gebhart/patrepeval huggingface dataset:
Elastomeric Transistor Stamps: Reversible Probing of Charge Transport in Organic Crystals (2004)

We introduce a method to fabricate high-performance field-effect transistors on the surface of freestanding organic single crystals. The transistors are constructed by laminating a monolithic elastomeric transistor stamp against the surface of a crystal. This method, which eliminates exposure of the fragile organic surface to the hazards of conventional processing, enables fabrication of rubrene transistors with charge carrier mobilities as high as approximately 15 cm2/V.s and subthreshold slopes as low as 2nF.V/decade.cm2. Multiple relamination of the transistor stamp against the same crystal does not affect the transistor characteristics; we exploit this reversibility to reveal anisotropic charge transport at the basal plane of rubrene.
Thermostable alanine racemase from Bacillus stearothermophilus: molecular cloning of the gene, enzyme purification, and characterization (1986)

The alanine racemase (EC 5.1.1.1) gene of a thermophilic bacterium, Bacillus stearothermophilus, was cloned and expressed in Escherichia coli C600 with vector plasmid pICR301, which was constructed from pBR322 and the L-alanine dehydrogenase gene derived from B. stearothermophilus. A coupled assay method with L-alanine dehydrogenase and tetrazolium salts was used to detect visually the alanine racemase activity in the clones. Alanine racemase overproduced in a clone carrying the plasmid pICR4, 12 kilobases of DNA, was purified from cell extracts about 340-fold to homogeneity by five steps including heat treatment. The overproduced enzyme was confirmed to originate from B. stearothermophilus by an immunochemical cross-reaction with the enzyme of B. stearothermophilus. The purified enzyme has a molecular weight of about 78 000 and consists of two identical subunits of Mr of 39 000. At the optimum temperature (50 degrees C), the enzyme has a specific activity of 1800 units/mg (Vmax, D- to L-alanine). Resolution and reconstitution experiments together with the absorption spectrum of the enzyme clearly indicate that alanine racemase of B. stearothermophilus is a pyridoxal 5'-phosphate enzyme.
Involvement of focal adhesion kinase in invasin-mediated uptake (1998)

High-efficiency entry of the enteropathogenic bacterium Yersinia pseudotuberculosis into nonphagocytic cells is mediated by the bacterial outer membrane protein invasin. Invasin-mediated uptake requires high affinity binding of invasin to multiple beta1 chain integrin receptors on the host eukaryotic cell. Previous studies using inhibitors have indicated that high-efficiency uptake requires tyrosine kinase activity. In this paper we demonstrate a requirement for focal adhesion kinase (FAK) for invasin-mediated uptake. Overexpression of a dominant interfering form of FAK reduced the amount of bacterial entry. Specifically, the autophosphorylation site of FAK, which is a reported site of c-Src kinase binding, is required for bacterial internalization, as overexpression of a derivative lacking the autophosphorylation site had a dominant interfering effect as well. Cultured cells expressing interfering variants of Src kinase also showed reduced bacterial uptake, demonstrating the involvement of a Src-family kinase in invasin-promoted uptake.
Replica Voting: a Distributed Middleware Service for Real-time Dependable Systems (2006)

In information assurance settings, majority voting among replica processes enhances the trust-worthiness of data collected from a hostile external environment. It allows a correct data fusion and dissemination by the end-users, in the presence of content corruptions and/or timing failures that may possibly occur during data collection. Two key elements are required of the voting functionality: i) fielding asynchronously generated real-time or near-real-time data, and ii) handling large sized non-numeric data sets with problem-specific interpretations-e.g., terrain images from radar stations. Under the constraints (i) and (ii), we describe a highly asynchronous voting service to effect a timely and low-overhead delivery of data to the users. The paper analyzes the service-level properties of a voting machinery to meet the stringent needs of IA applications. The externally visible properties are prescribed in terms of `safety' and `liveness' requirements of the underlying voting protocols that reflect the application-specific data integrity and availability constraints. When voting is provided as a middleware service, an application designer may prescribe the necessary service-level parameters: the level of resiliency and the performance aspects of data delivery
The gamma-carboxyglutamic acid and epidermal growth factor-like modules of factor IXa beta. Effects on the serine protease module and factor X activation. (1994)

