gebhart/patrepeval huggingface dataset:
Lymphoid precursor cells adhere to two different sites on fibronectin. (1987)

Several precursor lymphoid cell lines, blocked at specific stages of differentiation, adhere specifically to fibronectin in vitro. Whereas the Ba F3 cell line, which has both immunoglobulin heavy- and light-chain genes in germline configuration, interacts with the arg-gly-asp-containing cell-binding domain of fibronectin, the B-committed line PD 31, which is undergoing rearrangement of immunoglobulin light-chain genes, does not. Accordingly the Ba F3, but not the putative PD 31 surface fibronectin receptor, binds to an affinity matrix containing the 115-kD cell-binding domain of fibronectin. PD 31 cells recognize a different domain of the fibronectin molecule, which is contained within the carboxy terminal segment possessing a high-affinity binding site for heparin. A polyclonal antibody raised against the fibronectin receptor of mouse erythroleukemic cells inhibits adhesion of these lymphoid lines to fibronectin. It precipitates two major species of 140 and 70 kD from surface-radioiodinated Ba F3 cells and species of 140 and 120 kD from PD 31 cells. We propose that the two types of cells express different fibronectin receptors mediating substrate adhesion, and suggest that receptor(s) with different specificity might be expressed in the course of B cell maturation. Because we show that these adhesion properties are shared by normal bone marrow lymphoid precursors, we infer that these receptors may play a role in normal lymphopoiesis.
Alogliptin added to insulin therapy in patients with type 2 diabetes reduces HbA 1c without causing weight gain or increased hypoglycaemia (2009)

Adding alogliptin to previous insulin therapy (with or without metformin) significantly improved glycaemic control in patients with type 2 diabetes inadequately controlled on insulin, without causing weight gain or increasing the incidence of hypoglycaemia. Further studies are warranted to explore the role of alogliptin added to optimized basal insulin regimens.
Pharmacological selectivity of the cloned human P2U‐purinoceptor: potent activation by diadenosine tetraphosphate (1995)

1. The human P2U-purinoceptor was stably expressed in 1321N1 human astrocytoma cells and the pharmacological selectivity of the expressed receptor was studied by measurement of inositol lipid hydrolysis. 2. High basal levels of inositol phosphates occurred in P2U-purinoceptor-expressing cells. This phenomenon was shown to be due to release of large amounts of ATP from 1321N1 cells, and could be circumvented by adoption of an assay protocol that did not involve medium changes. 3. UTP, ATP and ATP gamma S were full and potent agonists for activation of phospholipase C with EC50 values of 140 nM, 230 nM, and 1.72 microM, respectively. 5BrUTP, 2C1ATP and 8BrATP were also full agonists although less potent than their natural congeners. Little or no effect was observed with the selective P2Y-, P2X-, and P2T-purinoceptor agonists, 2MeSATP, alpha,beta-MeATP, and 2MeSADP, respectively. 4. Diadenosine tetraphosphate, Ap4A, was a surprisingly potent agonist at the expressed P2U-purinoceptor with an EC50 (720 nM) in the range of the most potent P2U-purinoceptor agonists. Ap4A may be a physiologically important activator of P2U-purinoceptors.
Characterization of a Macaque Recombinant Monoclonal Antibody That Binds to a CD4-Induced Epitope and Neutralizes Simian Immunodeficiency Virus (2000)

A potent neutralizing Fab fragment from a long-term survivor of simian immunodeficiency virus (SIVsm) infection was used to construct a recombinant macaque immunoglobulin G1kappa (IgG1kappa) molecule, designated IgG1-201. A Chinese hamster ovary cell line expressing IgG1-201 was derived by stable transfection and optimized for antibody secretion by methotrexate selection and dihydrofolate reductase gene amplification. IgG1-201 effectively neutralized the homologous, molecularly cloned SIVsmH4 virus but had no activity against the heterologous SIVmac251/BK28 virus. The previously characterized, neutralization-resistant SIVsmE543-3 virus was also not neutralized by IgG1-201. Binding to SIVsmH4 gp120 was enhanced in the presence of recombinant soluble CD4, suggesting that IgG1-201 bound a CD4-induced epitope. IgG1-201 immunoprecipitated the SIVsmH4 but not the SIVsmE543-3 envelope despite a close relationship between these two clones. Immunoprecipitation of a panel of SIVsmH4/SIVsmE543-3 chimeric viruses tentatively assigned the neutralization epitope to the third constant domain, immediately C terminal to the V3 loop. These findings suggest the presence of at least one CD4-induced neutralization epitope on SIV, as is the case with human immunodeficiency virus type 1.
Hand-Eye Calibration (1995)

