gebhart/patrepeval huggingface dataset:
The Dual-Specific Binding of Dengue Virus and Target Cells for the Antibody-Dependent Enhancement of Dengue Virus Infection (2006)

Using flow cytometric assay and monoclonal anti-dengue Ab, we observed that both anti-E and anti-prM Abs could enhance dengue virus infection in a concentration-dependent but serotype-independent manner. Increases were found in both the percentage of dengue-infected cells and the expression of dengue E and NS1 protein per cell. Dengue virion binding and infection were enhanced on FcR-bearing cells via the Fc-FcgammaRII pathway. Furthermore, anti-prM Ab also enhanced dengue virion binding and infection on cells lacking FcR, such as BHK-21 or A549 cells, by the mechanism of peptide (CPFLKQNEPEDIDCW)-specific binding. Anti-prM Ab cross-reacted with BHK-21 or A549 cells and recognized self-Ags such as heat shock protein 60. In summary, a novel mechanism of anti-prM Ab-mediated enhancement on dengue virus infection was found to be mediated by dual specific binding to dengue virion and to target cells, in addition to the traditional enhancement on FcR-bearing cells.
Anti-leukemic activity and tolerability of anti-human CD47 monoclonal antibodies (2017)

CD47, a broadly expressed cell surface protein, inhibits cell phagocytosis via interaction with phagocyte-expressed SIRPα. A variety of hematological malignancies demonstrate elevated CD47 expression, suggesting that CD47 may mediate immune escape. We discovered three unique CD47-SIRPα blocking anti-CD47 monoclonal antibodies (mAbs) with low nano-molar affinity to human and cynomolgus monkey CD47, and no hemagglutination and platelet aggregation activity. To characterize the anti-cancer activity elicited by blocking CD47, the mAbs were cloned into effector function silent and competent Fc backbones. Effector function competent mAbs demonstrated potent activity in vitro and in vivo, while effector function silent mAbs demonstrated minimal activity, indicating that blocking CD47 only leads to a therapeutic effect in the presence of Fc effector function. A non-human primate study revealed that the effector function competent mAb IgG1 C47B222-(CHO) decreased red blood cells (RBC), hematocrit and hemoglobin by >40% at 1 mg/kg, whereas the effector function silent mAb IgG2σ C47B222-(CHO) had minimal impact on RBC indices at 1 and 10 mg/kg. Taken together, our findings suggest that targeting CD47 is an attractive therapeutic anti-cancer approach. However, the anti-cancer activity observed with anti-CD47 mAbs is Fc effector dependent as are the side effects observed on RBC indices.
Conformations of isolated fragments of pancreatic polypeptide (1990)

In spite of its short polypeptide chain, the pancreatic polypeptide molecule consists of a polyproline II type helix and alpha-helix. To understand the stability and formation of the alpha-helical region, we prepared some peptide fragments including the helical segment of chicken pancreatic polypeptide and studied their conformations by circular dichroism (CD). PP7-36 (a peptide fragment corresponding to residues 7-36 of chicken pancreatic polypeptide) showed a CD spectrum characteristic of the helix at pH 4.6 and at peptide concentrations as low as 1 microM. PP11-36 was able to form a helical conformation only at high peptide concentrations and not at concentrations lower than 10 microM. However, acetyl PP11-36 (in which the alpha-amino group is acetylated so that no positive charge exists at the N terminus) was able to form the helical conformation at pH 4.6 and at the peptide concentrations where PP11-36 could not. Succinyl PP12-36 (in which the alpha-amino group is succinylated to introduce a negative charge) was also able to form the helical conformation. The CD spectra of PP12-36 and PP13-36 were not characteristic of the helical conformation at all the pH values and peptide concentrations studied. Acetyl PP13-36, which has no charge at the N terminus, did not form the helix. On the other hand, succinyl PP13-36, which has a negative charge at the N-terminal end, did form the helix at pH 4.6. These findings indicate that the presence of the negative charge of carboxylate at the N-terminal region of a peptide fragment is important for helix formation.(ABSTRACT TRUNCATED AT 250 WORDS)
Fibronectin in multiple sclerosis lesions. (1989)