Blood coagulation factors IX and X are two serine proteases with a similar modular structure. The non-catalytic part of each protein consists of a gamma-carboxyglutamic acid (Gla)-containing module and two modules homologous to the epidermal growth factor (EGF) precursor. We have now found that the NH2-terminal EGF-like module of both factors IX and X inhibits factor Xa formation in a Gla-independent manner, both in the presence and absence of phospholipid and the cofactor, factor VIIIa. In contrast, the COOH-terminal EGF-like module has no such effect. Our data indicate that the NH2-terminal EGF-like module of factor IXa beta interacts either with the corresponding module or with the serine protease module in the substrate, factor X, without affecting the hydrolysis of low molecular weight substrates. Using antibodies as structural probes, we found that Ca2+ binding to the Gla module of factor IXa beta induces a conformational transition in the serine protease module. No evidence was found for a direct interaction between the Gla module and factor VIIIa. We therefore propose that the Gla module in factor IXa beta is indirectly involved in the cofactor interaction, in that Ca2+ binding to sites in this module induces a conformation in the serine protease module that is commensurate with factor VIIIa interaction. In addition, the immunochemical approach revealed a Gla-independent Ca2+ binding site in the serine protease module (apparent Kd of approximately 120 microM) that also might influence its conformation. Antibodies against the EGF-like modules of factor IX were used to probe Ca2+ binding to these modules in intact and in Gla-domainless factor IXa beta. The data indicate a Ca2+ binding site with an apparent Kd of approximately 50 microM in the NH2-terminal EGF-like module of both factor IX species.
Combined use of oligonucleotide and tissue microarrays identifies cancer/testis antigens as biomarkers in lung carcinoma. (2002)

High density oligonucleotide microarrays (OMAs) have been used recently to profile gene expression in lung carcinoma tissue homogenates. The length of the lists of potentially interesting genes generated by these studies is daunting, and biological and clinical relevance of these lists remains to be validated. Moreover, specific identification of individual biomarkers that might be used for early detection and surveillance has not been the objective of these early studies. We have developed a schema for combining the data derived from the OMA analysis of a few lung cancer cell lines with immunohistochemical testing of tissue microarrays to rapidly identify biomarkers of potential clinical relevance. Initially, we profiled gene expression in lung tumor cell lines using the Affymetrix HG-U95Av2 OMA. RNA from 2 non-small cell lung cancer (NSCLC) cell lines (A549 and H647) and 2 small cell lung cancer (SCLC) cell lines (SHP-77 and UMC-19) were tested. Cells from 1 histologically and cytogenetically normal bronchial epithelial primary culture from a volunteer who had never smoked and 10 samples of histologically unremarkable lung tissue from resection specimens served as normalization controls. Array results were analyzed with Gene Spring software. Results were confirmed by reverse transcription-PCR in an expanded number of cell lines. We then validated the cell line data by immunohistochemical testing for protein using a tissue microarray containing 187 NSCLC clinical samples. Of the 20 most highly expressed genes in the tumor lines, 6 were members of the cancer/testis antigen (CTAG) gene group including 5 MAGE-A subfamily members and NY-ESO-1. SCLC lines strongly expressed all of the MAGE-A genes as well as NY-ESO-1, whereas NSCLC lines expressed a subset of MAGE-A genes at a lower level of intensity and failed to express NY-ESO-1. Reverse transcription-PCR of an extended series of 25 lung cancer cell lines including 13 SCLC, 9 NSCLC, and 3 mesothelioma lines indicated that MAGE-A10 and NY-ESO-1 were expressed only by SCLC, and that MAGE-A1, 3, 6, 12, and 4b were expressed by both SCLC and NSCLC. By immunohistochemistry using the monoclonal antibody 6C1 that recognizes several MAGE-A gene subfamily members, 44% of NSCLC clearly expressed MAGE-A proteins in cytoplasm and/or nucleus. Expression of MAGE-A genes did not correlate with survival but did correlate with histological classification with squamous carcinomas more frequently MAGE-A positive than other NSCLC types (P < 0.00002). We conclude that expression of CTAG gene products, whereas apparently not of prognostic importance, may be useful for early detection and surveillance because of a high level of specificity for central airway squamous and small cell carcinomas.
Botulinum neurotoxin serotype F is a zinc endopeptidase specific for VAMP/synaptobrevin (1993)

