gebhart/patrepeval huggingface dataset:
Stable, Heat-Conducting Phosphor Composites for High-Power Laser Lighting (2018)

Solid-state lighting using laser diodes is an exciting new development that requires new phosphor geometries to handle the greater light fluxes involved. The greater flux from the source results in more conversion and therefore more conversion loss in the phosphor, which generates self-heating, surpassing the stability of current encapsulation strategies used for light-emitting diodes, usually based on silicones. Here, we present a rapid method using spark plasma sintering (SPS) for preparing ceramic phosphor composites of the canonical yellow-emitting phosphor Ce-doped yttrium aluminum garnet (Ce:YAG) combined with a chemically compatible and thermally stable oxide, α-Al<sub>2</sub>O<sub>3</sub>. SPS allows for compositional modulation, and phase fraction, microstructure, and luminescent properties of ceramic composites with varying compositions are studied here in detail. The relationship between density, thermal conductivity, and temperature rise during laser-driven phosphor conversion is elucidated, showing that only modest densities are required to mitigate thermal quenching in phosphor composites. Additionally, the scattering nature of the ceramic composites makes them ideal candidates for laser-driven white lighting in reflection mode, where Lambertian scattering of blue light offers great color uniformity, and a luminous flux >1000 lm is generated using a single commercial laser diode coupled to a single phosphor element.
Epitope Prediction Methods (1994)

Before beginning this discussion, a brief review of immunology is required. The following is a very abbreviated overview of the paradigm as it pertains to the subject of synthetic peptides as antigens. In the vigorous field of immunology, theories of antigen presentation and cell regulation, in particular, are especially dynamic. The following discussion was accurate at the time of publication.
3D-2D projective registration of free-form curves and surfaces (2002)

Some medical interventions require knowing the correspondence between an MRI/CT pre-operative image and the actual position of the patient. Examples occur in neurosurgery, radiotherapy, interventional radiology, but also in video surgery (laparoscopy). We present in this article three new techniques for performing this task without artificial markers. We find the 3D-2D projective transformation (composition of a rigid displacement and a perspective projection) which maps a 3D object onto a 2D image of this object. Depending on the object model (curve or surface), and on the 2D image acquisition system (X-Ray, video), the techniques are different but the framework is common. It does not depend on the initial relative positions of the objects and deals with the occlusions and the outliers. Results are presented on real medical data to demonstrate the validity of our approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Voronoi tessellated halftone masks (2010)

A new algorithm to build blue noise masks using centroidal Voronoi tessellations (CVT) and a variant of Lloyd's Algorithm is presented. The algorithm takes advantage of the optimality properties of CVTs and through a modified version of Lloyd's algorithm, achieves optimization of the stacked binary patterns that build the mask. A new ordering for binary pattern design is presented, as well as a new metric that allows the creation of quality profiles of the masks. The masks generated by this method are used to halftone sample images, and quality profiles are created. It is shown that CVT masks outperform masks created by DBS and VaC according to the new metric defined and thorough visual inspection of halftoned images.
The Effects of Short‐Term Application of a Combination of Platelet‐Derived and Insulin‐Like Growth Factors on Periodontal Wound Healing (1991)

Polypeptide growth factors are a class of potent natural biologic mediators which regulate many of the activities of wound healing including cell proliferation, migration, and metabolism. Platelet-derived growth factor (PDGF) and insulin-like growth factor-I (IGF-I) have been shown to regulate DNA and protein synthesis in bone cells in vitro and to interact synergistically to enhance soft tissue wound healing in vivo. We have hypothesized that the combination of PDGF and IGF-I may, therefore, enhance regeneration of both the soft and hard tissue components of the periodontium. To test this hypothesis we performed conventional periodontal surgery on all 4 quadrants of the mouth of 13 beagle dogs with naturally occurring periodontal disease. Following flap reflection, degranulation, and root planing, all premolar teeth in 2 quadrants of each dog received a combination of 3 micrograms of recombinant PDGF-B and IGF-I in a methylcellulose gel, while the premolar teeth in the contralateral quadrants received the gel alone. Teeth in 4 additional animals also received 125I-PDGF or 125I-IGF-I in the treated sites. The clearance rate of the 125I-labeled protein, changes in local bone metabolism, and amount of new bone and cementum with inserting collagen fibers were measured. The clearance studies revealed that the half-life of the factors at the site of application was 3.0 hours for IGF-I and to 4.2 hours for PDGF-B. Greater than 96% of the radio-labeled proteins was cleared by 96 hours and no radioactivity was detected 2 weeks after application. There was a significant (P less than 0.01) 2-fold increase in uptake of the bone-seeking radiopharmaceutical Technetium 99-MDP at 2 and 4 weeks in growth factor treated sites compared to controls, indicating that there was increased metabolic activity within the bone at these sites. Computer-aided histologic analyses of biopsies obtained at 2 and 5 weeks post-operatively revealed a significant (P less than 0.01), 5 to 10 fold increase in new bone and cementum in PDGF-B/IGF-I treated sites at both time points compared to controls receiving the placebo gel. The height and total area of new bone continued to increase from 2 to 5 weeks. The new bone underwent a normal maturation process as judged by histologic appearance. A physiologic periodontal ligament space was also formed between the new bone and new cementum. There was no increase in ankylosis in the treated sites.(ABSTRACT TRUNCATED AT 400 WORDS)
Mutations in the carboxy terminus of adeno-associated virus 2 capsid proteins affect viral infectivity: lack of an RGD integrin-binding motif (1994)