Cryostat sections of central nervous system (CNS) tissues of patients with multiple sclerosis (MS) and other CNS diseases were stained with antibodies to fibronectin, a macrophage fibronectin receptor component, fibrin/fibrinogen, and albumin using immunoperoxidase. In active, but not inactive, MS plaques vessel fibronectin was increased (to approximately 57% of Factor VIII+ vessels) over uninvolved MS and normal control white matter (P less than 0.001 for both). Fibronectin was primarily localized to vessel walls and amount of staining correlated with degree of inflammation. Active plaques and necrotic lesions also had extracellular fibronectin and fibrin/ogen. These molecules and the fibronectin receptor were found on macrophages. Albumin was more widely and diffusely distributed in lesions than fibronectin. Thus, in addition to extravasation from damaged vessels, fibronectin may be deposited on or synthesized by endothelial cells and macrophages in the CNS. Fibronectin could facilitate monocyte adhesion to endothelial cell luminal surfaces, promote migration of mononuclear cells, and enhance myelin phagocytosis in MS lesions.
Heat shock proteins, thermotolerance, and their relevance to clinical hyperthermia (1995)

Mammalian cells, when exposed to a non-lethal heat shock, have the ability to acquire a transient resistance to subsequent exposures at elevated temperatures, a phenomenon termed thermotolerance. The mechanism(s) for the development of thermotolerance is not well understood, but earlier experimental evidence suggests that protein synthesis may play a role in its manifestation. On the molecular level, heat shock activates a specific set of genes, so-called heat shock genes, and results in the preferential synthesis of heat shock proteins. The heat shock response, specifically the regulation, expression and functions of heat shock proteins, has been extensively studied in the past decades and has attracted the attention of a wide spectrum of investigators ranging from molecular and cell biologists to radiation and hyperthermia oncologists. There is much data supporting the hypothesis that heat shock proteins play important roles in modulating cellular responses to heat shock, and are involved in the development of thermotolerance. This review summarizes some current knowledge on thermotolerance and the functions of heat shock proteins, especially hsp70. The relationship between thermotolerance development and hsp70 synthesis in tumours and in normal tissues is examined. The possibility of using hsp70 as an indicator for thermotolerance is discussed.
Optimal diffusion coefficient estimation in single-particle tracking (2012)

Single-particle tracking is increasingly used to extract quantitative parameters on single molecules and their environment, while advances in spatial and temporal resolution of tracking techniques inspire new questions and avenues of investigation. Correspondingly, sophisticated analytical methods are constantly developed to obtain more refined information from measured trajectories. Here we point out some fundamental limitations of these approaches due to the finite length of trajectories, the presence of localization error, and motion blur, focusing on the simplest motion regime of free diffusion in an isotropic medium (Brownian motion). We show that two recently proposed algorithms approach the theoretical limit of diffusion coefficient uncertainty. We discuss the practical performance of the algorithms as well as some important implications of these results for single-particle tracking.
Second European evidence-based consensus on the diagnosis and management of ulcerative colitis: Special situations (2012)

Second European evidence-based consensus on the diagnosis and management of ulcerative colitis: Special situations Gert Van Assche⁎, Axel Dignass⁎⁎, Bernd Bokemeyer, Silvio Danese, Paolo Gionchetti, Gabriele Moser, Laurent Beaugerie, Fernando Gomollon, Winfried Hauser, Klaus Herrlinger, Bas Oldenburg, Julian Panes, Francisco Portela, Gerhard Rogler, Jurgen Stein, Herbert Tilg, Simon Travis, James O. Lindsay
Miss rate prediction across all program inputs (2003)

Improving cache performance requires understanding cache behavior. However, measuring cache performance for one or two data input sets provides little insight into how cache behavior varies across all data input sets. This paper uses our recently published locality analysis to generate a parameterized model of program cache behavior. Given a cache size and associativity, this model predicts the miss rate for arbitrary data input set sizes. This model also identifies critical data input sizes where cache behavior exhibits marked changes. Experiments show this technique is within 2% of the hit rate for set associative caches on a set of integer and floating-point programs.
Opsonophagocytosis of Fluorescent Polystyrene Beads Coupled to Neisseria meningitidis Serogroup A, C, Y, or W135 Polysaccharide Correlates with Serum Bactericidal Activity (2002)

