gebhart/patrepeval huggingface dataset:
Multi-objective aerodynamic and stealthy performance optimization for airfoil using Kriging surrogate model (2011)

The Class-Shape function Transformation (CST) method is used to describe the parameterized airfoil geometry. The parameterized models for aerodynamic and stealthy performance of airfoil are constructed. The aerodynamic analysis model of airfoil is constructed by Computational Fluid Dynamics (CFD) method based on N-S equations. And the stealthy performance analysis model of airfoil is constructed by Computational Electromagnetic Method (CEM) based Method of Moments (MoM). The multi-objective aerodynamic and stealthy performance optimization method for airfoil using Kriging surrogate model is presented in this paper. The Latin hypercube method is employed to get a set of sample points. The aerodynamic and stealthy performance Kriging models are built. The multi-objective aerodynamic and stealthy performance optimization of airfoil is optimized by combining Pareto genetic algorithm with Kriging surrogate model. The presented method is validated by two applications. The results of the investigation show that the constructed analysis models are reasonable and the presented multi-objective optimization design method is feasible, which can improve the performance of airfoil and the efficiency of optimization effectively.
Modeling and Control of Contact Between Constrained Rigid Bodies (2004)

This paper examines the phenomenon of frictionless contact between rigid bodies that are already subject to kinematic constraints from some other source. Such contacts occur frequently when robots interact with their environments, in which case, the additional constraints come from the robot mechanisms. A proper analysis of these contacts must consider both sets of constraints. This paper presents a general model of constrained-body contact, expressed in invariant terms; a method of resolving equations of motion into decoupled subsystems with respect to the contact's motion and force freedoms; an equation of motion for possibly redundant robots experiencing constrained-body contact, which employs a novel decomposition of the robot's joint space into dynamically decoupled subspaces; and a dynamically decoupled hybrid motion/force-control system based on the same decomposition. It is shown that disturbances from an unknown dynamic environment are automatically confined to the force-control subsystem, and that a modification to the control law can factor these disturbances out of the controlled response.
Evolutionarily conserved and functionally important residues in the I- CeuI homing endonuclease (1997)

Two approaches were used to discern critical amino acid residues for the function of the I- Ceu I homing endonuclease: sequence comparison of subfamilies of homologous proteins and genetic selection. The first approach revealed residues potentially involved in catalysis and DNA recognition. Because I- Ceu I is lethal in Escherichia coli , enzyme variants not perturbing cell viability were readily selected from an expression library. A collection of 49 variants with single amino acid substitutions at 37 positions was assembled. Most of these positions are clustered within or around the LAGLI-DADG dodecapeptide and the TQH sequence, two motifs found in all protein subfamilies examined. The Km and kcat values of the wild-type and nine variant enzymes synthesized in vitro were determined. Three variants, including one showing a substitution of the glutamine residue in the TQH motif, revealed no detectable endonuclease activity; five others showed reduced activity compared to the wild-type enzyme; whereas the remaining variant cleaved the top strand about three times more efficiently than the wild-type. Our results not only confirm recent reports indicating that amino acids in the LAGLI-DADG dodecapeptide are functionally critical, but they also suggest that some residues outside this motif directly participate in catalysis.
Aromatic Substituted Group 4 Metallocene Catalysts for the Polymerization of α-Olefins (1996)

Six new group 4 metallocene complexes were synthesized as precursors for the polymerization of α-olefins. The phenyl-substituted precursors 2b−4b when activated by methylaluminoxane (MAO) were highly active for the polymerization of ethylene but exhibited no activity for the polymerization of propylene. Bis(2-methylbenz[e]indenyl)zirconium dichloride (5b) was activated with both MAO and triphenylcarbenium tetrakis(pentafluorophenyl)borate (trityl)/triisobutylaluminum producing polypropylene with varying molecular weight depending on polymerization temperature. The titanium precursor 6b had lower activity for ethylene as compared to the zirconium analog 5b and virtually no activity for propylene when activated with either MAO or trityl.
Pegylated Arginine Deiminase Treatment of Patients With Unresectable Hepatocellular Carcinoma: Results From Phase I/II Studies (2004)

