gebhart/patrepeval huggingface dataset:
Field Ionization of Cold Atoms near the Wall of a Single Carbon Nanotube (2010)

We observe the capture and field ionization of individual atoms near the side wall of a single suspended nanotube. Extremely large cross sections for ionization from an atomic beam are observed at modest voltages due to the nanotube's small radius and extended length. The effects of the field strength on both the atomic capture and the ionization process are clearly distinguished in the data, as are prompt and delayed ionizations related to the locations at which they occur. Efficient and sensitive neutral atom detectors can be based on the nanotube capture and wall ionization processes.
The pleiotropic functions of the Y‐box‐binding protein, YB‐1 (2003)

The Y-box-binding protein (YB-1) represents the most evolutionary conserved nucleic-acid-binding protein currently known. YB-1 is a member of the cold-shock domain (CSD) protein superfamily. It performs a wide variety of cellular functions, including transcriptional regulation, translational regulation, DNA repair, drug resistance and stress responses to extracellular signals. As a result, YB-1 expression is closely associated with cell proliferation. In this review, we will begin by briefly describing the characteristics of YB-1 and will then summarize the pleiotropic functions brought about via DNA-RNA transaction and protein-protein interactions. In addition, we will discuss the diverse range of potential physiological and pathological functions of YB-1.
Activation of MyD88-dependent TLR1/2 signaling by misfolded α-synuclein, a protein linked to neurodegenerative disorders (2015)

Synucleinopathies, such as Parkinson's disease and diffuse Lewy body disease, are progressive neurodegenerative disorders characterized by selective neuronal death, abnormal accumulation of misfolded α-synuclein, and sustained microglial activation. In addition to inducing neuronal toxicity, higher-ordered oligomeric α-synuclein causes proinflammatory responses in the brain parenchyma by triggering microglial activation, which may exacerbate pathogenic processes by establishing a chronic neuroinflammatory milieu. We found that higher-ordered oligomeric α-synuclein induced a proinflammatory microglial phenotype by directly engaging the heterodimer TLR1/2 (Toll-like receptor 1 and 2) at the cell membrane, leading to the nuclear translocation of NF-κB (nuclear factor κB) and the increased production of the proinflammatory cytokines TNF-α (tumor necrosis factor-α) and IL-1β (interleukin-1β) in a MyD88-dependent manner. Blocking signaling through the TLR1/2 heterodimer with the small-molecule inhibitor CU-CPT22 reduced the nuclear translocation of NF-κB and secretion of TNF-α from cultured primary mouse microglia. Candesartan cilexetil, a drug approved for treating hypertension and that inhibits the expression of TLR2, reversed the activated proinflammatory phenotype of primary microglia exposed to oligomeric α-synuclein, supporting the possibility of repurposing this drug for synucleinopathies.
Solution Structure of Human Survivin and Its Binding Interface with Smac/Diablo (2004)

NMR studies of the antiapoptotic protein survivin have been used to determine the homodimer interface of the protein in solution and to identify residues of the protein that interact with Smac/Diablo. In solution, survivin(1-120) forms a bow-tie-shaped dimer whose interface is composed of its N-terminal residues as well as residues connecting its BIR domain to the C-terminal alpha helix. The solution structure resolves the controversy regarding the two possible dimer interfaces for survivin observed in X-ray crystal structures. The structural basis for the interaction between survivin and Smac/Diablo was also investigated. When Smac/Diablo or N-terminal Smac/Diablo peptide analogues are added to a solution of survivin, specific residues near alpha4 and beta3 are perturbed. NMR experiments indicate that the peptides bind across the third beta-strand of survivin in a manner similar to the way Smac/Diablo peptides bind to the BIR3 domain of X-linked IAP (XIAP).
Immediate Motor Effects of Stimulation through Electrodes Implanted in the Human Globus Pallidus (1998)

The immediate motor effects of stimulation through electrodes chronically implanted in the globus pallidus internus (GPI) were studied in 9 subjects with Parkinson's disease. Single stimuli (at >>0.4 Hz) produced short latency facilitation of voluntarily activated contralateral muscles in all subjects. The latency and distribution of the facilitation, its probably monosynaptic nature, and the short chronaxie and refractory period of the activated neural elements suggest that the facilitation results from the direct excitation of the fast conducting corticospinal pathway. The facilitation of motoneurons followed high frequency (e.g. 200 Hz) stimulation without decrement and occurred at stimulus intensities well below those required to produce a visible muscle contraction. We conclude that, while there may be other effects, GPI stimulation through electrodes may activate the corticospinal tract, even when the stimuli are below the threshold for a visible muscle contraction, and that continuous stimulation may do so continuously. This may be an unwanted side effect, but possible therapeutic actions are considered. The reproducible short latency facilitation enabled us to estimate current spread from the quadripolar electrodes used for deep brain stimulation. When the current is sufficient to excite large myelinated fibers near one of the quadripolar electrodes, an additional 1-mA current will activate similar fibers at an additional distance of 1.8 mm with bipolar stimulation and at a distance of 5.7 mm with monopolar stimulation.
Environment affects amino acid preference for secondary structure. (1992)

