gebhart/patrepeval huggingface dataset:
Focused Ion Beam Analysis of Low-K Dielectrics (2000)

Abstract The characteristics of an organic low-k dielectric during investigation by focused ion beam (FIB) are discussed for the different FIB application modes: cross-section imaging, specimen preparation for transmission electron microscopy, and via milling for device modification. It is shown that the material is more stable under the ion beam than under the electron beam in the scanning electron microscope (SEM) or in the transmission electron microscope (TEM). The milling of the material by H2O vapor assistance is strongly enhanced. Also by applying XeF2 etching an enhanced milling rate can be obtained so that both the polymer layer and the intermediate oxides can be etched in a single step.
Renal involvement in bone marrow transplantation (2005)

Bone marrow transplantation (BMT) is an effective therapeutic strategy for leukaemic malignancies and depressed bone marrow following cancer. However, its side effects on kidneys have been reported. Some drugs and irradiation are also suggested to be nephrotoxic. It is well known that haemolytic uraemic syndrome (HUS) after BMT develops as late-onset BMT nephropathy. Cyclosporine A (CsA) is a possible cause. Radiation nephropathy shows changes that are similar to the histology of HUS. These findings suggest that endothelial damage is closely associated with the pathogenesis of post-BMT nephropathy. Recently, some patients have developed glomerulonephritis accompanied by graft-versus-host disease (GVHD) after BMT. In these patients immune deposits are found mainly in subepithelium and mesangium equal to those of secondary membranous glomerulonephritis. A murine experimental model of GVHD manifests similar symptoms and histological changes to those of actual patients and may suggest the pathogenesis of glomerulonephritis.
EPITOPE TAGGING (1998)

Epitope tagging is a recombinant DNA method by which a protein encoded by a cloned gene is made immunoreactive to a known antibody. This review discusses the major advantages and limitations of epitope tagging and describes a number of recent applications. Major areas of application include monitoring protein expression, localizing proteins at the cellular and subcellular levels, and protein purification, as well as the analysis of protein topology, dynamics and interactions. Recently the method has also found use in transgenic and gene therapy studies and in the emerging fields of functional genomics and proteomics.
Co‐expression of native and introduced genes reveals cryptic regulation of HMG CoA reductase expression in Arabidopsis (1995)

In eukaryotes, all isoprenoid compounds share a common precursor, mevalonic acid, whose synthesis is catalyzed by the enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase. As one step towards a better understanding of the role that this enzyme plays in coordinating isoprenoid biosynthesis in plants, Arabidopsis thaliana HMG CoA reductase was ectopically expressed in transgenic Arabidopsis plants. By using this molecular genetic approach, several novel and fundamental observations have been made regarding isoprenoid biosynthesis in Arabidopsis. First, it was demonstrated that the overexpression of authentic Arabidopsis HMG CoA reductase is not sufficient to alter the bulk synthesis and accumulation of the abundant end products of the plant isoprenoid pathway. Second, active transcription of the transgene appears to co-activate and deregulate expression of the native gene, resulting in a striking elevation of HMG CoA reductase mRNA levels. Finally, although very high levels of HMG CoA reductase mRNA were expressed in these transgenic plants, only modest increases in enzyme activity could be detected. Taken together, these data suggest that HMG CoA reductase expression is regulated at multiple levels in plants as well as animals, and they provide a foundation for elucidating the molecular mechanisms for mevalonate regulation in A. thaliana.
A Modified Gaussian Integration Scheme in Element Free Method (2002)

ABSTRACT In this paper, a modified numerical integration scheme is presented that improves the accuracy of the numerical integration of the Galerkin weak form, within the integration cells of the analyzed domain in the element-free methods. A geometrical interpretation of the Gaussian quadrature rule is introduced to map the effective weighting territory of each quadrature point in an integration cell. Then, the conventional quadrature rule is extended to cover the overlapping area between the weighting territory of each quadrature point and the physical domain. This modified numerical integration scheme can lessen the errors due to misalignment between the integration cell and the boundary or interface of the physical domain. Some numerical examples illustrate that this newly proposed integration scheme for element-free methods does effectively improve the accuracy when solving solid mechanics problems.
Neuroprotective Flavonoids fromFlemingia macrophylla (2005)