Elimination of all detectable plasma arginine in patients with HCC was well tolerated and seemed to be effective in the treatment of some patients with HCC. Further testing of ADI-SS PEG 20,000 mw in a larger population of individuals with HCC as well as other human tumors auxotrophic for arginine is warranted.
Product of a New Gene, syd, Functionally Interacts with SecY when Overproduced in Escherichia coli (1995)

A mutant form of SecY, SecY-d1, was previously suggested to sequester a component(s) of the protein translocator complex. Its synthesis from a plasmid leads to interference with protein export in Escherichia coli. SecE is a target of this sequestration, and its overproduction cancels the export interference. We now report that overexpression of another gene, termed syd, also suppresses secY-d1. The nucleotide sequence of syd predicted that it encodes a protein of 181 amino acid residues, which has been identified by overproduction, purification, and determination of the amino-terminal sequence. Cell fractionation experiments suggested that Syd is loosely associated with the cytoplasmic surface of the cytoplasmic membrane. SecY may be involved in the membrane association of Syd since the association is saturable, the extent of which depends on the overproduction of SecY. SecY is rapidly degraded in vivo unless its primary partner, SecE, is sufficiently available. Overproduction of Syd was found to stabilize oversynthesized SecY. However, Syd cannot stabilize the SecY-d1 form of SecY. Thus, in the presence of both secY+ and secY-d1, Syd increases the effective SecY+/SecY-d1 ratio in the cell and cancels the dominant interference by the latter. We also found that overproduction of Syd dramatically inhibits protein export in the secY24 mutant cell in which SecY-SecE interaction has been weakened. These results indicate that Syd, especially when it is overproduced, has abilities to interact with SecY. Possible significance of such interactions is discussed in conjunction with the apparent lack of phenotypic consequences of genetic disruption of syd.
Replicative intermediates of hepatitis B virus in HepG2 cells that produce infectious virions (1988)

Clonal cells derived from HepG2 cells transfected with a plasmid containing hepatitis B virus (HBV) DNA secrete hepatitis B surface antigen particles, nucleocapsids, and virions (M. A. Sells, M.-L. Chen, and G. Acs, Proc. Natl. Acad. Sci. USA 84:1005-1009, 1987) which elicit acute hepatitis in chimpanzees (G. Acs, M. A. Sells, R. H. Purcell, P. Price, R. Engle, M. Shapiro, and H. Popper, Proc. Natl. Acad. Sci. USA 84:4641-4644, 1987). We report here the initial characterization of the viral nucleic acids produced in this culture system. Kinetic analyses of nuclear, cytoplasmic, and extracellular HBV DNAs were performed by Southern blotting with radiolabeled HBV strand-specific probes. The results from these analyses indicate that at the stationary cellular growth phase, there is a dramatic increase in the rate at which HBV DNA accumulates. Incomplete double- and single-stranded forms of the HBV genome were detected in the nuclear and cytoplasmic fractions as well as in the extracellular medium. In addition, the nuclear DNA apparently includes multiple complete copies of the HBV genome chromosomally integrated and full-length covalently closed circular HBV DNA. Multiple HBV-specific polyadenylated RNAs with lengths of 3.5, 2.5, and 2.1 kilobases were identified by Northern (RNA) blot analysis. S1 nuclease mapping and primer extension identified a single 3' end and multiple unique initiation sites corresponding to nucleotides just 5' to the pre-S1 region, as well as upstream and within the pre-S2 and precore regions. The nucleic acid profile obtained from these analyses is essentially a facsimile of that obtained by studying liver tissue from HBV-infected individuals.
Aptamers: An Emerging Class of Molecules That Rival Antibodies in Diagnostics (1999)

