gebhart/patrepeval huggingface dataset:
Delivery of Multiple Epitopes by Recombinant Detoxified Adenylate Cyclase ofBordetella pertussisInduces Protective Antiviral Immunity (2001)

CyaA, the adenylate cyclase toxin from Bordetella pertussis, can deliver its N-terminal catalytic domain into the cytosol of a large number of eukaryotic cells and particularly into professional antigen-presenting cells. We have previously identified within the primary structure of CyaA several permissive sites at which insertion of peptides does not alter the ability of the toxin to enter cells. This property has been exploited to design recombinant CyaA toxoids capable of delivering major histocompatibility complex (MHC) class I-restricted CD8(+) T-cell epitopes into antigen-presenting cells and to induce specific CD8(+) cytotoxic T-lymphocyte (CTL) responses in vivo. Here we have explored the capacity of the CyaA vector carrying several different CD8(+) T-cell epitopes to prime multiple CTL responses. The model vaccine consisted of a polyepitope made of three CTL epitopes from lymphocytic choriomeningitis virus (LCMV), the V3 region of human immunodeficiency virus gp120, and chicken ovalbumin, inserted at three different sites of the catalytic domain of genetically detoxified CyaA. Each of these epitopes was processed on delivery by CyaA and presented in vitro to specific T-cell hybridomas. Immunization of mice by CyaA toxoids carrying the polyepitope lead to the induction of specific CTL responses for each of the three epitopes, as well as to protection against a lethal viral challenge. Moreover, mice primed against the vector by mock CyaA or a recombinant toxoid were still able to develop strong CTL responses after subsequent immunization with a recombinant CyaA carrying a foreign CD8(+) CTL epitope. These results highlight the potency of the adenylate cyclase vector for induction of protective CTL responses with multiple specificity and/or broad MHC restriction.
The Internal Cavity of the Staphylococcal α-Hemolysin Pore Accommodates ∼175 Exogenous Amino Acid Residues (2005)

The cavity within the cap domain of the transmembrane staphylococcal alpha-hemolysin (alphaHL) pore is roughly a sphere of diameter approximately 45 A (molecular surface volume approximately 39,500 A(3)). We tested the ability of the cavity to accommodate exogenous polypeptide chains. Concatemerized Gly/Ser-containing sequences ("loops", L; number of repeats = n; number of residues = 10n + 5, n = 0-21) were inserted at a position located within the cavity of the fully assembled heptameric alphaHL pore. Homomeric pores containing 25 or less residues in each loop (n <or= 2) could be assembled. The pores were protease-resistant, indicating that they had been formed correctly, and produced currents in planar lipid bilayers. The pores showed an up to 70% reduction in unitary conductance, depending on the length of the inserted loop. Protease-resistant heteromeric pores containing wild-type (W) and L subunits were also assembled: when n = 3, up to five L subunits were tolerated; when n = 4, three L subunits were tolerated; and when n = 5 or 6, two L subunits were tolerated. For n >or= 7, only one L subunit was incorporated. As the inserted loop was lengthened, transient closures were observed in planar bilayer experiments with single pores. However, L(1)W(6) pores with very long loops (n = 14 and 21) had unitary conductance values close to those of W(7), suggesting that the loop is extruded through the opening in the cap of the pore into the external medium. Further analysis of bilayer recordings and electrophoretic migration patterns indicates that the upper capacity of the cavity is approximately 175 amino acids. The findings suggest that small functional peptides or proteins might be assembled within the alphaHL pore.
Prevention of cartilage degeneration and gait asymmetry by lubricin tribosupplementation in the rat following anterior cruciate ligament transection (2011)

Our findings indicate that a single intraarticular injection of concentrated lubricin following ACLT reduces type II collagen degradation and improves weight bearing in the affected rat joint. These findings support the practice of tribosupplementation with lubricin for retarding cartilage degeneration and possibly the development of posttraumatic osteoarthritis.
Thermoacoustic computed tomography–technical considerations (1999)