Whenever a sensor is mounted on a robot hand, it is important to know the relationship between the sensor and the hand. The problem of determining this relationship is referred to as the hand-eye calibration problem. Hand-eye calibration is impor tant in at least two types of tasks: (1) map sensor centered measurements into the robot workspace frame and (2) tasks allowing the robot to precisely move the sensor. In the past some solutions were proposed, particularly in the case of the sensor being a television camera. With almost no exception, all existing solutions attempt to solve a homogeneous matrix equation of the form AX = X B. This article has the following main contributions. First we show that there are two possible formulations of the hand-eye calibration problem. One formu lation is the classic one just mentioned. A second formulation takes the form of the following homogeneous matrix equation: MY = M'YB. The advantage of the latter formulation is that the extrinsic and intrinsic parameters of the camera need not be made explicit. Indeed, this formulation directly uses the 3 x4 perspective matrices (M andM' ) associated with two positions of the camera with respect to the calibration frame. Moreover, this formulation together with the classic one covers a wider range of camera-based sensors to be calibrated with respect to the robot hand: single scan-line cameras, stereo heads, range finders, etc. Second, we develop a common mathematical framework to solve for the hand-eye calibration problem using either of the two formulations. We represent rotation by a unit quaternion and present two methods: (1) a closed-form solution for solving for rotation using unit quaternions and then solving for translation and (2) a nonlinear technique for simultane ously solving for rotation and translation. Third, we perform a stability analysis both for our two methods and for the lin ear method developed by Tsai and Lenz (1989). This analysis allows the comparison of the three methods. In light of this comparison, the nonlinear optimization method, which solves for rotation and translation simultaneously, seems to be the most robust one with respect to noise and measurement errors.
Majorana fermions emerging from magnetic nanoparticles on a superconductor without spin-orbit coupling (2011)

There exists a variety of proposals to transform a conventional $s$-wave superconductor into a topological superconductor, supporting Majorana fermion midgap states. A necessary ingredient of these proposals is strong spin-orbit coupling. Here we propose an alternative system consisting of a one-dimensional chain of magnetic nanoparticles on a superconducting substrate. No spin-orbit coupling in the superconductor is needed. We calculate the topological quantum number of a chain of finite length, including the competing effects of disorder in the orientation of the magnetic moments and in the hopping energies, to identify the transition into the topologically nontrivial state (with Majorana fermions at the end points of the chain).
Hardware-based simulation and collision detection for large particle systems (2004)

Particle systems have long been recognized as an essential building block for detail-rich and lively visual environments. Current implementations can handle up to 10,000 particles in real-time simulations and are mostly limited by the transfer of particle data from the main processor to the graphics hardware (GPU) for rendering.This paper introduces a full GPU implementation using fragment shaders of both the simulation and rendering of a dynamically-growing particle system. Such an implementation can render up to 1 million particles in real-time on recent hardware. The massively parallel simulation handles collision detection and reaction of particles with objects for arbitrary shape. The collision detection is based on depth maps that represent the outer shape of an object. The depth maps store distance values and normal vectors for collision reaction. Using a special texture-based indexing technique to represent normal vectors, standard 8-bit textures can be used to describe the complete depth map data. Alternately, several depth maps can be stored in one floating point texture.In addition, a GPU-based parallel sorting algorithm is introduced that can be used to perform a depth sorting of the particles for correct alpha blending.
Efficient routing in all-optical networks (1994)