Antibodies, the most popular class of molecules providing molecular recognition needs for a wide range of applications, have been around for more than three decades. As a result, antibodies have made substantial contributions toward the advancement of diagnostic assays and have become indispensable in most diagnostic tests that are used routinely in clinics today. The development of the systematic evolution of ligands by exponential enrichment (SELEX) process, however, made possible the isolation of oligonucleotide sequences with the capacity to recognize virtually any class of target molecules with high affinity and specificity. These oligonucleotide sequences, referred to as "aptamers", are beginning to emerge as a class of molecules that rival antibodies in both therapeutic and diagnostic applications. Aptamers are different from antibodies, yet they mimic properties of antibodies in a variety of diagnostic formats. The demand for diagnostic assays to assist in the management of existing and emerging diseases is increasing, and aptamers could potentially fulfill molecular recognition needs in those assays. Compared with the bellwether antibody technology, aptamer research is still in its infancy, but it is progressing at a fast pace. The potential of aptamers may be realized in the near future in the form of aptamer-based diagnostic products in the market. In such products, aptamers may play a key role either in conjunction with, or in place of, antibodies. It is also likely that existing diagnostic formats may change according to the need to better harness the unique properties of aptamers.
Sclerostin Antibody Administration Converts Bone Lining Cells Into Active Osteoblasts (2016)

Sclerostin antibody (Scl-Ab) increases osteoblast activity, in part through increasing modeling-based bone formation on previously quiescent surfaces. Histomorphometric studies have suggested that this might occur through conversion of bone lining cells into active osteoblasts. However, direct data demonstrating Scl-Ab-induced conversion of lining cells into active osteoblasts are lacking. Here, we used in vivo lineage tracing to determine if Scl-Ab promotes the conversion of lining cells into osteoblasts on periosteal and endocortical bone surfaces in mice. Two independent, tamoxifen-inducible lineage-tracing strategies were used to label mature osteoblasts and their progeny using the DMP1 and osteocalcin promoters. After a prolonged "chase" period, the majority of labeled cells on bone surfaces assumed a thin, quiescent morphology. Then, mice were treated with either vehicle or Scl-Ab (25 mg/kg) twice over the course of the subsequent week. After euthanization, marked cells were enumerated, their thickness quantified, and proliferation and apoptosis examined. Scl-Ab led to a significant increase in the average thickness of labeled cells on periosteal and endocortical bone surfaces, consistent with osteoblast activation. Scl-Ab did not induce proliferation of labeled cells, and Scl-Ab did not regulate apoptosis of labeled cells. Therefore, direct reactivation of quiescent bone lining cells contributes to the acute increase in osteoblast numbers after Scl-Ab treatment in mice. © 2016 American Society for Bone and Mineral Research.
The Crown and Stem of the V3 Loop Play Distinct Roles in Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Interactions with the CCR5 Coreceptor (2002)

Human immunodeficiency virus type 1 envelope glycoprotein gp120 interacts with CD4 and the CCR5 coreceptor in order to mediate viral entry. A CD4-induced surface on gp120, primarily composed of residues in the V3 loop and the C4 domain, interacts with CCR5. In the present study, we generated envelope glycoproteins comprising chimeric V3 loops and/or V3 loops with deletions and studied their binding to CCR5 amino-terminal domain (Nt)-based sulfopeptides and cell surface CCR5, as well as their ability to mediate viral entry. We thus delineated two functionally distinct domains of the V3 loop, the V3 stem and the V3 crown. The V3 stem alone mediates soluble gp120 binding to the CCR5 Nt. In contrast, both the V3 stem and crown are required for soluble gp120 binding to cell surface CCR5. Within the context of a virion, however, the V3 crown alone determines coreceptor usage. Our data support a two-site gp120-CCR5 binding model wherein the V3 crown and stem interact with distinct regions of CCR5 in order to mediate viral entry.
P‐32: Parametric Characterization of Perceived Light Field Display Resolution (2016)

The perceived resolution of a light field display is examined from a human visual system perspective. Results show that the perceived resolution of the display depends largely on angular pitch and shows very little to no dependence on hogel pitch.
High-Rate Girth-Eight Low-Density Parity-Check Codes on Rectangular Integer Lattices (2004)

This letter introduces a combinatorial construction of girth-eight high-rate low-density parity-check codes based on integer lattices. The parity-check matrix of a code is defined as a point-line incidence matrix of a 1-configuration based on a rectangular integer lattice, and the girth-eight property is achieved by a judicious selection of sets of parallel lines included in a configuration. A class of codes with a wide range of lengths and column weights is obtained. The resulting matrix of parity checks is an array of circulant matrices.
Conditional transgenic technologies (2001)