Using site-directed mutagenesis, we tested whether a potential integrin-binding site, (composed of the amino acids RGD) which is predicted in the adeno-associated virus 2 (AAV-2) capsid open reading frame (ORF), plays a role in the infectivity of AAV-2. Nucleotide sequencing of wild-type and mutant capsid protein-coding sequences, however, revealed discrepancies with the published sequence data at several positions, including a frameshift in the carboxy terminus which cancels the RGD motif and extends the capsid ORF by 27 amino acids. This sequence was confirmed by protein sequencing of proteolytic fragments of VP3. Thus, the virus mutant (pTAV-p), in which the intention was to exchange D of the putative RGD motif for E, resulted in replacing I480 by S in the newly established ORF. A second virus mutant (pTAV-d), in which the intention was to delete the RGD peptide, in fact gave a shift into the ORF of the originally published sequence. The pTAV-p mutant showed a strongly reduced infectivity compared to wild-type AAV-2, whereas pTAV-d was not infectious at all. Neither mutant accumulated viral ssDNA as detected by Hirt extraction. Analysis of virus particle formation and subcellular localization of the capsid proteins revealed a defect of the mutant capsid proteins in capsid assembly. This shows that the newly established C-terminal sequence of the AAV capsid proteins plays an important role in viral assembly.
Diagnosis of and therapy for solid tumors with radiolabeled antibodies and immune fragments. (1984)

Antibodies which are directed against human tumor-associated antigens can potentially be used as carriers of radioactivity for in vivo diagnosis (radioimmunodetection) or treatment (radioimmunotherapy) of solid tumors, including colon, hepatoma, cholangiocarcinoma, and melanoma. Murine monoclonal antibodies (MOAB), produced by the hybridoma technique of Kohler and Milstein, are replacing conventional heterosera as sources of antibodies, because MOAB can be produced in large quantities as reproducible reagents with homogeneous binding properties. We have studied human melanoma using MOAB IgG and Fab fragments that recognize the human melanoma-associated antigens p97 and "high-molecular-weight antigen." Both antigens are found in the membrane of melanomas at much larger concentrations than in normal adult tissues. We have performed radioimmunodetection studies with whole immunoglobulin and have detected 88% of lesions greater than 1.5 cm. We have used Fab fragments for radioimmunotherapy and have found that large doses of radiolabeled antibodies (up to 342 mCi) can be repetitively given to patients without excessive end-organ toxicity. Two of three patients treated with high-dose radiolabeled antimelanoma Fab showed an effect from the treatment. Although both technical and biologic problems remain, the use of radiolabeled antibodies that are directed against tumor-associated antigens holds future promise as a new therapeutic approach to solid tumors that are resistant to conventional therapy.
Characterization of outer membranes isolated from Treponema pallidum, the syphilis spirochete (1995)

Previous freeze-fracture electron microscopy (EM) studies have shown that the outer membrane (OM) of Treponema pallidum contains sparse transmembrane proteins. One strategy for molecular characterization of these rare OM proteins involves isolation of T. pallidum OMs. Here we describe a simple and extremely gentle method for OM isolation based upon isopycnic sucrose density gradient ultracentrifugation of treponemes following plasmolysis in 20% sucrose. Evidence that T. pallidum OMs were isolated included (i) the extremely low protein/lipid ratio of the putative OM fraction, (ii) a paucity of antigenic and/or biochemical markers for periplasmic, cytoplasmic membrane, and cytosolic compartments, and (iii) freeze-fracture EM demonstrating that the putative OMs contained intramembranous particles highly similar in size and density to those in native T. pallidum OMs. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis revealed that the OMs contained a relatively small number of treponemal proteins, including several which did not appear to correspond to previously characterized T. pallidum antigens. Interestingly, these candidate rare OM proteins reacted poorly with syphilitic sera as determined by both conventional immunoblotting and enhanced chemiluminescence. Compared with whole cells, T. pallidum OMs were deficient in cardiolipin, the major lipoidal antigen reactive with antibodies in syphilitic sera. Also noteworthy was that other lipoidal constituents of OMs, including the recently discovered glycolipids, did not react with human syphilitic sera. These latter observations suggest that the poor antigenicity of virulent T. pallidum is a function of both the lipid composition and the low protein content of its OM.
[Topoisomerase I inhibitors. Review of phase II trials with irinotecan (CPT-11) and topotecan]. (1995)