Three equivocal amino acid sequences were synthesized that are predicted to be alpha-helical from amino acid preference but are found to be primarily beta-strand from x-ray diffraction of their respective proteins. In some solvent systems we recover the alpha-helical structure predicted by amino acid preference, whereas in other systems we mimic the interior of the protein and produce a beta-strand. These results are experimental proof that the environment is important in determining the secondary structure formed by an amino acid sequence; therefore schemes that predict secondary structure from amino acid sequence alone can never be totally successful.
The Next Oil Crisis Looms Large--and Perhaps Close (1998)

Many economists foresee another half-century of cheap oil, but a growing contingent of geologists warns that oil will begin to run out much sooner--perhaps in only 10 years. The optimists are mainly those who put their faith in new technology for finding and extracting oil and expect that production will meet rise in demand until about 50 years from now--plenty of time for the development of alternatives. But the pessimists say that even taking into account the best efforts of the explorationists and the discovery of new fields in frontier areas like the Caspian Sea (see sidebar on
 p. 1130), sometime between 2010 and 2020 the gush of oil from wells around the world will peak at 80 million barrels per day, then begin a steady, inevitable decline.
The working population (1997)

The fourth book in a four-volume series that explores what the 1991 census can tell us about ethnicity in Britain. The particular focus of this volume is the relative situation of minority ethnic groups in respect of education, employment and housing.
Bioabsorbable Fixation Devices (1997)

With time, more and more types of medical devices become available to assist the surgeon in managing patients. Bioabsorbable fixation devices, which have been directed toward the orthopedic surgeon over the past 10 years, are but one example. One aim of this article is to present the current status of bioabsorbable devices in medical practice to the craniomaxillofacial surgeon who may not be aware of the inroads this technology has made. A bioabsorbable fixation system has become available for use by the craniomaxillofacial surgeon, which is described. A further aim of this article is to present concisely the testing rigor required of such devices before their introduction to the U.S. market. This has the added benefit of explaining the important role of the surgeon in developing and helping reduce to standard clinical practice the use of new technologies.
An architecture for a configurable mixed-signal device (2003)

The mixed-signal programmable system-on-chip (PSOC) architecture for high-volume low-cost applications is presented. Programmable analog, digital, and clocking circuits are combined with flash memory and a microcontroller to provide a platform for single-chip solutions for low-cost consumer applications. Both programmable analog and digital circuits are designed to support a moderate level of abstraction, balancing flexibility against cost and performance. A rough comparison of alternative approaches based on functionality and cost is presented.
Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds (2002)

Formation of the sugar-amino acid linkage is a crucial event in the biosynthesis of the carbohydrate units of glycoproteins. It sets into motion a complex series of posttranslational enzymatic steps that lead to the formation of a host of protein-bound oligosaccharides with diverse biological functions. These reactions occur throughout the entire phylogenetic spectrum, ranging from archaea and eubacteria to eukaryotes. It is the aim of this review to describe the glycopeptide linkages that have been found to date and specify their presence on well-characterized glycoproteins. A survey is also made of the enzymes involved in the formation of the various glycopeptide bonds as well as the site of their intracellular action and their affinity for particular peptide domains is evaluated. This examination indicates that 13 different monosaccharides and 8 amino acids are involved in glycoprotein linkages leading to a total of at least 41 bonds, if the anomeric configurations, the phosphoglycosyl linkages, as well as the GPI (glycophosphatidylinositol) phosphoethanolamine bridge are also considered. These bonds represent the products of N- and O-glycosylation, C-mannosylation, phosphoglycation, and glypiation. Currently at least 16 enzymes involved in their formation have been identified and in many cases cloned. Their intracellular site of action varies and includes the endoplasmic reticulum, Golgi apparatus, cytosol, and nucleus. With the exception of the Asn-linked carbohydrate and the GPI anchor, which are transferred to the polypeptide en bloc, the sugar-amino acid linkages are formed by the enzymatic transfer of an activated monosaccharide directly to the protein. This review also deals briefly with glycosidases, which are involved in physiologically important cleavages of glycopeptide bonds in higher organisms, and with a number of human disease states in which defects in enzymatic transfer of saccharides to protein have been implicated.
Confinement And Control Of Oil Pollution On Water With Monomolecular Surface Films (1969)