Transgenic technology has been revolutionised by the development of techniques that allow temporo-spatial control of gene deletion or expression in transgenic animals. The ability to switch gene expression 'on' or 'off' in restricted tissues at specific times allows unprecedented flexibility for exploring gene function in both health and disease. As use of these techniques grows in all areas of biomedical research, an understanding of this topic is essential. In this review we examine the theory, application and limitations of these strategies, with particular reference to endocrine research.
Phase Fluorometric Optical Carbon Dioxide Gas Sensor for Fermentation Off‐Gas Monitoring (1996)

We demonstrated an optical carbon dioxide gas sensor suitable for replacement of gas chromatographs and mass spectrometers for the measurement of carbon dioxide in the off-gas of a bioreactor for fermentation and cell culture applications. The sensor is based upon the change in lifetime of a donor fluorophore, sulforhodamine 101 (SR101), induced by fluorescence resonance energy transfer to a pH-sensitive, nonfluorescent acceptor, <i>m</i>-cresol purple (MCP). Carbon dioxide diffusing into the sensor produces carbonic acid, changing the absorbance spectrum of the MCP, and thus its spectral overlap with the SR101, changing its lifetime. This lifetime change was measured in the frequency, rather than the time domain, as a change in the phase angle of the fluorescence relative to the modulated excitation light. The sensor was calibrated by correlating the phase response to carbon dioxide concentrations. The calibration remained valid over the life of the sensor, which has been shown to be greater than 2 weeks. The sensor was most sensitive at low CO<sub>2</sub> concentrations and responded to concentration changes in seconds. The sensor film is very inexpensive to produce and the light source is an inexpensive light-emitting diode. Furthermore, lower cost detection electronics can be developed since only one modulation frequency is required. In addition, this sensor can potentially be used <i>in vivo</i>, with a fiber optic both delivering the excitation light and collecting the emission.
P‐32: Vacuum In‐Line Sealing Technology with Auxiliary Heating Line for PDP Packaging (2002)

Abstract Sealing of two glass plates composing of PDP panel was done in a vacuum chamber by using an auxiliary heating line(AHL). In order to improve the uniformity of sealing temperature and reduce the panel temperature during sealing, the AHL was introduced by a screen printing method inside a frit glass and used as a part of heating source for the frit melting. Outgassing and bubbling can be also severe problems during the heating process of the frit glass inside a vacuum chamber. Our specially prepared frit glass was successfully applied for the vacuum in‐line sealing approach without bubbles. By using the AHL technology and the specially prepared frit glass, we have successfully sealed a PDP test panel without bubbles and any leak through the frit glass.
Theory of photoinduced charge transfer in weakly coupled donor-acceptor conjugated polymers: application to an MEH-PPV: CN-PPV pair (1998)

In a pair of coupled donor-acceptor conjugated polymer chains, it is possible for an exciton photoexcited on either polymer to decay into a hole in the donor polymer's valence band and an electron in the conduction band of the acceptor polymer. We calculate the corresponding exciton decay rate and its dependence on inter-polymer distance. For a pair of derivatives of poly(phenylene vinylene), PPV, specifically poly[2-methoxy, 5-(2′-ethyl-hexyloxy)-1,4 PPV], MEH-PPV, and poly(2,5-hexyloxy p-phenylene cyanovinylene), CN-PPV, at a separation of 6 Å the characteristic decay time is 2.2 ps, whereas at 4 Å it is ∼ 50 fs.
DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history (1999)

A detailed analysis of the polbeta superfamily of nucleotidyltransferases was performed using computer methods for iterative database search, multiple alignment, motif analysis and structural modeling. Three previously uncharacterized families of predicted nucleotidyltransferases are described. One of these new families includes small proteins found in all archaea and some bacteria that appear to consist of the minimal nucleotidyltransferase domain and may resemble the ancestral state of this superfamily. Another new family that is specifically related to eukaryotic polyA polymerases is typified by yeast Trf4p and Trf5p proteins that are involved in chromatin remodeling. The TRF family is represented by multiple members in all eukaryotes and may be involved in yet unknown nucleotide polymerization reactions required for maintenance of chromatin structure. Another new family of bacterial and archaeal nucleotidyltransferases is predicted to function in signal transduction since, in addition to the nucleotidyltransferase domain, these proteins contain ligand-binding domains. It is further shown that the catalytic domain of gamma proteobacterial adenylyl cyclases is homologous to the polbeta superfamily nucleotidyltransferases which emphasizes the general trend for the origin of signal-transducing enzymes from those involved in replication, repair and RNA processing. Classification of the polbeta superfamily into distinct families and examination of their phyletic distribution suggests that the evolution of this type of nucleotidyltransferases may have included bursts of rapid divergence linked to the emergence of new functions as well as a number of horizontal gene transfer events.
Postsynthetic Modification of a Metal–Organic Framework for Stabilization of a Hemiaminal and Ammonia Uptake (2011)