Using an Abeta-induced neurotoxicity blocking assay to direct fractionation, three new flavonoids, fleminginin (1), flemingichromone (2), and flemingichalcone (3), and twenty known compounds were isolated from the active fractions of the aerial parts of Flemingia macrophylla. The structures of 1 - 3 were elucidated on the basis of spectroscopic data. When tested for neuroprotective activity, compound 2, osajin ( 4), 5,7,4'-trihydroxy-6,8-diprenylisoflavone (5), 5,7,4'-trihydroxy-6,3'-diprenylisoflavone (6), and aureole (7) protected neuronal cells from Abeta-induced damage with EC50 values of 31.43 +/- 3.16, 5.01 +/- 1.28, 11.25 +/-1.51, 4.47 +/- 0.65, 12.09 +/- 2.55 microM, respectively.
Herpes simplex virus type 1 glycoprotein C-negative mutants exhibit multiple phenotypes, including secretion of truncated glycoproteins (1984)

A virus-neutralizing monoclonal antibody specific for glycoprotein C (gC) of herpes simplex virus type 1 strain KOS was used to select a number of neutralization-resistant mutants. A total of 103 of these mutants also were resistant to neutralization by a pool of gC-specific antibodies and thus were operationally defined as gC-. Analysis of mutant-infected cell mRNA showed that a 2.7-kilobase mRNA, comparable in size to the wild-type gC mRNA, was produced by nearly all mutants. However, six mutants, gC-5, gC-13, gC-21, gC-39, gC-46, and gC-98, did not produce the normal-size gC mRNA but rather synthesized a novel 1.1-kilobase RNA species. These mutants had deletions of 1.6 kilobases in the coding sequence of the gC structural gene, which explains their gC- phenotype. Despite the production of an apparently normal mRNA by the remaining 97 mutants, only 7 mutants produced a detectable gC polypeptide. In contrast to wild-type gC, which is a membrane-bound glycoprotein with an apparent molecular weight of 130,000 (130K), five of these mutants quantitatively secreted proteins of lower molecular weight into the culture medium. These were synLD70 (101K), gC-8 (109K), gC-49 (112K), gC-53 (108K), and gC-85 (106K). The mutant gC-3 secreted a protein that was indistinguishable in molecular weight from wild-type KOS gC. Another mutant, gC-44, produced a gC protein which also was indistinguishable from wild-type gC by molecular weight and which remained cell associated. Pulse-labeling of infected cells in the presence and absence of the glycosylation inhibitor tunicamycin demonstrated that these proteins were glycosylated and provided estimates of the molecular weights of the nonglycosylated primary translation products. The smallest of these proteins was produced by synLD70 and was 48K, about two-thirds the size of the wild-type polypeptide precursor (73K). Physical mapping of the mutations in synLD70 and gC-8 by marker rescue placed these mutations in the middle third of the gC coding sequence. Mapping of the mutations in other gC- mutants, including two in which no protein product was detected, also placed these mutations within or very close to the gC gene. The biochemical and genetic data available on mutants secreting gC gene products suggest that secretion is due to the lack of a functional transmembrane anchor sequence on these mutant glycoproteins.
Representations of Language Varieties Are Reliable Given Corpus Similarity Measures (2021)

This paper measures similarity both within and&#13;\nbetween 84 language varieties across nine languages. These corpora are drawn from digital sources (the web and tweets), allowing&#13;\nus to evaluate whether such geo-referenced&#13;\ncorpora are reliable for modelling linguistic&#13;\nvariation. The basic idea is that, if each&#13;\nsource adequately represents a single underlying language variety, then the similarity between these sources should be stable across&#13;\nall languages and countries. The paper shows&#13;\nthat there is a consistent agreement between&#13;\nthese sources using frequency-based corpus&#13;\nsimilarity measures. This provides further evidence that digital geo-referenced corpora consistently represent local language varieties.
Targeted drug delivery to tumor vasculature by a carbohydrate mimetic peptide (2011)