Botulinum neurotoxin serotype F contains the zinc binding motif of zinc endopeptidases. Atomic adsorption analysis of highly purified toxin preparation revealed the presence of one atom of zinc per molecule of toxin, which could be removed with EDTA or o-phenanthroline. The light chain of the neurotoxin was shown to have a zinc-dependent protease activity specific for VAMP/synaptobrevin, an integral membrane protein of synaptic vesicles. Both isoforms of rat VAMP were cleaved at the same site corresponding to the single Gln-Lys peptide bond present in their sequences. This proteolytic activity was inhibited by EDTA, o-phenanthroline, and captopril as well as by VAMP peptides spanning the cleavage site.
Characterization of UHMWPE hip cups run on joint simulators (1987)

The density and crystallinity of UHMWPE-hip cups were investigated as a function of thickness from the inner stressed surface to the unstressed outer surface. The effects of mechanical strain and chemical reactions during simulation tests, and damage of the material due to pretreatments and storage, resulted in changes of the structure, as indicated by variations in the crystallinity. Independent of either the batch of UHMWPE supplied or the manufacturer and the type of simulator used, the individual sample-sets showed a similar characteristic curve of density versus wall thickness. Infrared spectroscopic evaluations indicated the presence of oxidative degradation, and answers the question as to which areas of the polymers are changed by aging and which compounds are newly formed. The characteristic carbonyl groups were also determined. The concentration trend of carbonyl groups versus wall thickness obtained agrees surprisingly well with the locally determined density and crystallinity trend. As these compounds are formed by reactions which produce stable oxidative degradation products and also crosslinking, we have determined the degree of cross-linking. The determination of the soluble constituents after extraction showed lower degree of crosslinking on the surface than in the middle of the material. Hence it follows that on the surfaces oxidative chain scission is prevailing, whereas in the interior mainly crosslinking is developed. These results indicate that the samples used for the simulation tests had distinct differences in characteristics. Generally the results show that wear tests in joint simulators lead to property changes in UHMWPE which differ considerably from test results previously obtained on retrieved hip cups.
Fredericamycin A a new antitumor antibiotic. I. Production, isolation and physicochemical properties. (1981)

A new antitumor antibiotic, fredericamycin A (FCRC-A48, NSC-305263), has been isolated from a strain of Streptomyces griseus (FCRC-48). Based on its unique ultraviolet-visible spectrum, infrared spectrum, proton and carbon-13 nuclear magnetic resonance spectra and mass spectra, it is judged to be a novel acid-base indicator type of compound. Its production, isolation and physicochemical properties are discussed. The isolation, ultraviolet-visible spectrum and some biological properties of two minor components, fredericamycin B and fredericamycin C, are also described.
Cloning and endonuclease restriction analysis of uidA and uidR genes in Escherichia coli K-12: determination of transcription direction for the uidA gene. (1982)

The two genes of the Escherichia coli K-12 uid region (the structural gene uidA and the regulatory gene uidR) were isolated on a ColE1-uid hybrid plasmid from the bank of Clarke and Carbon. We made a restriction map of this region and correlated it with the genetic map by subcloning the uid restriction fragments into plasmids pBR322, pBR325, and pACYC177. In these plasmids, amplification of the products of the uidA and uidR genes occurred. The enzyme coded for by uidA was identified by polyacrylamide gel electrophoresis of crude extracts from strains containing the uidA plasmid. A 1-megadalton EcoRI-BamHI segment contained the uidAo operator, and the direction of transcription of the uidA gene was determined. The restriction analysis also suggested that the order of the loci in this region is manA, uidA, uidAo, uidR.
A Novel Function of IL-12p40 as a Chemotactic Molecule for Macrophages (1999)