In our study, we show by solid-state (15)N NMR measurements that an important zirconium metal-organic framework (UiO-66) with amino-functionalized links is composed of a mixture of amino and -NH(3)(+)Cl(-) salt functionalities rather than all amino functionality to give a composition of Zr(6)O(4)(OH)(4)(BDC-NH(2))(4)(BDC-NH(3)(+)Cl(-))(2) (UiO-66-A). UiO-66-A was postsynthetically modified to form a mixture of three functionalities, where the hemiaminal functionality is the majority species in UiO-66-B and aziridine is the majority functionality in UiO-66-C. UiO-66-A-C are all porous with surface areas ranging from 780 to 820 m(2)/g and have chemical stability, as evidenced by reversible ammonia uptake and release showing capacities ranging from 134 to 193 cm(3)/g.
Communication protocols and concurrency: an Occam implementation of X.25 (2003)

Experience with the use of the current software and hardware offerings is presented and discussed in relation to practical implementation of the CCITT recommendation X-25. An implementation of X.25 is made using the concurrent programming language Occam and its associated hardware, the transputer. Their suitability in such an application is investigated. In particular, the simplicity of software design of communication systems based on concurrent implementation methods is reported. The implementation and its consequences are discussed, and conclusions regarding this approach are drawn.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Detection of C-polysaccharide in serum of patients with Streptococcus pneumoniae bacteraemia. (1995)

This study demonstrates that C-polysaccharide antigen commonly circulates in patients with S pneumoniae bacteraemia but its presence is masked by ligands present in serum.
Smart Vest: Wearable multi-parameter remote physiological monitoring system (2007)

The wearable physiological monitoring system is a washable shirt, which uses an array of sensors connected to a central processing unit with firmware for continuously monitoring physiological signals. The data collected can be correlated to produce an overall picture of the wearer's health. In this paper, we discuss the wearable physiological monitoring system called ‘Smart Vest’. The Smart Vest consists of a comfortable to wear vest with sensors integrated for monitoring physiological parameters, wearable data acquisition and processing hardware and remote monitoring station. The wearable data acquisition system is designed using microcontroller and interfaced with wireless communication and global positioning system (GPS) modules. The physiological signals monitored are electrocardiogram (ECG), photoplethysmogram (PPG), body temperature, blood pressure, galvanic skin response (GSR) and heart rate. The acquired physiological signals are sampled at 250 samples/s, digitized at 12-bit resolution and transmitted wireless to a remote physiological monitoring station along with the geo-location of the wearer. The paper describes a prototype Smart Vest system used for remote monitoring of physiological parameters and the clinical validation of the data are also presented.
The 1- and 2-Naphthylalanine Analogs of Oxytocin and Vasopressin (1995)

Solid phase technique on p -methylbenzhydrylamine resin was used for the synthesis of four analogs of oxytocin and four analogs of vasopressin with the non-coded amino acids L- or D- and 1- or 2-naphthylalanine and D-homoarginine. [L-1-Nal2]oxytocin, [D-1-Nal2]oxytocin, [L-2-Nal2]oxytocin, [D-2-Nal2]oxytocin, [L-1-Nal2, D-Har8]vasopressin, [D-1-Nal2, D-Har8]vasopressin, [L-2-Nal2, D-Har8]vasopressin and [D-2-Nal2, D-Har8]vasopressin were synthesized. All eight analogs were found to be uterotonic inhibitors in vitro and in vivo. Analogs with 2-naphthylalanine are stronger inhibitors, particularly in the vasopressin series than the analogs with 1-naphthylalanine. Analogs with 1-naphthylalanine have no activity in the pressor test, analogs with 2-naphthylalanine are weak pressor inhibitors.