Article Efficient routing in all-optical networks Share on Authors: Prabhakar Raghavan IBM T.J. Watson Research Center, Yorktown IBM T.J. Watson Research Center, YorktownView Profile , Eli Upfal The Weizmann Institute, Israel and IBM Almaden Research Center, California The Weizmann Institute, Israel and IBM Almaden Research Center, CaliforniaView Profile Authors Info & Claims STOC '94: Proceedings of the twenty-sixth annual ACM symposium on Theory of ComputingMay 1994 Pages 134–143https://doi.org/10.1145/195058.195119Published:23 May 1994 156citation832DownloadsMetricsTotal Citations156Total Downloads832Last 12 Months35Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
β‐Substituierte Enamine, X: Darstellung und Umsetzungen von 3‐Arylamino‐2‐halogencrotononitrilen (1976)

Abstract 3‐Arylamino‐2‐halogencrotononitrile (5) werden durch Kondensation von 2‐Halogen‐3‐oxo‐butyronitril (2) mit primären aromatischen Aminen oder durch Einwirkung von N ‐Halogen‐succinimid auf 3‐Arylaminocrotononitrile (6) gewonnen. Ihre Halogenatome können nucleophil gegen Dialkylamino‐ oder gegen Arylthiogruppen ausgetauscht werden, wobei die Endiamine 10a, b , das Phenylthio‐enamin 10c oder aua o ‐Phenylendiaminen unter Ringschluß Chinoxaline 11 entstehen.
Calcitonin gene-related peptide reduces brain injury in a rat model of focal cerebral ischemia. (1994)

These findings lend support for the potential use of this peptide in the prophylactic treatment of delayed cerebral ischemia after aneurysmal subarachnoid hemorrhage.
Natural auto- and polyreactive antibodies differing from antigen-induced antibodies in the H chain CDR3 (1991)

We describe three sets of natural (preimmune) polyreactive antibodies and Ag-induced antibodies that share the same VH-VL combinations. The amino acid homology in the VH and VL segments averaged 92%. These sets were found among 49 neonatal and adult natural mAb that were compared with 35 Ag-induced monoclonals produced during the memory response to phosphocholine (PC)-keyhole limpet hemocyanin. Both groups of monoclonals had been selected on the basis of a restricted fine specificity pattern, namely the ability to recognize PC-protein and p-nitrophenyl phosphocholine but not PC. All of the antibodies were tested for reactivity against a panel of 15 self and foreign Ag. Despite their common fine specificity as the basis for selection, 33/49 natural antibodies were poly/auto reactive whereas 0/35 Ag-induced antibodies had such poly/auto reactive properties. The natural antibodies were encoded by genes representing nine different VH families and several V kappa and V lambda families. There were a few replacement substitutions distinguishing the Ag-induced antibodies from the natural antibodies in each set; however, the most noteworthy difference was the extreme variability of CDR3 in the natural antibodies that differed in both length and amino acid sequence from each other and from Ag-induced antibodies. The results suggest that CDR3 of the H chain may play a critical role in distinguishing poly- from monospecific combining sites in natural and Ag-induced antibodies.
Mutational studies with the trp repressor of Escherichia coli support the helix-turn-helix model of repressor recognition of operator DNA. (1985)

Several classes of trp repressor mutants were selected and analyzed in vivo. Mutants that produced repressors with either enhanced or reduced activity were obtained. One class of mutants produced inactive or slightly active repressors that were trans-dominant to the wild-type repressor. The amino acid substitutions in many of these repressors were clustered in a segment of the polypeptide that is homologous to the DNA recognition domain of the lambda cro repressor. A second functionally important region of the trp repressor was identified; this region could participate in L-tryptophan binding. Observations with trpR nonsense mutants suggest that the first 67 residues of the repressor polypeptide are sufficient for subunit association.
Specification of Guaranteed Quality of Service (1997)

This memo describes the network element behavior required to deliver a guaranteed service (guaranteed delay and bandwidth) in the Internet. Guaranteed service provides firm (mathematically provable) bounds on end-to-end datagram queueing delays. This service makes it possible to provide a service that guarantees both delay and bandwidth. This specification follows the service specification template described in [1].
RNA interference blocks gene expression and RNA synthesis from hepatitis C replicons propagated in human liver cells (2003)