Abstract Under favorable conditions monomolecular surface films can be used to guide, confine and condense petroleum spills on water. Composed of water-insoluable, non-toxic organic material, these films spread rapidly and spontaneously into a one-molecule-thick layer. Consequently, small quantities of piston-film material will clear thin oil layers from large areas of a water surface. The effects of wind, the chemical character of the pollution and its thickness upon the usefulness of the piston film will be discussed. In addition to clearing water surfaces of oil, one of the most useful applications may be the ability of the surface film to confine and condense a small oil spill into layers as thick as one centimeter. Since the petroleum is thickened and compressed into a much reduced surface area, the efficiency of oil retrieval techniques would be enhanced.
Pathogenesis, Immunology, and Diagnosis of LatentMycobacterium tuberculosisInfection (2010)

Phagocytosis of tubercle bacilli by antigen-presenting cells in human lung alveoli initiates a complex infection process by Mycobacterium tuberculosis and a potentially protective immune response by the host. M. tuberculosis has devoted a large part of its genome towards functions that allow it to successfully establish latent or progressive infection in the majority of infected individuals. The failure of immune-mediated clearance is due to multiple strategies adopted by M. tuberculosis that blunt the microbicidal mechanisms of infected immune cells and formation of distinct granulomatous lesions that differ in their ability to support or suppress the persistence of viable M. tuberculosis. In this paper, current understanding of various immune processes that lead to the establishment of latent M. tuberculosis infection, bacterial spreading, persistence, reactivation, and waning or elimination of latent infection as well as new diagnostic approaches being used for identification of latently infected individuals for possible control of tuberculosis epidemic are described.
A New Potent Secondary Amphipathic Cell–penetrating Peptide for siRNA Delivery Into Mammalian Cells (2008)

RNA interference constitutes a powerful tool for biological studies, but has also become one of the most challenging therapeutic strategies. However, small interfering RNA (siRNA)-based strategies suffer from their poor delivery and biodistribution. Cell-penetrating peptides (CPPs) have been shown to improve the intracellular delivery of various biologically active molecules into living cells and have more recently been applied to siRNA delivery. To improve cellular uptake of siRNA into challenging cell lines, we have designed a secondary amphipathic peptide (CADY) of 20 residues combining aromatic tryptophan and cationic arginine residues. CADY adopts a helical conformation within cell membranes, thereby exposing charged residues on one side, and Trp groups that favor cellular uptake on the other. We show that CADY forms stable complexes with siRNA, thereby increasing their stability and improving their delivery into a wide variety of cell lines, including suspension and primary cell lines. CADY-mediated delivery of subnanomolar concentrations of siRNA leads to significant knockdown of the target gene at both the mRNA and protein levels. Moreover, we demonstrate that CADY is not toxic and enters cells through a mechanism which is independent of the major endosomal pathway. Given its biological properties, we propose that CADY-based technology will have a significant effect on the development of fundamental and therapeutic siRNA-based applications.
Glycan Array on Aluminum Oxide-Coated Glass Slides through Phosphonate Chemistry (2010)

A new type of glycan array covalently or noncovalently attached to aluminum oxide-coated glass (ACG) slides has been developed for studies of enzymatic reactions and protein binding. To prepare the noncovalent array, glycans with a polyfluorinated hydrocarbon (-C(8)F(17)) tail are spotted robotically onto the ACG slide surface containing a layer of polyfluorinated hydrocarbon terminated with phosphonate. After incubation and washing, the noncovalent array can be characterized by MS-TOF via ionization/desorption at a low laser energy without addition of matrix. A representative cellotetraose array was developed to study the activity and specificity of different cellulases and to differentiate the exo- and endoglucanase activities. To prepare the covalent array, glycans with a phosphonic acid tail were synthesized and spotted robotically onto the ACG slide surface. After incubation, the slides can be used directly for quantitative protein binding analysis. Compared to the preparation of glycan arrays on glass slides and other surfaces, this method of arraying using phosphonic acid reacting with ACG is more direct, convenient, and effective and represents a new platform for the high-throughput analysis of protein-glycan interactions.
Pathogenicity Island 2 Mutants ofSalmonella typhimuriumAre Efficient Carriers for Heterologous Antigens and Enable Modulation of Immune Responses (1999)

