gebhart/patrepeval huggingface dataset:
A novel von Willebrand factor binding protein expressed by Staphylococcus aureus a aThe GenBank accession number for the sequence reported in this paper is AY032850. (2002)

When a shotgun phage-display library of Staphylococcus aureus Newman was affinity selected (panned) against recombinant von Willebrand factor (vWf), a novel von Willebrand factor binding protein (vWbp) was found. Experimental data indicate that the interaction between vWbp and vWf is very specific and mediated by a region of 26 aa residues in the C-terminal part of vWbp. vWbp has an N-terminal secretory signal sequence but no cell wall anchoring motif, suggesting a soluble extracellular location. Mature vWbp could be purified from the culture supernatant and the identity of the protein was confirmed by N-terminal sequencing. vWbp migrates with an apparent molecular mass of 66 kDa and the deduced protein consists of 482 aa. The gene encoding vWbp, named vwb, was present in all S. aureus strains investigated.
Prostaglandins, NSAIDs, and Gastric Mucosal Protection: Why Doesn't the Stomach Digest Itself? (2008)

Except in rare cases, the stomach can withstand exposure to highly concentrated hydrochloric acid, refluxed bile salts, alcohol, and foodstuffs with a wide range of temperatures and osmolarity. This is attributed to a number of physiological responses by the mucosal lining to potentially harmful luminal agents, and to an ability to rapidly repair damage when it does occur. Since the discovery in 1971 that prostaglandin synthesis could be blocked by aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs), there has been great interest in the contribution of prostaglandins to gastric mucosal defense. Prostaglandins modulate virtually every aspect of mucosal defense, and the importance of this contribution is evident by the increased susceptibility of the stomach to injury following ingestion of an NSAID. With chronic ingestion of these drugs, the development of ulcers in the stomach is a significant clinical concern. Research over the past two decades has helped to identify some of the key events triggered by NSAIDs that contribute to ulcer formation and/or impair ulcer healing. Recent research has also highlighted the fact that the protective functions of prostaglandins in the stomach can be carried out by other mediators, in particular the gaseous mediators nitric oxide and hydrogen sulfide. Better understanding of the mechanisms through which the stomach is able to resist injury in the presence of luminal irritants is helping to drive the development of safer anti-inflammatory drugs, and therapies to accelerate and improve the quality of ulcer healing.
Biophysical and biochemical characterization of five animal viruses with bisegmented double-stranded RNA genomes (1979)

Infectious pancreatic necrosis virus of fish, infectious bursal disease virus of chickens, Tellina virus and oyster virus of bivalve molluscs, and drosophila X virus of Drosophila melanogaster are naked icosahedral viruses with an electron microscopic diameter of 58 to 60 nm. The genome of each of these viruses consists of two segments of double-stranded RNA (molecular weight range between 2.6 x 10(6) and 2.2 x 10(6), and the virion, capsid proteins fall into three size class categories (large, medium, and small; ranging from 100,000 to 27,000) as determined by polyacrylamide slab gel electrophoresis. The hydrodynamic properties of the five viruses are similar as determined by analytical ultracentrifugation and laser quasi-elastic, light-scattering spectroscopy. The calculated particle weights range between 55 x 10(6) and 81 x 10(6). Tryptic peptide comparisons of 125I-labeled virion proteins showed that five viruses are different from each other, although there was considerable overlap in the peptide maps of the three aquatic viruses, indicting a degree of relatedness. Cross-neutralization tests indicated that drosophila X, infectious pancreatic necrosis, and infectious bursal disease viruses were different from each other and from oyster and Tellina viruses. The same test showed oyster and Tellina viruses to be related. The biochemical and biophysical properties of the five viruses cannt be included in the family Reoviridae or in any of the present virus genera.
SnoopLigase peptide-peptide conjugation enables modular vaccine assembly (2019)