RNA interference represents an exciting new technology that could have therapeutic applications for the treatment of viral infections. Hepatitis C virus (HCV) is a major cause of chronic liver disease and affects >270 million individuals worldwide. The HCV genome is a single-stranded RNA that functions as both a messenger RNA and replication template, making it an attractive target for the study of RNA interference. Double-stranded small interfering RNA (siRNA) molecules designed to target the HCV genome were introduced through electroporation into a human hepatoma cell line (Huh-7) that contained an HCV subgenomic replicon. Two siRNAs dramatically reduced virus-specific protein expression and RNA synthesis to levels that were 90% less than those seen in cells treated with negative control siRNAs. These same siRNAs protected naive Huh-7 cells from challenge with HCV replicon RNA. Treatment of cells with synthetic siRNA was effective >72 h, but the duration of RNA interference could be extended beyond 3 weeks through stable expression of complementary strands of the interfering RNA by using a bicistronic expression vector. These results suggest that a gene-therapeutic approach with siRNA could ultimately be used to treat HCV.
The Contribution of Horizontal Gene Transfer to the Evolution of Fungi. (2007)

The genomes of the hemiascomycetes Saccharomyces cerevisiae and Ashbya gossypii have been completely sequenced, allowing a comparative analysis of these two genomes, which reveals that a small number of genes appear to have entered these genomes as a result of horizontal gene transfer from bacterial sources. One potential case of horizontal gene transfer in A. gossypii and 10 potential cases in S. cerevisiae were identified, of which two were investigated further. One gene, encoding the enzyme dihydroorotate dehydrogenase (DHOD), is potentially a case of horizontal gene transfer, as shown by sequencing of this gene from additional bacterial and fungal species to generate sufficient data to construct a well-supported phylogeny. The DHOD-encoding gene found in S. cerevisiae, URA1 (YKL216W), appears to have entered the Saccharomycetaceae after the divergence of the S. cerevisiae lineage from the Candida albicans lineage and possibly since the divergence from the A. gossypii lineage. This gene appears to have come from the Lactobacillales, and following its acquisition the endogenous eukaryotic DHOD gene was lost. It was also shown that the bacterially derived horizontally transferred DHOD is required for anaerobic synthesis of uracil in S. cerevisiae. The other gene discussed in detail is BDS1, an aryl- and alkyl-sulfatase gene of bacterial origin that we have shown allows utilization of sulfate from several organic sources. Among the eukaryotes, this gene is found in S. cerevisiae and Saccharomyces bayanus and appears to derive from the alpha-proteobacteria.
Multiple Roles for Sialylated Glycans in Determining the Cardiopulmonary Tropism of Adeno-Associated Virus 4 (2013)

Adeno-associated virus 4 (AAV4) is one of the most divergent serotypes among known AAV isolates. Mucins or O-linked sialoglycans have been identified as the primary attachment receptors for AAV4 in vitro. However, little is known about the role(s) played by sialic acid interactions in determining AAV4 tissue tropism in vivo. In the current study, we first characterized two loss-of-function mutants obtained by screening a randomly mutated AAV4 capsid library. Both mutants harbored several amino acid residue changes localized to the 3-fold icosahedral symmetry axes on the AAV4 capsid and displayed low transduction efficiency in vitro. This defect was attributed to decreased cell surface binding as well as uptake of mutant virions. These results were further corroborated by low transgene expression and recovery of mutant viral genomes in cardiac and lung tissue following intravenous administration in mice. Pharmacokinetic analysis revealed rapid clearance of AAV4 mutants from the blood circulation in conjunction with low hemagglutination potential ex vivo. These results were recapitulated with mice pretreated intravenously with sialidase, directly confirming the role of sialic acids in determining AAV4 tissue tropism. Taken together, our results support the notion that blood-borne AAV4 particles interact sequentially with O-linked sialoglycans expressed abundantly on erythrocytes followed by cardiopulmonary tissues and subsequently for viral cell entry.
Preparation, Structure, and Thermal Stability of New NixCo1-2xMnx(OH)2 (0 ≤ x ≤ 1/2) Phases (2003)