ABSTRACT The potential use as vaccine delivery system of Salmonella typhimurium strains harboring defined mutations in the sseC (HH104) and sseD (MvP101) genes, which encode putative effector proteins of the type III secretion system of Salmonella pathogenicity island 2, was evaluated and compared with that of the well-characterized aroA mutant strain SL7207 by using β-galactosidase (β-Gal) as a model antigen. When orally administered to immune-competent or gamma interferon-deficient (IFN-γ −/− ) BALB/c mice, both mutants were found to be highly attenuated (50% lethal dose, &gt;10 9 bacteria). Both strains were also able to efficiently colonize and persist in Peyer’s patches. Immunization with HH104 and MvP101 triggered β-Gal-specific serum and mucosal antibody responses equivalent to or stronger than those observed in SL7207-immunized mice. Although immunoglobulin G2 (IgG2) serum antibodies were dominant in all groups, IgG1 was also significantly increased in mice vaccinated with MvP101 and SL7207. Comparable β-Gal-specific IgA and IgG antibodies were detected in intestinal lavages from mice immunized with the different strains. Antigen-specific CD4 + T-helper cells were generated after vaccination with all vaccine prototypes; however, responses were significantly more efficient when HH104 and MvP101 were used ( P &lt; 0.05). Significantly higher levels of IFN-γ were produced by restimulated spleen cells from mice immunized with HH104 than from those vaccinated with the MvP101 or SL7207 derivatives ( P ≤ 0.05). Interestingly, the three strains induced major histocompatibility complex class I-restricted CD8 + cytotoxic T cells against β-Gal; however, cytotoxic T-lymphocyte responses were significantly stronger after immunization with HH104 ( P &lt; 0.05). These novel S. typhimurium attenuated strains constitute promising delivery systems for vaccine antigens. The qualitative differences observed in the obtained responses with different carriers may be useful for those applications in which a targeted immunomodulation is required.
Obesity: a prognostic factor of severity in acute pancreatitis. (1999)

This study was conducted to assess the prognostic value of obesity in acute pancreatitis and to determine the role played by obesity-associated diseases in the course of the disease. We prospectively studied 49 patients with acute pancreatitis who were divided into three groups according to their body mass index (BMI). There were 22 patients in group I (BMI < or = 25 kg/m2, normal or low weight); 15 in group II (BMI >25 and < or = 29 kg/m2, overweight); and 12 in group III (BMI >29 kg/m2, obese). Other anthropometric parameters also were measured. The severity of pancreatitis was assessed according to the Atlanta classification system. Systemic complications were significantly more common among obese than nonobese patients (p < 0.05). Patients with severe pancreatitis had a higher body-fat percentage, measured by the subscapular skin-fold thickness, and a larger abdominal circumference than patients with mild pancreatitis. Although hypertensive or diabetic patients developed more systemic complications, the multivariate analysis demonstrated that the presence of these underlying diseases did not modify the prognostic role of obesity in acute pancreatitis. We conclude that obesity is a prognostic factor of outcome in acute pancreatitis. Obesity-associated diseases do not vary the prognostic value of obesity. It seems that truncal adiposity is the kind of obesity related to worse outcome of acute pancreatitis.
Kinetic studies of superoxide dismutases: properties of the manganese-containing protein from Thermus thermophilus (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetic studies of superoxide dismutases: properties of the manganese-containing protein from Thermus thermophilusChristopher Bull, Eric C. Niederhoffer, Tatsuro Yoshida, and James A. FeeCite this: J. Am. Chem. Soc. 1991, 113, 11, 4069–4076Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/ja00011a003https://doi.org/10.1021/ja00011a003research-articleACS PublicationsRequest reuse permissionsArticle Views714Altmetric-Citations140LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Object-oriented conceptual modeling of video data (2002)

We propose a graphical data model for specifying spatio-temporal semantics of video data. The proposed model segments a video clip into subsegments consisting of objects. Each object is detected and recognized, and the relevant information of each object is recorded. The motions of objects are modeled through their relative spatial relationships as time evolves. Based on the semantics provided by this model, a user can create his/her own, object-oriented view of the video database. Using the propositional logic, we describe a methodology for specifying conceptual queries involving spatio-temporal semantics and expressing views for retrieving various video clips. Alternatively, a user can sketch the query, by exemplifying the concept. The proposed methodology can be used to specify spatio-temporal concepts at various levels of information granularity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Natural Language Processing (1996)

Work in computational linguistics began very soon after the development of the first computers (Booth, Brandwood and Cleave 1958), yet in the intervening four decades there has been a pervasive feeling that progress in computer understanding of natural language has not been commensurate with progress in other computer applications. Recently, a number of prominent researchers in natural language processing met to assess the state of the discipline and discuss future directions (Bates and Weischedel 1993). The consensus of this meeting was that increased attention to large amounts of lexical and domain knowledge was essential for significant progress, and current research efforts in the field reflect this point of view.
Interleukin 15: biology and relevance to human disease (2001)

Since the cloning of interleukin (IL)-15 six years ago, there have been numerous studies examining the molecular and cellular biology of this cytokine. IL-15 and IL-2 have similar biologic properties in vitro, consistent with their shared receptor (R) signaling components (IL-2/15Rβγc). However,