We developed a polysaccharide-specific flow cytometric opsonophagocytic assay (OPA) for the simultaneous measurement of functional antibody to Neisseria meningitidis serogroups A, C, Y, and W135. OPA titers significantly correlated with serum bactericidal assay titers for all serogroups tested (mean r = 0.96; P < 0.001). OPA could be used in meningococcal vaccine evaluation.
An entirely beaded poly(dimethylacrylamide) support for peptide synthesis (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn entirely beaded poly(dimethylacrylamide) support for peptide synthesisGlenn L. Stahl, Clark W. Smith, and Roderich WalterCite this: J. Org. Chem. 1979, 44, 19, 3424–3425Publication Date (Print):September 1, 1979Publication History Published online1 May 2002Published inissue 1 September 1979https://pubs.acs.org/doi/10.1021/jo01333a037https://doi.org/10.1021/jo01333a037research-articleACS PublicationsRequest reuse permissionsArticle Views84Altmetric-Citations8LEARN 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
Polite computing (2005)

Abstract This paper presents politeness as a key social requirement for computer human interaction (CHI). Politeness is defined, in information terms, as offering the locus of control of a social interaction to another party. Software that creates pop-up windows is not illegal, but is impolite, as it preempts user choice. It is proposed that impolite software drives users away, while polite software attracts them. Specifying politeness suggests four requirements: (1) Respect user choice (2) Disclose yourself (3) Offer useful choices (4) Remember past choices. Software that ignores these rules may fail not by logic error but by social error. "Mr. Clippy" is an example of software that users often disable because it is impolite. Operating systems could support application politeness by providing an application source registry and a general meta-choice console. A future is envisaged where software politeness is a critical software success requirement.
The TraT lipoprotein as a vehicle for the transport of foreign antigenic determinants to the cell surface of Escherichia coli K12: structure–function relationships in the TraT protein (1990)

The TraT protein is a surface-exposed lipoprotein, specified by plasmids of the IncF group, that mediates serum resistance and surface exclusion. The structure and function of the TraT protein determined by plasmid R6-5 was probed by genetic insertion of a foreign antigenic determinant, the C3 epitope of polio virus, at residues 61, 125, 180, 200 or 216 of the protein. The chimaeric proteins were transported to the outer membrane and, in three cases, immunoassays with an anti-C3 monoclonal antibody indicated that the C3 epitope was exposed on the cell surface. Three of the hybrids, with insertions at residues 125, 180 and 200, assembled into the trypsin-resistant oligomeric form characteristic of the wild-type protein, which suggested that these regions are not involved in TraT subunit:subunit interactions. Additionally, the hybrid protein carrying the C3 epitope at position 180 functioned in a genetic suppression assay and retained partial surface-exclusion activity. Thus, its localization, folding and organization does not appear to be grossly altered from that of the wild-type protein. Applications of the protein for the transport of foreign antigenic determinants to the cell surface are discussed.
Characterization of truncated alpha chain products from human, rat, and mouse high affinity receptor for immunoglobulin E (1991)

The high affinity receptor for immunoglobulin E (IgE) is a tetrameric structure (alpha beta gamma 2) consisting of non-covalently associated subunits: one IgE-binding alpha chain, one 4-fold membrane spanning beta chain, and two disulfide-linked gamma chains. Here, we have engineered alpha cDNA constructs (alpha trunc) encoding exclusively the leader peptide and the extracellular domain of the alpha subunit. Transfection of human alpha trunc into COS-7 cells resulted in the secretion of soluble IgE-binding polypeptides. By contrast, the polypeptides generated from rat and mouse alpha trunc transfections were sequestered in the endoplasmic reticulum and degraded even though they appeared to fold properly as judged by their capacity to bind IgE. Stable transfectants with human alpha trunc were obtained from a dihydrofolate reductase-deficient Chinese hamster ovary cell line. Several clones secreted substantial amounts (0.1 microgram/ml/10(6) cells) of IgE-binding polypeptides. The dissociation rate of bound IgE from this soluble truncated alpha (kappa-1 = 4.9 x 10(-6) s-1 at 25 degrees C) was characteristic of receptors on intact cells. After treatment with tunicamycin, the transfectants secreted unglycosylated 18-kDa polypeptides which could also bind IgE. These unglycosylated products had a tendency to form dimers and higher oligomers which were resistant to treatment by sodium dodecyl sulfate and reducing agents. These data demonstrate unequivocally that the extracellular domain of the alpha subunit is sufficient to mediate high affinity binding of IgE. Furthermore, posttranslational addition of carbohydrates is not required for proper folding and function of the receptor binding site. The truncated human alpha should be a suitable reagent for crystallographic analysis and for detailed analysis of the receptor binding sites.
Roles of Mycobacterium smegmatis d -Alanine: d -Alanine Ligase and d -Alanine Racemase in the Mechanisms of Action of and Resistance to the Peptidoglycan Inhibitor d -Cycloserine (2002)