IL-12p70 plays a pivotal role in regulating the Th1/Th2 balance in the initial stage of immune responses. In contrast, IL-12p40, which is produced excess over IL-12p70, has been known to down-regulate IL-12p70-mediated responses by acting as an antagonist. To investigate in vivo function of IL-12p40, RH7777 rat hepatoma cells were engineered to inducibly express mouse IL-12p40 under the tight control of doxycycline (dox). In the absence of dox, s.c. injection of these cells into syngeneic rat was shown to generate tumors. However, the induction of IL-12p40 by dox was sufficient for inhibiting tumor formation, as well as for tumor regression. Immunohistochemical analysis showed that macrophages, but not CD4+ T, CD8+ T, and NK cells, were predominantly recruited into tumor sites as early as 3 days after IL-12p40 induction. These results were further supported by the observation that IL-12p40, but not C-terminal deletion mutants by more than 5 amino acids, was able to chemoattract peritoneal macrophages in vitro, suggesting that IL-12p40, when produced in a large excess over IL-12p70 in vivo, can initially amplify the immune responses against tumors by directly recruiting macrophages. Our findings indicate that IL-12p40 may function as an effector molecule as well as an antagonist of IL-12p70.
A modular DNA signal translator for the controlled release of a protein by an aptamer (2006)

Owing to the intimate linkage of sequence and structure in nucleic acids, DNA is an extremely attractive molecule for the development of molecular devices, in particular when a combination of information processing and chemomechanical tasks is desired. Many of the previously demonstrated devices are driven by hybridization between DNA 'effector' strands and specific recognition sequences on the device. For applications it is of great interest to link several of such molecular devices together within artificial reaction cascades. Often it will not be possible to choose DNA sequences freely, e.g. when functional nucleic acids such as aptamers are used. In such cases translation of an arbitrary 'input' sequence into a desired effector sequence may be required. Here we demonstrate a molecular 'translator' for information encoded in DNA and show how it can be used to control the release of a protein by an aptamer using an arbitrarily chosen DNA input strand. The function of the translator is based on branch migration and the action of the endonuclease FokI. The modular design of the translator facilitates the adaptation of the device to various input or output sequences.
Pulp response to collagen and glutaraldehyde in pulpotomized primary teeth of baboons. (1991)

This investigation assessed histologically the pulp tissue reaction to glutaraldehyde (GA) and to a commercial collagen preparation in pulpotomized primary teeth of baboons. One hundred and eighty-eight primary teeth were pulpotomized; in half of them inflammation was induced prior to the treatment. The teeth were divided into five groups: in three of them GA was used as a pulp dressing and applied for 1 min (group 1), 5 min (group 2), or mixed into the paste (group 3); collagen was used in group 4 and in group 5 (control) IRM was placed directly over the pulp stumps. Follow-up times were two, eight, and 24 weeks. Total necrosis was observed only in the collagen group. Partial necrosis and severe inflammation also were seen mainly in this group, and when the GA was incorporated into the paste. Slight to moderate inflammation was evident in all groups two and eight weeks postoperatively; however, 78% of the teeth of group 2 (GA 5 min) were inflammation-free after 24 weeks. Partial dentin bridges were seen in 92% of the teeth of the control group, in 82% of group 2, and 50% each of groups 1 and 3 eight weeks postoperatively. Dentin bridges were present in only 4% of the collagen group. After 24 weeks, all the teeth in group 2 and 83% of group 1 had dentin bridges. We conclude that Zyderm (Colagen Corp. Palo Alto, CA) led to unacceptable results, 5 min application of GA presented the best healing response, and GA 1 min and IRM also were satisfactory.
A NH2 Tau Fragment Targets Neuronal Mitochondria at AD Synapses: Possible Implications for Neurodegeneration (2010)