For many infectious diseases there is still no vaccine, even though potential protective antigens have been identified. Suitable platforms and conjugation routes are urgently needed to convert the promise of such antigens into broadly protective and scalable vaccines. Here we apply a newly established peptide-peptide ligation approach, SnoopLigase, for specific and irreversible coupling of antigens onto an oligomerization platform. SnoopLigase was engineered from a Streptococcus pneumoniae adhesin and enables isopeptide bond formation between two peptide tags: DogTag and SnoopTagJr. We expressed in bacteria DogTag linked to the self-assembling coiled-coil nanoparticle IMX313. This platform was stable over months at 37 °C when lyophilized, remaining reactive even after boiling. IMX-DogTag was efficiently coupled to two blood-stage malarial proteins (from PfEMP1 or CyRPA), with SnoopTagJr fused at the N- or C-terminus. We also showed SnoopLigase-mediated coupling of a telomerase peptide relevant to cancer immunotherapy. SnoopLigase-mediated nanoassembly enhanced the antibody response to both malaria antigens in a prime-boost model. Including or depleting SnoopLigase from the conjugate had little effect on the antibody response to the malarial antigens. SnoopLigase decoration represents a promising and accessible strategy for modular plug-and-display vaccine assembly, as well as providing opportunities for robust nanoconstruction in synthetic biology.
Gene‐based SNP genetic association study of the corticotropin‐releasing hormone receptor‐2 (CRHR2) in major depression (2002)

An increasing amount of data suggests that affective disorders are related to dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis, the stress-response system. Corticotropin-releasing hormone receptor-2 (CRHR2)-deficient mice display a stress-sensitive and anxiety-like phenotype suggesting that the CRHR2 is a plausible functional candidate gene influencing the reactivity of the HPA axis and therefore the liability to develop affective disorders. In this study, a gene-based single nucleotide polymorphism (SNP) map of the corticotropin-releasing hormone receptor 2 (CRHR2) was constructed containing one synonymous cSNP in exon 10, two intronic SNPs, and two SNPs in the 5' upstream regulatory region. No significant difference in allele or genotype frequency was found for four out of the five SNPs between Belgian unipolar (UP) patients and age-, gender-, and ethnicity-matched controls. The cSNP did show allelic and genotypic association with borderline significance (P=0.04). However, a replication study of this cSNP in a bipolar sample of Belgian origin and a Swedish UP sample did not show significant differences in allele and genotype frequencies.
Type-preserving compilation for large-scale optimizing object-oriented compilers (2008)

Type-preserving compilers translate well-typed source code, such as Java or C#, into verifiable target code, such as typed assembly language or proof-carrying code. This paper presents the implementation of type-preserving compilation in a complex, large-scale optimizing compiler. Compared to prior work, this implementation supports extensive optimizations, and it verifies a large portion of the interface between the compiler and the runtime system. This paper demonstrates the practicality of type-preserving compilation in complex optimizing compilers: the generated typed assembly language is only 2.3% slower than the base compiler's generated untyped assembly language, and the type-preserving compiler is 82.8% slower than the base compiler.
Alteration of argyrophilic nucleolar organizer region associated (Ag‐NOR) proteins in apoptosis‐induced human salivary gland cells and human oral squamous carcinoma cells (2001)

