gebhart/patrepeval huggingface dataset:
Recombinant Listeria monocytogenes as a live vaccine vehicle and a probe for studying cell‐mediated immunity (1997)

Summary: The ability of Listeria monocytogenes (L. monocytogenes) to enter the cytosol of host cells allows secreted proteins lo efficiently enter the endogenous antigen‐processing pathway leading to presentation by MHC class I molecules. L. monocytogenes has recently been exploited as a live vaccine vehicle for the induction of immunological memory against heterologous antigens. We have established a genetic system for site‐specific integration of antigen expression cassettes into the imam genome which allows regulated expression and secretion of heterologous proteins. The ability of recombinant strains to stimulate long‐term immunological memory and CD8+ T‐cell‐mediated protective immunity was investigated using the lymphocytic choriomeningitis virus (LCMV) murine infection model. Vaccination of mice with recombinant Listeria strains expressing LCMV antigens induced LCMV‐specific CD8+ T cells which protected mice against LCMV challenge. We have also used a cottontail rabbit papilloma‐virus model to test the ability of recombinant Listeria strains to stimulate protective antitumor immunity in domestic rabbits. These studies have demonstrated the protective efficacy of recombinant L. monocytogenes vaccines and have established an experimental system for systematic analysis of cytotoxic T cell induction by an intracellular bacterium.
PEYER'S PATCHES: AN ENRICHED SOURCE OF PRECURSORS FOR IGA-PRODUCING IMMUNOCYTES IN THE RABBIT (1971)

The proliferative and differentiative potential of Peyer's patch, peripheral blood, and popliteal lymph node cells was assessed by allogeneic cell transfer followed by quantitation of donor immunocytes by immunofluorescence. It was found that Peyer's patches are a highly enriched source of cells which have the potential to proliferate and differentiate into IgA-producing immunocytes and that the Peyer's patch cells are far more efficient in seeding the gut of irradiated recipient rabbits with donor cells that give rise to immunoglobulin-producing cells than cells from peripheral blood or popliteal lymph nodes.
Molecular cloning, identification, and sequence of the hyaluronan synthase gene from group A Streptococcus pyogenes. (1993)

The hyaluronan (HA) synthase of Group A Streptococci has been identified by transposon mutagenesis and deletion analysis. The genes for the HA synthase and a recently identified UDP-Glc dehydrogenase (Dougherty, B. A., and van de Rijn, I. (1993) J. Biol. Chem. 268, 7118-7124) reside on a contiguous stretch of 3.2-kilobase pair DNA that can direct HA biosynthesis in Enterococcus faecalis and Escherichia coli as well as mutant Streptococcus (DeAngelis, P. L., Papaconstantinou, J., and Weigel, P. H. (1993) J. Biol. Chem. 268, 14568-14571). The synthase contains 395 residues (calculated Mr = 45,063) and migrates on SDS-PAGE with a molecular mass of 42 kDa. E. coli K5, which synthesizes UDP-glucuronic acid for production of its endogenous capsular polysaccharide, can make HA if it contains a plasmid encoding the intact 42-kDa protein. E. coli SURE or chi 1448 cells containing the same construct, however, cannot produce HA since these strains cannot make both required sugar nucleotide precursors. The HA synthase is predicted to be an integral membrane protein with four membrane-associated helices, which is consistent with the location of the enzyme activity in Streptococci. There is significant homology between the HA synthase and the Rhizobium nodC gene product, an enzyme that synthesizes chitin-like oligomers. This is the first description at the molecular level of an enzyme shown to synthesize a glycosaminoglycan.
Polymeric integrated selective enrichment target (ISET) for solid‐phase‐based sample preparation in MALDI–TOF MS (2007)

A polymer microfabricated proteomic sample preparation and MALDI MS sample presentation device, the integrated selective enrichment target (ISET), comprising an array of perforated nanovials is reported. Each perforated nanovial can be filled with selective extraction media (microbeads) for purification and concentration of protein/peptides prior to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The main areas covered are the influence of the molding-process-induced surface roughness and how to address the lack of inherent conductivity in the polyetheretherketone (PEEK) material for optimal MALDI MS readout. Application of the disposable polymeric ISET devices for solid-phase extraction and phosphopeptide capture is also demonstrated.
Oversampling Delta-Sigma Data Converters (1991)