Synapses are ultrastructural sites for memory storage in brain, and synaptic damage is the best pathologic correlate of cognitive decline in Alzheimer's disease (AD). Post-translational hyperphosphorylation, enzyme-mediated truncation, conformational modifications, and aggregation of tau protein into neurofibrillary tangles (NFTs) are hallmarks for a heterogeneous group of neurodegenerative disorders, so-called tauopathies. AD is a secondary tauopathy since it is pathologically distinguished by the presence of amyloid-beta (Abeta)-containing senile plaques and the presence of tau-positive NFTs in the neocortex and hippocampus. Here, we report that a 20-22 kDa NH2-truncated tau fragment is largely enriched in human mitochondria from cryopreserved synaptosomes of AD brains and that its amount in terminal fields correlates with the pathological synaptic changes and with the organelle functional impairment. This NH2-truncated tau form is also found in other human, not AD-tauopathies, while its presence in AD patients is linked to Abeta multimeric species and likely to pathology severity. Finally native, patient-derived, Abeta oligomers-enriched extracts likely impair the mitochondrial function by the in vitro production of 20-22 kDa NH2-tau fragments in mature human SY5Y and in rat hippocampal neurons. Thus our findings suggest that the mitochondrial NH2-derived tau peptide distribution may exacerbate the synapse degeneration occurring in tauopathies, including AD, and sustain the in vivo NH-2 tau cleavage inhibitors as an alternative drug discovery strategies for AD therapy.
Vascular endothelial growth factor (VEGF) and its receptors (1999)

Vascular endothelial growth factor (VEGF) is a highly specific mitogen for vascular endothelial cells. Five VEGF isoforms are generated as a result of alternative splicing from a single VEGF gene. These isoforms differ in their molecular mass and in biological properties such as their ability to bind to cell-surface heparan-sulfate proteoglycans. The expression of VEGF is potentiated in response to hypoxia, by activated oncogenes, and by a variety of cytokines. VEGF induces endothelial cell proliferation, promotes cell migration, and inhibits apoptosis. In vivo VEGF induces angiogenesis as well as permeabilization of blood vessels, and plays a central role in the regulation of vasculogenesis. Deregulated VEGF expression contributes to the development of solid tumors by promoting tumor angiogenesis and to the etiology of several additional diseases that are characterized by abnormal angiogenesis. Consequently, inhibition of VEGF signaling abrogates the development of a wide variety of tumors. The various VEGF forms bind to two tyrosine-kinase receptors, VEGFR-1 (flt-1) and VEGFR-2 (KDR/flk-1), which are expressed almost exclusively in endothelial cells. Endothelial cells express in addition the neuropilin-1 and neuropilin-2 coreceptors, which bind selectively to the 165 amino acid form of VEGF (VEGF165). This review focuses on recent developments that have widened considerably our understanding of the mechanisms that control VEGF production and VEGF signal transduction and on recent studies that have shed light on the mechanisms by which VEGF regulates angiogenesis.
Clinical performance of human papillomavirus E6, E7 mRNA flow cytometric assay compared to human papillomavirus DNA typing. (2011)

The HPV assay provides an early predictor of persistent HPV infection and may improve cervical cancer screening by increasing the specificity of detecting high-grade lesions.
Bronchiolitis-Associated Hospitalizations Among US Children, 1980-1996 (1999)

During 1980-1996, rates of hospitalization of infants with bronchiolitis increased substantially, as did the proportion of total and lower respiratory tract hospitalizations associated with bronchiolitis. Annual bronchiolitis hospitalizations associated with RSV infection among infants may be greater than previous estimates for RSV bronchiolitis and pneumonia hospitalizations combined.
Helicobacter pylori Infection and the Risk of Gastric Carcinoma (1991)

Infection with H. pylori is associated with an increased risk of gastric adenocarcinoma and may be a cofactor in the pathogenesis of this malignant condition.
Biology of human respiratory syncytial virus: a review (2010)

Acute lower respiratory tract infection is one of the major causes of mortality and morbidity in young children worldwide. Respiratory syncytial virus (RSV) is the single most important viral cause of lower respiratory tract infection during infancy and early childhood worldwide. Respiratory syncytial virus belongs to the Pneumovirinae subfamily of the Paramyxoviridae family of enveloped single stranded negative sense RNA viruses. The virus accounts for approximately 50% of all pneumonia and up to 90% of the reported cases of bronchiolitis in infancy. It is a common community–acquired respiratory pathogen without ethnic, socioeconomic, gender, age or geographic boundaries. Moreover, the epidemiological and ecological relationships between Human Respiratory syncytial virus, man and environment have aroused increasing interest in this viral, specie. The present review looks at the nature of this virus with the view to provide more information about its biology which may be useful to the present and future researchers.