We have constructed a thermoacoustic computed tomography scanner for imaging soft tissue in the human body. Thermoacoustic signals are induced in soft tissue by irradiation with 434 MHz rf energy. The thermoacoustic signals are detected by an array of transducers mounted on a hemispherical bowl. A three-dimensional, filtered backprojection algorithm is used to reconstruct rf absorption patterns within soft tissue. We have demonstrated soft tissue differentiation sufficient to delineate the normal internal structures of an excised lamb kidney using safe levels of rf radiation.
Rearrangements in the p53 gene in Philadelphia chromosome positive chronic myelogenous leukemia [see comments] (1989)

Molecular structural analysis of the p53 gene in patients with Philadelphia chromosome-positive chronic myelogenous leukemia (CML) indicates a significant incidence of gene rearrangements in patients at either accelerated phase or blastic crisis. Southern blot analysis of genomic DNA hybridizing with either genomic or cDNA p53 specific probes indicated that 30% of the CML patients at blastic crisis phase exhibited rearrangements, mostly mapping downstream to the first non-coding exon. This is compatible with the observation that the progression of CML from the chronic to the acute phase involves frequent aberrations in chromosome 17, to which the p53 oncogene has been mapped. Therefore, we suggest that one of the pathways of development of CML to the acute phase is associated with aberrations in the p53 nuclear oncogene.
The PNH phenotype cells that emerge in most patients after CAMPATH‐1H therapy are present prior to treatment (1999)

Paroxysmal nocturnal haemoglobinuria (PNH) cells are deficient in glycosylphosphatidylinositol (GPI) linked antigens due to a somatic mutation of the PIG-A gene in a haemopoietic stem cell. It appears that a PNH clone reaches detectable proportions only when there is selection in its favour. GPI-deficient T lymphocytes have been identified in patients treated with CAMPATH-1H, a monoclonal antibody against the GPI-linked CD52 molecule. CAMPATH-1H selects for cells that are deficient in CD52 (such as PNH-like cells) promoting the development of a PNH-like clone (analogous to PNH). We report that 10/15 patients with chronic lymphocytic leukaemia developed PNH-like lymphocytes after therapy with CAMPATH-1H. The remaining five patients developed no PNH-like cells at any stage, including one patient who received 12 weeks of therapy. The inactivating PIG-A mutation has been identified in one patient. This mutation was detectable by an extremely sensitive mutation-specific PCR-based analysis in the patient's mononuclear cells prior to CAMPATH-1H therapy. The frequency and phenotype of GPI-deficient lymphocytes after CAMPATH-1H and the detection of a PIG-A mutation in the lymphocytes prior to CAMPATH-1H therapy indicated that such mutations were present in a very small proportion of cells prior to selection in their favour by CAMPATH-1H. This suggests that a large proportion of individuals have cells with PIG-A mutations that are not detectable by flow cytometry and thus may have the potential to develop PNH.
Semantic Labeling of Online Information Sources (2007)

In order to combine data from various heterogeneous sources, software agents must first understand the semantics of the sources, expressed in the source model. Currently, source modeling is manual, but as large numbers of sources come online, it is impractical to expect users to continue modeling them by hand. We describe two machine learning techniques for automatically modeling information sources: one that uses source’s metadata, contained in a Web Service Definition file, and one that uses the source’s content, to classify the semantics of the data it uses. We go beyond previous works and verify predictions by invoking the source with sample data of the predicted type. We provide performance results of both methods and validate our approach on several live Web sources. In addition, we describe the application of semantic modeling within the CALO project.
Potential Role of Human Cytomegalovirus and p53 Interaction in Coronary Restenosis (1994)

A subset of patients who have undergone coronary angioplasty develop restenosis, a vessel renarrowing characterized by excessive proliferation of smooth muscle cells (SMCs). Of 60 human restenosis lesions examined, 23 (38 percent) were found to have accumulated high amounts of the tumor suppressor protein p53, and this correlated with the presence of human cytomegalovirus (HCMV) in the lesions. SMCs grown from the lesions expressed HCMV protein IE84 and high amounts of p53. HCMV infection of cultured SMCs enhanced p53 accumulation, which correlated temporally with IE84 expression. IE84 also bound to p53 and abolished its ability to transcriptionally activate a reporter gene. Thus, HCMV, and IE84-mediated inhibition of p53 function, may contribute to the development of restenosis.
Adenovirus-mediated gene transfer for cystic fibrosis: quantitative evaluation of repeated in vivo vector administration to the lung. (1994)