D-Cycloserine (DCS) targets the peptidoglycan biosynthetic enzymes D-alanine racemase (Alr) and D-alanine:D-alanine ligase (Ddl). Previously, we demonstrated that the overproduction of Alr in Mycobacterium smegmatis determines a DCS resistance phenotype. In this study, we investigated the roles of both Alr and Ddl in the mechanisms of action of and resistance to DCS in M. smegmatis. We found that the overexpression of either the M. smegmatis or the Mycobacterium tuberculosis ddl gene in M. smegmatis confers resistance to DCS, but at lower levels than the overexpression of the alr gene. Furthermore, a strain overexpressing both the alr and ddl genes displayed an eightfold-higher level of resistance. To test the hypothesis that inhibition of Alr by DCS decreases the intracellular pool of D-alanine, we determined the alanine pools in M. smegmatis wild-type and recombinant strains with or without DCS treatment. Alr-overproducing strain GPM14 cells not exposed to DCS displayed almost equimolar amounts of L- and D-alanine in the steady state. The wild-type strain and Ddl-overproducing strains contained a twofold excess of L- over D-alanine. In all strains, DCS treatment led to a significant accumulation of L-alanine and a concomitant decease of D-alanine, with approximately a 20-fold excess of L-alanine in the Ddl-overproducing strains. These data suggest that Ddl is not significantly inhibited by DCS at concentrations that inhibit Alr. This study is of significance for the identification of the lethal target(s) of DCS and the development of novel drugs targeting the D-alanine branch of mycobacterial peptidoglycan biosynthesis.
Fundamentals of Ceramics (2002)

Fundamentals of Ceramics presents readers with an exceptionally clear and comprehensive introduction to ceramic science. This Second Edition updates problems and adds more worked examples, as well as adding new chapter sections on Computational Materials Science and Case Studies. The Computational Materials Science sections describe how today density functional theory and molecular dynamics calculations can shed valuable light on properties, especially ones that are not easy to measure or visualize otherwise such as surface energies, elastic constants, point defect energies, phonon modes, etc. The Case Studies sections focus more on applications, such as solid oxide fuel cells, optical fibers, alumina forming materials, ultra-strong and thin glasses, glass-ceramics, strong and tough ceramics, fiber-reinforced ceramic matrix composites, thermal barrier coatings, the space shuttle tiles, electrochemical impedance spectroscopy, two-dimensional solids, field-assisted and microwave sintering, colossal magnetoresistance, among others.
Normal-pressure hydrocephalus associated with spinal cord tumor (1987)

While the association of spinal cord tumor and high-pressure hydrocephalus is well known, only 5 cases of spinal cord tumor associated with normotensive hydrocephalus have been reported. Two further cases are described here, discussing the possible pathophysiological mechanism. It is suggested that these patients go through a subclinical stage of high-pressure hydrocephalus and become normotensive later on, a process which might influence the surgical results.
NT-3-mediated TrkC receptor activation promotes proliferation and cell survival of rodent progenitor oligodendrocyte cells in vitro and in vivo (1998)