Topoisomerase I inhibitors are a new therapeutic class whose clinical evaluation began a few years ago; Irinotecan (CPT-11) gave interesting results in colon cancer; side effects were neutropenia, diarrhea, vomiting and a cholinergic syndrome. Topotecan was useful in lung and ovarian cancer; side effects were mostly hematologic. Undergoing studies concern dose optimization, mode of administration and therapeutic associations.
Sensing techniques for mobile interaction (2000)

We describe sensing techniques motivated by unique aspects of human-computer interaction with handheld devices in mobile settings. Special features of mobile interaction include changing orientation and position, changing venues, the use of computing as auxiliary to ongoing, real-world activities like talking to a colleague, and the general intimacy of use for such devices. We introduce and integrate a set of sensors into a handheld device, and demonstrate several new functionalities engendered by the sensors, such as recording memos when the device is held like a cell phone, switching between portrait and landscape display modes by holding the device in the desired orientation, automatically powering up the device when the user picks it up the device to start using it, and scrolling the display using tilt. We present an informal experiment, initial usability testing results, and user reactions to these techniques.
Energy-efficient deployment strategies in structural health monitoring using wireless sensor networks (2012)

Structural health monitoring using wireless sensor networks has drawn considerable attention in recent years. The ease of deployment of tiny wireless devices that are coupled with sensors and actuators enhances the data collection process and makes prognostic and preventive maintenance of an infrastructure much easier. In this paper, the deployment problem is considered for finding node locations to reliably diagnose the health of a structure while consuming minimum energy during data collection. A simple shear structure is considered and modal analysis is performed. The example verifies the expectation that placing nodes further apart from each other reduces the mode shape errors but increases the energy consumption during data collection. A min–max, energy-balanced routing tree and an optimal grid separation formulation are proposed that minimize the energy consumption as well as provide fine grain measurements. Copyright © 2012 John Wiley & Sons, Ltd.
OISTI (an Oral-Interface System to provide Tourist-Information inside a car) (2002)

We present a positioning system implemented in Java that is designed to provide tourist information for car users. Most of this multimedia information is stored in a local database in the car, but it is possible to increase or update it by accessing a remote database by mobile telephone. The system can be controlled like any standard computer by keyboard or by mouse, but also offers hands-free control based on an oral interface module, which is very important for a system designed to be used inside a car.
Acrolein Impairs ATP Binding Cassette Transporter A1-dependent Cholesterol Export from Cells through Site-specific Modification of Apolipoprotein A-I (2005)

Acrolein is a highly reactive alpha,beta-unsaturated aldehyde, but the factors that control its reactions with nucleophilic groups on proteins remain poorly understood. Lipid peroxidation and threonine oxidation by myeloperoxidase are potential sources of acrolein during inflammation. Because both pathways are implicated in atherogenesis and high density lipoprotein (HDL) is anti-atherogenic, we investigated the possibility that acrolein might target the major protein of HDL, apolipoprotein A-I (apoA-I), for modification. Tandem mass spectrometric analysis demonstrated that lysine 226, located near the center of helix 10 in apoA-I, was the major site modified by acrolein. Importantly, this region plays a critical role in the cellular interactions and ability of apoA-I to transport lipid. Indeed, we found that conversion of Lys-226 to N(epsilon)-(3-methylpyridinium)lysine by acrolein associated quantitatively with decreased cholesterol efflux from cells via the ATP-binding cassette transporter A1 pathway. In the crystal structure of truncated apoA-I, Glu-234 lies adjacent to Lys-226, suggesting that negatively charged residues might direct the modification of specific lysine residues in proteins. Finally, immunohistochemical studies with a monoclonal antibody revealed co-localization of apoA-I with acrolein adducts in human atherosclerotic lesions. Our observations suggest that acrolein might interfere with normal reverse cholesterol transport by HDL by modifying specific sites in apoA-I. Thus, acrolein might contribute to atherogenesis by impairing cholesterol removal from the artery wall.
Evaluation of the effects of Neptune Krill Oil on the clinical course of hyperlipidemia. (2004)