Although numerous carbohydrates play significant roles in mammalian cells, carbohydrate-based drug discovery has not been explored due to the technical difficulty of chemically synthesizing complex carbohydrate structures. Previously, we identified a series of carbohydrate mimetic peptides and found that a 7-mer peptide, designated I-peptide, inhibits hematogenous carbohydrate-dependent cancer cell colonization. During analysis of the endothelial surface receptor for I-peptide, we found that I-peptide bound to annexin 1 (Anxa1). Because Anxa1 is a highly specific tumor vasculature surface marker, we hypothesized that an I-peptide-like peptide could target anticancer drugs to the tumor vasculature. This study identifies IFLLWQR peptide, designated IF7, as homing to tumors. When synthetic IF7 peptide was conjugated to fluorescent Alexa 488 (A488) and injected intravenously into tumor-bearing mice, IF7-A488 targeted tumors within minutes. IF7 conjugated to the potent anticancer drug SN-38 and injected intravenously into nude mice carrying human colon HCT116 tumors efficiently suppressed tumor growth at low dosages with no apparent side effects. These results suggest that IF7 serves as an efficient drug delivery vehicle by targeting Anxa1 expressed on the surface of tumor vasculature. Given its extremely specific tumor-targeting activity, IF7 may represent a clinically relevant vehicle for anticancer drugs.
Quantum Dot Molecular Beacons for DNA Detection (2009)

Molecular beacons have become an important fluorescent probe for sequence-specific DNA detection. To improve the sensitivity and robustness of molecular beacon assays, fluorescent semiconductor quantum dots (QDs) are now being used as the fluorescent moiety for molecular beacon synthesis. Multiple linkage strategies can be used for attaching molecular beacon DNA to QDs, and multiple quenchers, including gold particles, can be used for fluorescence quenching. Covalent attachment of QDs to DNA can be achieved through amide linkage, and affinity-based attachment can be achieved with streptavidin-biotin linkage. We have shown that these linkage strategies can be used to successfully create quantum dot molecular beacons that can be used in DNA detection assays with high specificity.
Dynamic multidimensional histograms (2002)

Histograms are a concise and flexible way to construct summary structures for large data sets. They have attracted a lot of attention in database research due to their utility in many areas, including query optimization, and approximate query answering. They are also a basic tool for data visualization and analysis.In this paper, we present a formal study of dynamic multidimensional histogram structures over continuous data streams. At the heart of our proposal is the use of a dynamic summary data structure (vastly different from a histogram) maintaining a succinct approximation of the data distribution of the underlying continuous stream. On demand, an accurate histogram is derived from this dynamic data structure. We propose algorithms for extracting such an accurate histogram and we analyze their behavior and tradeoffs. The proposed algorithms are able to provide approximate guarantees about the quality of the estimation of the histograms they extract.We complement our analytical results with a thorough experimental evaluation using real data sets.
Detecting bit-flip errors in a logical qubit using stabilizer measurements (2015)

Quantum data are susceptible to decoherence induced by the environment and to errors in the hardware processing it. A future fault-tolerant quantum computer will use quantum error correction to actively protect against both. In the smallest error correction codes, the information in one logical qubit is encoded in a two-dimensional subspace of a larger Hilbert space of multiple physical qubits. For each code, a set of non-demolition multi-qubit measurements, termed stabilizers, can discretize and signal physical qubit errors without collapsing the encoded information. Here using a five-qubit superconducting processor, we realize the two parity measurements comprising the stabilizers of the three-qubit repetition code protecting one logical qubit from physical bit-flip errors. While increased physical qubit coherence times and shorter quantum error correction blocks are required to actively safeguard the quantum information, this demonstration is a critical step towards larger codes based on multiple parity measurements.
The Novel Nucleoside Analog R1479 (4′-Azidocytidine) Is a Potent Inhibitor of NS5B-dependent RNA Synthesis and Hepatitis C Virus Replication in Cell Culture (2005)

Hepatitis C virus (HCV) polymerase activity is essential for HCV replication. Targeted screening of nucleoside analogs identified R1479 (4'-azidocytidine) as a specific inhibitor of HCV replication in the HCV subgenomic replicon system (IC(50) = 1.28 microM) with similar potency compared with 2'-C-methylcytidine (IC(50) = 1.13 microM). R1479 showed no effect on cell viability or proliferation of HCV replicon or Huh-7 cells at concentrations up to 2 mM. HCV replicon RNA could be fully cleared from replicon cells after prolonged incubation with R1479. The corresponding 5'-triphosphate derivative (R1479-TP) is a potent inhibitor of native HCV replicase isolated from replicon cells and of recombinant HCV polymerase (NS5B)-mediated RNA synthesis activity. R1479-TP inhibited RNA synthesis as a CTP-competitive inhibitor with a K(i) of 40 nM. On an HCV RNA-derived template substrate (complementary internal ribosome entry site), R1479-TP showed similar potency of NS5B inhibition compared with 3'-dCTP. R1479-TP was incorporated into nascent RNA by HCV polymerase and reduced further elongation with similar efficiency compared with 3'-dCTP under the reaction conditions. The S282T point mutation in the coding sequence of NS5B confers resistance to inhibition by 2'-C-MeATP and other 2'-methyl-nucleotides. In contrast, the S282T mutation did not confer cross-resistance to R1479.
The activation of prothrombin complex concentrates by calcium in vitro. (1977)