Adenoviral vectors have an important role as in vivo gene delivery vehicles in developing human gene therapy for the fatal pulmonary component of cystic fibrosis. In this study we evaluated the immune responses to wild-type adenovirus and replication-deficient, first generation adenoviral (Av1) vectors in the cotton rat (Sigmodon hispidus) and then quantitatively evaluated the efficiency of gene delivery and expression of single and repeated in vivo administration of Av1 vectors to the respiratory tract. Av1 vector reporter gene expression was quantitatively evaluated by employing a luciferase expression vector (Av1Luc1) and measuring luciferase activity in whole lung tissue homogenates by routine luminometry. Gene transfer and expression in naive animals (e.g. first Av1 vector dose) was efficient. A repeat dose also resulted in successful gene transfer and expression, although at a significantly reduced level (p < 0.01) compared with naive animals. This reduction inversely correlated with serum human adenovirus neutralizing antibody (HANA) titers. Importantly, increasing doses of Av1Cf2, an Av1 vector expressing the human CFTR cDNA, resulted in a graded HANA response consistent with a lack of in vivo replication. These observations have significant implications for repeated administration of adenoviral vectors to the lungs of individuals with cystic fibrosis.
Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily (2015)

Orthosomycins are oligosaccharide antibiotics that include avilamycin, everninomicin, and hygromycin B and are hallmarked by a rigidifying interglycosidic spirocyclic ortho-δ-lactone (orthoester) linkage between at least one pair of carbohydrates. A subset of orthosomycins additionally contain a carbohydrate capped by a methylenedioxy bridge. The orthoester linkage is necessary for antibiotic activity but rarely observed in natural products. Orthoester linkage and methylenedioxy bridge biosynthesis require similar oxidative cyclizations adjacent to a sugar ring. We have identified a conserved group of nonheme iron, α-ketoglutarate-dependent oxygenases likely responsible for this chemistry. High-resolution crystal structures of the EvdO1 and EvdO2 oxygenases of everninomicin biosynthesis, the AviO1 oxygenase of avilamycin biosynthesis, and HygX of hygromycin B biosynthesis show how these enzymes accommodate large substrates, a challenge that requires a variation in metal coordination in HygX. Excitingly, the ternary complex of HygX with cosubstrate α-ketoglutarate and putative product hygromycin B identified an orientation of one glycosidic linkage of hygromycin B consistent with metal-catalyzed hydrogen atom abstraction from substrate. These structural results are complemented by gene disruption of the oxygenases evdO1 and evdMO1 from the everninomicin biosynthetic cluster, which demonstrate that functional oxygenase activity is critical for antibiotic production. Our data therefore support a role for these enzymes in the production of key features of the orthosomycin antibiotics.
Extracellular Signal-regulated Protein Kinase Activation Is Required for the Anti-hypertrophic Effect of Atrial Natriuretic Factor in Neonatal Rat Ventricular Myocytes (1999)

Atrial natriuretic factor (ANF) inhibits proliferation in non-myocardial cells and is thought to be anti-hypertrophic in cardiomyocytes. We investigated the possibility that the anti-hypertrophic actions of ANF involved the mitogen-activated protein kinase signal transduction cascade. Cultured neonatal rat ventricular myocytes treated for 48 h with the alpha(1)-adrenergic agonist phenylephrine (PE) had an 80% increase in cross-sectional area (CSA). ANF alone had no effect but inhibited PE-induced increases in CSA by approximately 50%. The mitogen-activated protein kinase/ERK kinase (MEK) inhibitor PD098059 minimally inhibited PE-induced increases in CSA, but it completely abolished ANF-induced inhibition of PE-induced increases. ANF-induced extracellular signal-regulated protein kinase (ERK) nuclear translocation was also eliminated by PD098059. ANF treatment caused MEK phosphorylation and activation but failed to activate any of the Raf isoforms. ANF induced a rapid increase in ERK phosphorylation and in vitro kinase activity. PE also increased ERK activity, and the combined effect of ANF and PE appeared to be additive. ANF-induced ERK phosphorylation was eliminated by PD098059. ANF induced minimal phosphorylation of JNK or p38, indicating that its effect on ERK was specific. ANF-induced activation of ERK was mimicked by cGMP analogs, suggesting that ANF-induced ERK activation involves the guanylyl cyclase activity of the ANF receptor. These data suggest that there is an important linkage between cGMP signaling and the mitogen-activated protein kinase cascade and that selective ANF activation of ERK is required for the anti-hypertrophic action of ANF. Thus, ANF expression might function as the natural defense of the heart against maladaptive hypertrophy through its ability to activate ERK.
[Methods of production and perspectives for use of transgenic domestic animals]. (1997)