The level of argyrophilic nucleolar organizer regions (AgNORs) and AgNOR-associated proteins (Ag-NOR proteins) varies with cell activity, including ribosomal biogenesis occurring in proliferating cells. Proteins associated with some AgNORs are detected by a specific silver staining. To investigate a possible relationship between apoptosis and the AgNORs or Ag-NOR proteins, we examined the changes of AgNORs and Ag-NOR proteins during apoptosis in a human salivary gland cell line, HSG cells, and a human oral squamous carcinoma cell line, SCC-25 cells. Apoptosis was induced by treatment of HSG and SCC-25 cells with okadaic acid. Proteins prepared from HSG and SCC-25 cells treated with varying concentrations of okadaic acid (OA) were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by transferring to transfer membranes and staining for Ag-NOR proteins by modified Western blot analysis. Four major bands (110 kDa, 43 kDa, 39kDa, and 37 kDa) were detected in the proteins obtained from the control cells. The level of the 110-kDa protein decreased in the proteins prepared from OA-induced apoptotic cells; however, the reaction intensity of the other three bands was changed in apoptotic cells. An additional band of an 80-kDa Ag-NOR protein appeared and increased in the apoptotic cells. Cellular fractionation of HSG cells and SCC-25 cells was done with or without apoptotic induction. An 80-kDa Ag-NOR protein was detected in the nuclear fraction prepared from the apoptotic cells, while the 110-kDa protein decreased in the nuclear fraction of these cells. The 110-kDa Ag-NOR protein may be nucleolin (C23) as deduced from its AgNOR staining features, including molecular weight. The 80-kDa protein may be the cleavage product of the 110-kDa protein. In the cell-free apoptotic system, in which intact nuclei of HSG cells were incubated with the cytosol fraction of apoptotic HSG and SCC-25 cells, the 80-kDa Ag-NOR protein was detected in nuclei incubated with the cytosol fraction of apoptotic cells, while the level of the 110-kDa protein decreased. The changes of Ag-NOR proteins in nuclei prepared from SCC-25 cells incubated with cytosol fractions prepared from HSG and SCC-25 cells were identical to those of the HSG cells. The alternation of AgNORs in apoptosis-induced HSG cells was also examined using double staining with Hoechst 33342 and silver nitrate. Hoechst staining revealed typical apoptotic nuclei, which exhibited highly fluorescent condensed chromatin in OA-treated HSG cells. Silver grains representing AgNORs were not detected in the cells undergoing apoptosis. The dual-imposition view confirmed that AgNORs, which are visible as dots in nucleoli in the control cells, disappeared from the apoptotic nuclei of HSG cells. Our results indicate that the 110-kDa nucleolar Ag-NOR protein is associated with apoptosis and is cleaved during apoptosis.
Clinical Applications of PCR (2006)

In this updated second edition, leading researchers apply molecular diagnostics to the many recent advances that have occurred in polymerase chain reaction( PCR)-based technologies. Highlights include
The Plenoptic Function and the Elements of Early Vision (1991)

What are the elements of early vision? This question might be taken to mean, What are the fundamental atoms of vision?—and might be variously answered in terms ofsuch candidate structures as edges, peaks, corners, and so on. In this chapter we adopt a rather different point of view and ask the question, What are the fundamentalsubstances of vision? This distinction is important becausewe wish to focus on the first steps in extraction of visualinformation. At this level it is premature to talk aboutdiscrete objects, even such simple ones as edges and corners.There is general agreement that early vision involvesmeasurements of a number of basic image properties in-cluding orientation, color, motion, and so on. Figure l.lshows a caricature (in the style of Neisser, 1976), of the sort of architecture that has become quite popular as a model for both human and machine vision. The first stageof processing involves a set of parallel pathways, eachdevoted to one particular-visual property. We propose that the measurements of these basic properties be con-sidered as the elements of early vision. We think of earlyvision as measuring the amounts of various kinds of vi-sual substances present in the image (e.g., redness orrightward motion energy). In other words, we are inter- ested in how early vision measures “stuff” rather than in how it labels “things.”What, then, are these elementary visual substances?Various lists have been compiled using a mixture of intui-tion and experiment. Electrophysiologists have describedneurons in striate cortex that are selectively sensitive tocertain visual properties; for reviews, see Hubel (1988) and DeValois and DeValois (1988). Psychophysicists haveinferred the existence of channels that are tuned for cer- tain visual properties; for reviews, see Graham (1989), Olzak and Thomas (1986), Pokorny and Smith (1986), and Watson (1986). Researchers in perception have foundaspects of visual stimuli that are processed pre-attentive- ly (Beck, 1966; Bergen & Julesz, 1983; Julesz & Bergen,
IGNORING ECONOMICS IN DEALING WITH THE SAVINGS AND LOAN AND COMMERCIAL BANKING CRISIS (1991)

This paper describes how the government has largely ignored economics in its recent attempts to deal with the deterioration of federally insured depository institutions. The most recent example was the Financial Institutions Recovery, Reform, and Enforcement Act (FIRREA) of 1989. Well documented and widely distributed studies have pointed out the decline of commercial banks. However, the FIRREA completely ignored commercial banks. The paper discusses the pervasive regulatory laxity and forbearance that existed toward banks during the 1980s despite the consequences of similar regulatory behavior toward savings and loans. The paper also shows how the FIRREA's major provisions regarding savings and loans ignore economic analyses. The paper discusses the implications of economic analysis for more appropriate government responses to the continuing deterioration of depositories.
Biochemistry, Cellular and Molecular Biology, and Physiological Roles of the Iodothyronine Selenodeiodinases (2002)

