. When the capillary was coated with a thin solid film composed of an oxazine perchlorate dye, the device was demonstrated to be capable of reversibly sensing ammonia vapors. Ammonia-vapor concentrations from 1000 parts in 106 (ppm) to less than 60 ppm were easily and reproducibly detected. A preliminary qualitative kinetic model is proposed to describe the vapor–film interaction.
Characterization of Supported Nanoporous Carbon Membranes (2000)

A new method for the fabrication of supported nanoporous carbon membranes, involving ultrasonic deposition of the polymer precursor, is presented here. The method has been used to produce mechanically robust, continuous films of nanoporous carbon on tubular, macroporous stainless steel supports using polyfurfuryl alcohol as the polymer precursor. The films, which were characterized using microscopy and spectrometry, show unprecedented molecular sieving selectivities for very small molecules, such as oxygen, nitrogen, helium, and hydrogen.
DNA - Nanoelectronics: Realization of a Single Electron Tunneling Transistor and a Quantum Bit Element (1998)

Based on the understanding that chemical bonds can act as tunnel junctions in the Coulomb blockade regime, and on the technical ability to coat a DNA strand with metal, we suggest that DNA can be used to built logical devices. We discuss two explicit examples: a Single Electron Tunneling Transistor (SET) and a Quantum Bit Element. These devices would be literally in the nano-meter scale and would be able to operate at room temperature. In addition they would be identical to each other, highly stable and would have a self assembly property.