The technique of microinjection is so far the only successful method of gene transfer in farm animals. Fertilized oocytes are collected from superovulated donors by flushing the oviducts and the exogenous gene construct is injected into the male pronucleus of zygotes before transfer into the oviducts or uteri of synchronized recipients. The resulting pups have to be tested for integration and expression of the foreign gene. Potential applications of gene transfer in farm animals are the improvement of growth parameters, the increase of disease resistance, the enhancement of reproduction rates, the increase of wool production of sheep, the alteration of metabolic pathways, the production of human hemoglobin in the blood of transgenic animals, the generation of transgenic animals as organ donors and the proteins in the milk of transgenic animals. Many studies showed, that farm animals are able to direct the expression of partially large amounts of foreign proteins for biomedical purposes into their milk. Therefore transgenic livestock could be an attractive alternative for conventional production methods.
Selective silencing of NaV1.7 decreases excitability and conduction in vagal sensory neurons (2011)

There has been much information learned in recent years about voltage gated sodium channel (Na(V)) subtypes in somatosensory pain signalling, but much less is known about the role of specific sodium channel subtypes in the vagal sensory system. In this study, we developed a technique using adeno-associated viruses (AAVs) to directly introduce shRNA against Na(V)1.7 subtype gene into the vagal sensory ganglia of guinea pigs in vivo. Na(V)1.7 gene expression in nodose ganglia was effectively and selectively reduced without influencing the expression of other sodium channel subtype genes including Na(V)1.1, 1.2, 1.3 1.6, 1.8, or 1.9. Using a whole cell patch-clamp technique, this effect on Na(V)1.7 gene expression coincided with a reduction in tetrodotoxin-sensitive sodium current, a requirement for much larger depolarizing stimulus to initiate action potentials, and reduction in repetitive action potential discharge. Extracellular recordings in the isolated vagus nerve revealed that the conduction of action potentials in sensory A- and C-fibres in many neurons was effectively abolished after Na(V)1.7 shRNA introduction. Moreover, bilateral Na(V)1.7 shRNA injected animals survived for several months and the vagal reflex behaviour, exemplified by citric acid-induced coughing, was significantly suppressed. These data indicate that selectively silencing Na(V)1.7 ion channel expression leads to a substantial decrease in neural excitability and conduction block in vagal afferent nerves.
Vibrational spectroscopy and photodissociation properties of ions as determined by two-laser photodissociation techniques (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVibrational spectroscopy and photodissociation properties of ions as determined by two-laser photodissociation techniquesJeffrey P. Honovich and Robert C. DunbarCite this: J. Phys. Chem. 1983, 87, 19, 3755–3758Publication Date (Print):September 1, 1983Publication History Published online1 May 2002Published inissue 1 September 1983https://pubs.acs.org/doi/10.1021/j100242a036https://doi.org/10.1021/j100242a036research-articleACS PublicationsRequest reuse permissionsArticle Views69Altmetric-Citations15LEARN 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 options Get e-Alerts
IFN-α and IL-10 Induce the Differentiation of Human Type 1 T Regulatory Cells (2001)