The goal of this review is to place the exciting advances that have occurred in our understanding of the molecular biology of the types 1, 2, and 3 (D1, D2, and D3, respectively) iodothyronine deiodinases into a biochemical and physiological context. We review new data regarding the mechanism of selenoprotein synthesis, the molecular and cellular biological properties of the individual deiodinases, including gene structure, mRNA and protein characteristics, tissue distribution, subcellular localization and topology, enzymatic properties, structure-activity relationships, and regulation of synthesis, inactivation, and degradation. These provide the background for a discussion of their role in thyroid physiology in humans and other vertebrates, including evidence that D2 plays a significant role in human plasma T(3) production. We discuss the pathological role of D3 overexpression causing "consumptive hypothyroidism" as well as our current understanding of the pathophysiology of iodothyronine deiodination during illness and amiodarone therapy. Finally, we review the new insights from analysis of mice with targeted disruption of the Dio2 gene and overexpression of D2 in the myocardium.
Irinotecan Delivery by Lipid-Coated Mesoporous Silica Nanoparticles Shows Improved Efficacy and Safety over Liposomes for Pancreatic Cancer (2016)

Urgent intervention is required to improve the 5 year survival rate of pancreatic ductal adenocarcinoma (PDAC). While the four-drug regimen, FOLFIRINOX (comprising irinotecan, 5-fluorouracil, oxaliplatin, and leucovorin), has a better survival outcome than the more frequently used gemcitabine, the former treatment platform is highly toxic and restricted for use in patients with good performance status. Since irinotecan contributes significantly to FOLFIRINOX toxicity (bone marrow and gastrointestinal tract), our aim was to reduce the toxicity of this drug by a custom-designed mesoporous silica nanoparticle (MSNP) platform, which uses a proton gradient for high-dose irinotecan loading across a coated lipid bilayer (LB). The improved stability of the LB-coated MSNP (LB-MSNP) carrier allowed less drug leakage systemically with increased drug concentrations at the tumor sites of an orthotopic Kras-derived PDAC model compared to liposomes. The LB-MSNP nanocarrier was also more efficient for treating tumor metastases. Equally important, the reduced leakage and slower rate of drug release by the LB-MSNP carrier dramatically reduced the rate of bone marrow, gastrointestinal, and liver toxicity compared to the liposomal carrier. We propose that the combination of high efficacy and reduced toxicity by the LB-MSNP carrier could facilitate the use of irinotecan as a first-line therapeutic to improve PDAC survival.
Combined Selective Mapping and Binary Cyclic Codes for PAPR Reduction in OFDM Systems (2007)

In this paper, we consider reduction of PAPR in OFDM systems with BPSK subcarriers by combining SLM and binary cyclic codes. This combining strategy can be used for both error correction and PAPR reduction. We decompose a binary cyclic code into direct sum of two cyclic subcodes: the correction subcode used for error correction and the scrambling subcode for PAPR reduction. The transmitted OFDM signal is selected that achieves minimum PAPR, from the set of binary cyclic codewords. The received signal can be easily decoded without the need of any side information. Simulations show that the proposed scheme with simplex code as scrambling subcode achieves good PAPR reduction.
Introduction to the special issue on word sense disambiguation: the state of the art (1998)

Compte tenu du progres effectue recemment dans le domaine de la desambiguisation du sens des mots, les As. font ici le point sur l'etat de la recherche dans ce domaine depuis ces 50 dernieres annees et considerent les prochaines etapes a franchir. Dans un 1 e r temps, ils passent en revue les principales approches de la desambiguisation du sens des mots : des premieres tentatives effectuees dans le cadre de la traduction automatique aux methodes actuelles basees sur les corpus, en passant par les methodes basees sur l'intelligence artificielle et les methodes utilisant des bases de connaissance. Dans un 2 n d temps, ils examinent les problemes laisses en suspens (le role du contexte, la division des sens, l'evaluation des resultats) et proposent quelques orientations pour la recherche future
External validation of IMP3 expression as an independent prognostic marker for metastatic progression and death for patients with clear cell renal cell carcinoma (2008)