The results of the present study demonstrate within high levels of confidence that krill oil is effective for the management of hyperlipidemia by significantly reducing total cholesterol, LDL, and triglycerides, and increasing HDL levels. At lower and equal doses, krill oil was significantly more effective than fish oil for the reduction of glucose, triglycerides, and LDL levels.
New Functional Materials Based on Self-Assembling Organogels: From Serendipity towards Design (2000)

Small organic gelling agents very efficiently self-assemble into an entangled network in a wide variety of organic solvents, thereby turning the liquid into a gel. Recent progress in the design of organogelators led to tailor-made gelling agents for supercritical CO2. Furthermore, such agents can be used as templates for the construction of novel materials and as responsive gel systems. The picture shows switchable organogels and indicates schematically how viscoelastic properties can be affected.
JPred4: A protein secondary structure prediction server (2015)

JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.
Production and Utilization of Coalbed Methane Gas in Island Creek Coal Company Mines (1982)

ABSTRACT Occidental Research Corporation has for the past five years been actively engaged in a research program of draining methane gas from the Pocahontas #3 coal seam. This work is being conducted in Island Creek Coal Company's deep mines in the Virginia Pocahontas Division. The technique consists of drilling long horizontal inseam holes in advance of mining. The initial objective of the program was to reduce methane emissions in mine workings in order to improve mine safety and productivity. As the research program evolved, potential for commercial scale production and utilization of the gas resource became apparent. Current research activities include production and capturing of the gas and utilization at the mine plant for drying the coal. To date 27 horizontal holes have been drilled in three mines for an aggregate depth of over 6,400 meters (21,000 feet). The longest hole is 835 meters (2,740 feet). Over 18.4 million cubic meters (650 MMCF) of pipeline quality gas has been drained and transported safely to the surface through a network of underground pipelines. Coal dryers have been retrofitted with gas burners to replace #2 fuel oil and pulverized coal for drying coal.
Expression of the Extracellular Domain of the Thyrotropin Receptor in the Baculovirus System Using a Promoter Active Earlier than the Polyhedrin Promoter (1995)

Conventional baculovirus vectors that utilize the very late polyhedrin promoter have not proved successful for expressing a thyrotropin (TSH) receptor capable of ligand and Graves' disease autoantibody binding comparable to the receptor produced in mammalian cells. Because of the clinical importance of high level expression of this protein, we reassessed the baculovirus system using a new transfer vector (pAcMP3) containing the late basic protein promoter, which functions earlier than the classical polyhedrin promoter. Maximal synthesis of the [35S]methionine-labeled TSH receptor extracellular domain, affinity-purified using a 6-histidine tag, occurred earlier (1 day after insect cell infection) than with a vector (pVL1393) containing the polyhedrin promoter. The pAcMP3-derived TSH receptor extracellular domain was larger (approximately 68 kDa) than the pVL1393-derived protein (approximately 63 kDa). Only the 68-kDa product was secreted, albeit in trace amounts detectable only by precursor labeling. Enzymatic deglycosylation reduced both 68- and 63-kDa cellular proteins to approximately 54 kDa, indicating that the pAcMP3 vector generated a protein with greater carbohydrate content. However, despite its greater degree of glycosylation, most of the 68-kDa protein remained within the cell, almost entirely in the particulate fraction. Remarkably, the trace amounts of 68-kDa receptor protein affinity-purified from the soluble cytosolic fraction of infected insect cells completely neutralized TSH receptor autoantibodies in patients' sera and partly inhibited TSH binding. In conclusion, a baculovirus vector with a promoter active earlier than the conventional polyhedrin promoter generates a more glycosylated and functional TSH receptor extracellular domain protein, albeit at low levels. These data carry important implications for the expression by baculovirus vectors of functional, highly glycosylated proteins.
Grafting T Cells with Tumor Specificity: The Chimeric Receptor Strategy for Use in Immunotherapy of Malignant Diseases (1999)

Appreciation of the complementary nature of T-cell- and antibody-based immunotherapy stimulated interest in developing approaches that combine their advantages and minimize their limitations. A recent strategy is based on permanent grafting of cytotoxic T cells with a recombinant chimeric receptor designed for cellular targeting with antibody-like specificity and for cellular activation after binding to antigen. The extracellular moiety of the chimeric receptor consists of an antigen-binding domain derived from an antibody, the intracellular moiety consists of a signalling domain for cellular activation, thus combining the broad specificity of antibody-based and major histocompatibility complex (MHC)-independent recognition with the potent antitumor activity of T cells. By generation of specific T cells against any antigen for which a suitable monoclonal antibody (MAb) exists, the chimeric receptor strategy has the potential to extend the adoptive immunotherapy for a variety of malignant and infectious diseases. However, little is known about the optimized design of this type of receptor. We here discuss our results in grafting T cells with chimeric receptors of various design with regard to efficient cellular activation.