CD4(+) T regulatory type 1 (Tr1) cells suppress Ag-specific immune responses in vitro and in vivo. Although IL-10 is critical for the differentiation of Tr1 cells, the effects of other cytokines on differentiation of naive T cells into Tr1 cells have not been investigated. Here we demonstrate that endogenous or exogenous IL-10 in combination with IFN-alpha, but not TGF-beta, induces naive CD4(+) T cells derived from cord blood to differentiate into Tr1 cells: IL-10(+)IFN-gamma(+)IL-2(-/low)IL-4(-). Naive CD4(+) T cells derived from peripheral blood require both exogenous IL-10 and IFN-alpha for Tr1 cell differentiation. The proliferative responses of the Tr1-containing lymphocyte populations, following activation with anti-CD3 and anti-CD28 mAbs, were reduced. Similarly, cultures containing Tr1 cells displayed reduced responses to alloantigens via a mechanism that was partially mediated by IL-10 and TGF-beta. More importantly, Tr1-containing populations strongly suppressed responses of naive T cells to alloantigens. Collectively, these results show that IFN-alpha strongly enhances IL-10-induced differentiation of functional Tr1 cells, which represents a first major step in establishing specific culture conditions to generate T regulatory cells for biological and biochemical analysis, and for cellular therapy to induce peripheral tolerance in humans.
Expression and Functional Characterization of the β-Isoform of the Folate Receptor on CD34+ Cells (1999)

Abstract We have investigated the expression and functional competence of folate receptor (FR) isoforms on human hematopoietic cells. Using immunofluorescence and reverse transcriptase-polymerase chain reaction (RT-PCR) methodology, we find that a substantial fraction of low-density mononuclear and CD34+ cells express both the β and γ isoforms of FR. The  isoform of FR (the form most commonly found on cancer cells) was surprisingly absent from all hematopoietic cells examined. Compared with KB cells (a human cell line known for its elevated expression of FR-), the abundance of FR-β on CD34+ cell surfaces was relatively low (≈8% of KB cell levels). Because many antifolates and folic acid-linked chemotherapeutic agents enter malignant cells at least partially via FR endocytosis, it was important to evaluate the ability of FR on CD34+ cells to bind folic acid (FA). Based on three FR binding assays, freshly isolated CD34+ cells were found to display no affinity for FA. Thus, regardless of whether steps were taken to remove endogenous folates before receptor binding assays, FR on primitive hematopoietic cells failed to bind 3H-FA, fluorescein isothiocyanate (FITC)-linked FA, or FA-derivatized liposomes. In contrast, analogous studies on KB cells showed high levels of receptor binding for all three FR probes. These studies show that although multipotent hematopoietic progenitor cells express FR, the receptor does not transport significant amounts of FA. Consequently, antifolates and FA-linked chemotherapeutic agents that can be engineered to enter malignant cells exclusively through the FR should not harm progenitor/stem cell function.
Synthesis of methyl (R)- and (S)-[18O]phosphorothioates and determination of the absolute configuration at phosphorus of the diastereoisomers of adenosine 5′-(1-thiotriphosphate) (1979)

A general route for the synthesis of enantiomeric [18O]phosphorothioate esters of known absolute configuration has been developed, and isomer A of adenosine 5′-(1-thiotriphosphate) shown to have the (S)-configuration at Pα.
Vaccination against autoimmune encephalomyelitis (EAE): Attenuated autoimmune T lymphocytes confer resistance to induction of active EAE but not to EAE mediated by the intact T lymphocyte line (1981)

Autoimmune encephalomyelitis (EAE) can be induced in genetically susceptible rats by active immunization against myelin basic protein (BP) or by passive transfer or anti-BP lymphocytes. We have developed in vitro lines of T lymphocytes reactive only against BP that produce EAE upon i.v. inoculation of syngeneic rats. The object of the present study was to learn whether attenuated anti-BP line cells could be used to vaccinate rats against passive as well as active EAE. We inoculated rats i.v. with anti-BP line cells that were attenuated by irradiation or treatment by mitomycin C. A single inoculation was sufficient to protect about 70% of rats from subsequent EAE induced actively. However, even repeated vaccination could not protect against EAE mediated by passive transfer of anti-BP line cells. Thus, attenuated cells of EAE effector lines cannot vaccinate the autoreactive effects of preformed effector T lymphocytes.