Using a large and independent cohort of ccRCC patients, the authors confirmed that tumor cell IMP3 expression represents an independent predictor of aggressive ccRCC tumor behavior.
Membrane binding and conformational properties of peptides representing the NH2 terminus of influenza HA-2. (1987)

Synthetic peptides representing amino acid residues 1-16 and 1-20, a proposed fusogenic region of the HA-2 subunit of influenza virus hemagglutinin, bind to phosphatidylcholine vesicles with submicromolar dissociation constants. The 1-20, but not the 1-16, peptide appears to adopt a helical conformation when bound to vesicles and cooperatively promotes vesicle fusion.
An In Vitro Model of Human Red Blood Cell Production From Hematopoietic Progenitor Cells (1998)

Hemoglobinopathies, such as beta-thalassemias and sickle cell anemia (SCA), are among the most common inherited gene defects. Novel models of human erythropoiesis that result in terminally differentiated red blood cells (RBCs) would be able to address the pathophysiological abnormalities in erythrocytes in congenital RBC disorders and to test the potential of reversing these problems by gene therapy. We have developed an in vitro model of production of human RBCs from normal CD34(+) hematopoietic progenitor cells, using recombinant growth factors to promote terminal RBC differentiation. Enucleated RBCs were then isolated to a pure population by flow cytometry in sufficient numbers for physiological studies. Morphologically, the RBCs derived in vitro ranged from early polylobulated forms, resembling normal reticulocytes to smooth biconcave discocytes. The hemoglobin pattern in the in vitro-derived RBCs mimicked the in vivo adult or postnatal pattern of beta-globin production, with negligible gamma-globin synthesis. To test the gene therapy potential using this model, CD34(+) cells were genetically marked with a retroviral vector carrying a cell-surface reporter. Gene transfer into CD34(+) cells followed by erythroid differentiation resulted in expression of the marker gene on the surface of the enucleated RBC progeny. This model of human erythropoiesis will allow studies on pathophysiology of congenital RBC disorders and test effective therapeutic strategies.
Concrete Crack Identification Using a UAV Incorporating Hybrid Image Processing (2017)

Crack assessment is an essential process in the maintenance of concrete structures. In general, concrete cracks are inspected by manual visual observation of the surface, which is intrinsically subjective as it depends on the experience of inspectors. Further, it is time-consuming, expensive, and often unsafe when inaccessible structural members are to be assessed. Unmanned aerial vehicle (UAV) technologies combined with digital image processing have recently been applied to crack assessment to overcome the drawbacks of manual visual inspection. However, identification of crack information in terms of width and length has not been fully explored in the UAV-based applications, because of the absence of distance measurement and tailored image processing. This paper presents a crack identification strategy that combines hybrid image processing with UAV technology. Equipped with a camera, an ultrasonic displacement sensor, and a WiFi module, the system provides the image of cracks and the associated working distance from a target structure on demand. The obtained information is subsequently processed by hybrid image binarization to estimate the crack width accurately while minimizing the loss of the crack length information. The proposed system has shown to successfully measure cracks thicker than 0.1 mm with the maximum length estimation error of 7.3%.
Simple proton spectroscopic imaging. (1984)

Simple modification of a spin echo imaging pulse sequence generates useful spectroscopic information at 0.35 T. New images are produced that show water only, fat only, and the difference between water and fat intensity. Imaging speed, spatial resolution, and signal-to-noise ratio are comparable with ordinary imaging. The method provides new parameters for tissue characterization and improved contrast between some organs.
Industrial applications of metal–organic frameworks (2009)

New materials are prerequisite for major breakthrough applications influencing our daily life, and therefore are pivotal for the chemical industry. Metal-organic frameworks (MOFs) constitute an emerging class of materials useful in gas storage, gas purification and separation applications as well as heterogeneous catalysis. They not only offer higher surface areas and the potential for enhanced activity than currently used materials like base metal oxides, but also provide shape/size selectivity which is important both for separations and catalysis. In this critical review an overview of the potential applications of MOFs in the chemical industry is presented. Furthermore, the synthesis and characterization of the materials are briefly discussed from the industrial perspective (88 references).