The activation of prothrombin concentrate mixtures incubated "in vitro" was investigated. "Activation" was assessed by the correcting effect of suct mixtures on the APTT of a test plasma containing a factor VIII inhibitor and also by the generation of free thrombin. Thrombin itself was found to have insignificant activating effect. Prothrombin concentrates incubated with near-physiological levels of calcium appeared to correct the abnormal APTT to an increasing degree as the calcium concentration was increased. Free thrombin was generated with calcium cencentrations greater than those required for APTT correction. The activation process could be stopped at any stage by adding citrate which removed ionized calcium from the incubation mixture.
Efficacy of two cannabis based medicinal extracts for relief of central neuropathic pain from brachial plexus avulsion: results of a randomised controlled trial (2004)

The objective was to investigate the effectiveness of cannabis-based medicines for treatment of chronic pain associated with brachial plexus root avulsion. This condition is an excellent human model of central neuropathic pain as it represents an unusually homogenous group in terms of anatomical location of injury, pain descriptions and patient demographics. Forty-eight patients with at least one avulsed root and baseline pain score of four or more on an 11-point ordinate scale participated in a randomised, double-blind, placebo-controlled, three period crossover study. All patients had intractable symptoms regardless of current analgesic therapy. Patients entered a baseline period of 2 weeks, followed by three, 2-week treatment periods during each of which they received one of three oromucosal spray preparations. These were placebo and two whole plant extracts of Cannabis sativa L.: GW-1000-02 (Sativex), containing Delta(9)tetrahydrocannabinol (THC):cannabidiol (CBD) in an approximate 1:1 ratio and GW-2000-02, containing primarily THC. The primary outcome measure was the mean pain severity score during the last 7 days of treatment. Secondary outcome measures included pain related quality of life assessments. The primary outcome measure failed to fall by the two points defined in our hypothesis. However, both this measure and measures of sleep showed statistically significant improvements. The study medications were generally well tolerated with the majority of adverse events, including intoxication type reactions, being mild to moderate in severity and resolving spontaneously. Studies of longer duration in neuropathic pain are required to confirm a clinically relevant, improvement in the treatment of this condition.
Increased serum levels of endostatin in patients with idiopathic pulmonary fibrosis (2005)

Endostatin is an angiogenesis inhibitor that is an endogenously produced proteolytic fragment of type XVIII collagen. Serum levels of endostatin have been studied extensively in patients with malignant diseases. Recently, elevated serum endostatin levels were observed in patients with systemic sclerosis accompanying pulmonary fibrosis. To determine whether elevated serum endostatin can be observed in patients with idiopathic pulmonary fibrosis (IPF), we measured serum levels of endostatin in 69 patients with benign respiratory disease using an ELISA kit. The median of the serum endostatin levels in these patients was 50.8 pg/mL. Seven of 11 patients (63.6%) with collagen disease-associated pulmonary fibrosis (CDPF), and 19 of 24 patients (79.2%) with IPF had higher serum endostatin levels than the median level of the 69 patients. There was no statistical difference in serum endostatin levels between the patients with IPF and those with CDPF (P=0.7898). Serum endostatin levels in 24 patients with IPF were significantly higher than those in 34 patients with respiratory diseases other than IPF and CDPF (P=0.0001). Elevated serum levels of endostatin were observed in patients with IPF. Although the mechanisms are unclear, elevated serum levels of endostatin may be related to the fibrosing process in the lung.
A continuous multi-size particle separator using negative dielectrophoretic virtual pillars induced by a planar spot electrode array (2007)