We have previously described the expression of a functional full-length trkC transcript for neurotrophin-3 (NT-3) receptor in oligodendroglia (OL) cells (Kumar and de Vellis, 1996). To date, the role of NT-3 and its signal transduction cascade in OL remains poorly defined. We report that the NT-3 responsive population of cells in the OL lineage are the progenitor cells and that the addition of NT-3 results in the autophosphorylation of p145TrkC. Furthermore, NT-3-mediated activation of p21ras and mitogen-activated protein kinase (MAPK), extracellular signal-regulated protein kinase2 (ERK2), were also observed in the progenitor OL cells. These protein tyrosine kinase (PTK)-induced responses were sensitive to the presence of K252a, an inhibitor for tyrosine kinase. We have determined that NT-3 promotes progenitor OL cell commitment to enter into S-phase of cell cycle to initiate DNA synthesis, in a manner similar to platelet-derived growth factor-AA (PDGF-AA). NT-3 thus plays a role in cell proliferation when present alone, while augmenting the proliferation capacity of PDGF-AA as indicated by the nuclear binding activity of the transcription factor, E2F-1. Both the initiation and progression of mitotic events were confirmed by the expression of c-myc and cdc2 in the presence of NT-3, PDGF-AA or NT-3 plus PDGF-AA. A cell survival assay examining interleukin 1-beta-converting enzyme (ICE)-like protease-mediated cleavage of poly (ADP-ribose) polymerase (PARP) revealed an increase in OL progenitor cell death in the absence of NT-3 or PDGF-AA. In corroboration with our in vitro studies, in vivo results show an increased expression of the progenitor OL cell marker, glycerol phosphate dehydrogenase (GPDH) within 48 hr following an intracranial injection of NT-3, PDGF-AA, or NT-3 plus PDGF-AA in PN4-5 rats. These novel findings suggest that PDGF-AA potentiates the OL progenitor cell's ability to enter into the S-phase of the cell cycle and that NT-3 can augment this activity. Furthermore, PDGF-AA and NT-3 can block ICE-like protease-mediated PARP fragmentation in progenitor OL cells. These results provide important information which further delineates the signal transduction cascades and the role of NT-3 and PDGF-AA on OL progenitor cells.
A Randomized Trial of Factor VIII and Neutralizing Antibodies in Hemophilia A (2016)

Patients treated with plasma-derived factor VIII containing von Willebrand factor had a lower incidence of inhibitors than those treated with recombinant factor VIII. (Funded by the Angelo Bianchi Bonomi Foundation and others; ClinicalTrials.gov number, NCT01064284; EudraCT number, 2009-011186-88.).
Analysis of SOX9 Expression in Colorectal Cancer (2008)

Our purpose was to investigate the role of SOX9, a novel downstream molecule of β-catenin, in colorectal cancer. Expression of SOX9 and β-catenin was detected by immunostaining, quantitative real-time reverse transcription–polymerase chain reaction (Q-PCR), and Western blot in colorectal cancer. The correlation between SOX9 or β-catenin expression and clinicopathologic parameters was also analyzed. Immunostaining, Q-PCR, and Western blot consistently confirmed SOX9 up-regulation in colorectal cancer compared with normal mucosa (P < .05). Immunostaining showed more SOX9+ cells in the lower zone of colonic crypts than in the upper zone (P < .05). Cancers with strong SOX9 immunostaining were significantly associated with a lower 5-year overall survival (40% [17/43] vs low expression, 69% [66/95]; P <.01). The Cox proportional hazards model showed that strong SOX9 expression was an independent adverse prognosticator in colorectal cancer (P < .05). The detection of SOX9 expression might contribute to predicting clinical outcomes for patients with colorectal cancer.
Factors in the natural history of chronic subdural hematomas that influence their postoperative recurrence (2001)

Classification of CSDHs according to the internal architecture and intracranial extension may be useful for predicting the risk of postoperative recurrence.
Particulate Interactions in Dry Powder Formulation for Inhalation (2000)

Interactions between drug particulates are crucial in determining drug dispersion and deaggregation, and ultimately delivery efficiency. This book combines principles established in surface and colloidal chemistry with pharmaceutical powder technology. It discusses some of the factors affecting particulate interactions, and particle-fluid interaction in the respiratory tract. It review some of the studies carried out in dry powder formulation development, and proposes possible strategies in improving DPI efficiency. The majority of these principles are applicable to other pharmaceutical solid dosage forms (e.g. tablets and capsules).