The preparation, characterization, and thermal stability of NixCo1-2xMnx(OH)2 (0 ≤ x ≤ 1/2) is reported. These hydroxides are prepared by coprecipitation as the first step in the preparation of the corresponding Li[NixCo(1-2x)Mnx]O2 (0 ≤ x ≤ 1/2) oxides. Precipitates dried at room temperature adopt the hexagonal CdI2 structure. Thermal studies show that the hexagonal CdI2 type (RT) structure transforms to a cubic spinel-type solid solution (NixCo(1-2x)Mnx]3O4 (0 ≤ x ≤ 3/8) above about 150 °C that becomes well-crystallized at 600 °C. An intermediate turbostratic structure phase occurs between room temperature and 150 °C. This phase is present in small amounts in room-temperature-dried NixCo1-2xMnx(OH)2 materials with x ≥ 3/8. The results show that the drying method of the precipitate induces different phases with different bulk and tap density. This could have a major influence on the morphology, composition, density, and cell performance of Li[NixCo(1-2x)Mnx]O2 (0 ≤ x ≤ 1/2) oxides obtained from these dried precipitates.
Skin as a route of exposure and sensitization in chronic beryllium disease. (2003)

Chronic beryllium disease is an occupational lung disease that begins as a cell-mediated immune response to beryllium. Although respiratory and engineering controls have significantly decreased occupational beryllium exposures over the last decade, the rate of beryllium sensitization has not declined. We hypothesized that skin exposure to beryllium particles would provide an alternative route for sensitization to this metal. We employed optical scanning laser confocal microscopy and size-selected fluorospheres to demonstrate that 0.5- and 1.0- micro m particles, in conjunction with motion, as at the wrist, penetrate the stratum corneum of human skin and reach the epidermis and, occasionally, the dermis. The cutaneous immune response to chemical sensitizers is initiated in the skin, matures in the local lymph node (LN), and releases hapten-specific T cells into the peripheral blood. Topical application of beryllium to C3H mice generated beryllium-specific sensitization that was documented by peripheral blood and LN beryllium lymphocyte proliferation tests (BeLPT) and by changes in LN T-cell activation markers, increased expression of CD44, and decreased CD62L. In a sensitization-challenge treatment paradigm, epicutaneous beryllium increased murine ear thickness following chemical challenge. These data are consistent with development of a hapten-specific, cell-mediated immune response following topical application of beryllium and suggest a mechanistic link between the persistent rate of beryllium worker sensitization and skin exposure to fine and ultrafine beryllium particles.
Padlock oligonucleotides for duplex DNA based on sequence-specific triple helix formation (1999)

An oligonucleotide was circularized around double-stranded DNA thanks to triple helix formation. Short oligonucleotides are known to be able to form DNA triple helices by binding into the DNA major groove at an oligopurine.oligopyrimidine sequence. After sequence-specific recognition of a double-stranded DNA target through triple helix formation, the ends of the triplex-forming oligonucleotide were joined through the action of T4 DNA ligase, thus creating a circular DNA molecule catenated to the plasmid containing the target sequence. The labeling of the double-stranded DNA sequence has been carried out without any chemical or enzymatic modification of this sequence. These "padlock" oligonucleotides provide a tool to attach a noncovalent tag in an irreversible way to supercoiled plasmid or other double-stranded DNAs. Such a complex may find applications in the development of new techniques for duplex DNA detection or plasmid delivery methods for gene therapy.
Discovering all most specific sentences by randomized algorithms (1997)

Data mining can in many instances be viewed as the task of computing a representation of a theory of a model or of a database. In this paper we present a randomized algorithm that can be used to compute the representation of a theory in terms of the most specific sentences of that theory. In addition to randomization, the algorithm uses a generalization of the concept of hypergraph transversals. We apply the general algorithm in two ways, for the problem of discovering maximal frequent sets in 0/1 data, and for computing minimal keys in relations. We present some empirical results on the performance of these methods on real data. We also show some complexity theoretic evidence of the hardness of these problems.