We present a continuous size-dependent particle separator based on the virtual pillars induced by negative dielectrophoretic (DEP) force on a planar spot electrode array for separation of multi-sized particles. The present particle separator eliminates particle clogging in microchannel using virtual barriers. Also, the present particle separator easily changes separable particle sizes by adjusting applied voltage. Experimental study verifies the size-dependent particle separation capability for 6, 8, 10, and 12μm-diameter polystyrene beads and the voltage-tuning separation by adjusting applied voltages.
Enhancement of laser/EUV conversion by shaped laser pulse interacting with Li-contained targets for EUV lithography (2004)

The advantages of droplet and claster Li-contained targets for debris free EUV generation are estimated on base of analytical modeling and simulation. Conversion efficiency of laser energy into EUV energy from such targets is found to reach a few percents. The laser prepulse is proposed to enhance the laser energy conversion into emission at wavelength of 13.5 nm.
The UNITE database for molecular identification of fungi – recent updates and future perspectives (2010)

Udgivelsesdato: April 2010
Variants of the Antibody Herceptin That Interact with HER2 and VEGF at the Antigen Binding Site (2009)

The interface between antibody and antigen is often depicted as a lock and key, suggesting that an antibody surface can accommodate only one antigen. Here, we describe an antibody with an antigen binding site that binds two distinct proteins with high affinity. We isolated a variant of Herceptin, a therapeutic monoclonal antibody that binds the human epidermal growth factor receptor 2 (HER2), on the basis of its ability to simultaneously interact with vascular endothelial growth factor (VEGF). Crystallographic and mutagenesis studies revealed that distinct amino acids of this antibody, called bH1, engage HER2 and VEGF energetically, but there is extensive overlap between the antibody surface areas contacting the two antigens. An affinity-improved version of bH1 inhibits both HER2- and VEGF-mediated cell proliferation in vitro and tumor progression in mouse models. Such "two-in-one" antibodies challenge the monoclonal antibody paradigm of one binding site, one antigen. They could also provide new opportunities for antibody-based therapy.
Glycosylimidate, 25. Muraminsäure als Glycosyldonor und ‐akzeptor (1987)

Abstract Aus den 3‐ O ‐ungeschützten 2‐Azido‐2‐desoxy‐ D ‐glucose‐Derivaten 3 und 4 und Trifluormethansulfonaten von ( S )‐Milchsäureestern als Alkylierungsmittel konnten diastereospezifisch und in hohen Ausbeuten die Muraminsäurederivate 8a–10a erhalten werden. ( S )‐2‐Chlorpropionsäureester lieferte in dieser Reaktion Diastereomere. Die Muraminsäurederivate 8a–10a können in Glycosylakzeptoren und Glycosyldonoren übergeführt werden. So wurde aus 8a und 10a durch Entacetalisierung und selektive 6‐ O ‐Silylierung das Muraminsäurederivat 11 als Akzeptor erhalten, der mit dem α‐Trichloracetimidat 14 als Donor das β‐verknüpfte Disaccharid 15‐β lieferte. Schutzgruppenabspaltung führte zur Disaccharid‐Grundeinheit 19 des Zellwand‐Peptidoglycans von Bakterien. Selektive 1‐Entsilylierung des Muraminsäurederivates 8a und Bildung des α‐Trichloracetimidats 28‐α ergab einen Muraminsäure‐Glycosyldonor. Mit verschiedenen Akzeptoren wurden in Abhängigkeit vom Katalysator und von den Reaktionsbedingungen selektiv und in hohen Ausbeuten β‐ oder α‐Glycoside und ‐Disaccharide synthetisiert.
Using plane + parallax for calibrating dense camera arrays (2004)

A light field consists of images of a scene taken from different viewpoints. Light fields are used in computer graphics for image-based rendering and synthetic aperture photography, and in vision for recovering shape. In this paper, we describe a simple procedure to calibrate camera arrays used to capture light fields using a plane + parallax framework. Specifically, for the case when the cameras lie on a plane, we show (i) how to estimate camera positions up to an affine ambiguity, and (ii) how to reproject light field images onto a family of planes using only knowledge of planar parallax for one point in the scene. While planar parallax does not completely describe the geometry of the light field, it is adequate for the first two applications which, it turns out, do not depend on having a metric calibration of the light field. Experiments on acquired light fields indicate that our method yields better results than full metric calibration.