This now famous anthology brings together various aspects of oversampling methods and compares and evaluates design approaches. It describes the theoretical analysis of converter performances, the actual design of converters and their simulation, circuit implementations, and applications
NiCord® Expanded Hematopoietic Progenitor Cells (HPC) Are Capable of Prolonged Myeloid and Lymphoid Engraftment Following Myeloablative Dual Umbilical Cord Blood (UCB) Transplantation (2012)

Human transplantation of expanded HPCs resulting in durable, robust donor myeloid and T-cell engraftment has yet to be reported. We report here preliminary results of a pilot study of myeloablative dual UCB transplantation where one UCB unit is expanded ex vivo using the NiCord technology. The NiCord UCB graft consists of an expanded AC133+ and a re-frozen unexpanded AC133- fraction. HPCs were expanded for 21 days in media containing hematopoietic cytokines supplemented with nicotinamide (NAM), a vitamin B3 derivative that delays differentiation and improves engraftment efficiency of human HPCs. Patients were conditioned with total body irradiation (1350cGy) and fludarabine 160mg/m2. Graft versus host disease (GVHD) prophylaxis consisted of tacrolimus and mycophenolate mofetil. Four patients (median age 46; range 41-61) with AML (n = 2) or MDS (n = 2) received a NiCord-containing dual UCB graft. The unmanipulated unit was HLA 4/6 (n = 3) or 5/6 (n = 1) matched with the patient and contained a median cryopreserved TNC dose of 3 x 107/kg. The expanded unit was 4/6 matched (n = 2) or 5/6 HLA-matched (n = 2) with the patient and contained a median cryopreserved TNC dose of 2.3 x 107/kg. After expansion of the AC133+ cell fraction, the TNC and CD34+ cell dose increased a median 455 fold (range 321-577 fold) and 75 fold (range 46-100 fold), respectively. Patients received the NiCord unit that contained a median TNC and CD34+ cell dose of 3.1 x 107/kg (range 1.8-4.3) and 4.6 x 106/kg, respectively. The transplanted negative fraction contained a median of 1.8 x 105 (range 0.8-2.8) CD3+ T-cells/kg. All patients are durably engrafted, with a median time to ANC>500 of 13 days (range 11-18) and platelets >20,000 of 32 days (range 30-36). Peripheral blood CD3+ and CD15+ cell chimerism from the 4 patients at the time of last follow-up are reported. Patient 1, day +280; CD3 (NiCord-2%, unmanipulated-80%, host-18%), CD15 (NiCord-64%, unmanipulated-36%). Patient 2, day +180; CD3 (NiCord-100%), CD15 (NiCord-100%). Patient 3, day +60; CD3 (NiCord-93%, host-7%), CD15 (NiCord-98%, host-2%) Patient 4, day +60; CD3 (unmanipulated-100%), CD15 (unmanipulated-100%). There were no infusion-related or unexpected adverse events and all patients are alive and well without GVHD. These data demonstrate prompt and prolonged engraftment of both myeloid and lymphoid cells derived from expanded HPCs (NiCord) in 3 of 4 patients treated to date. Longer follow-up is required to confirm durability.
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences (2008)

The Molecular Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous gene sequences either from multigene families or from different species with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools for statistical analysis of data, MEGA provides many convenient facilities for the assembly of sequence data sets from files or web-based repositories, and it includes tools for visual presentation of the results obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here we discuss the motivation, design principles and priorities that have shaped the development of MEGA. We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods.
An Antigen Recognized by Autologous CTLs on a Human Bladder Carcinoma (1998)

By stimulating blood lymphocytes with autologous bladder carcinoma cells that had been transfected with B7-1, we obtained a panel of CTL clones which lyse specifically the bladder tumor cells in an MHC class I-restricted fashion. Based on inhibition with anti-HLA Abs and the recognition of allogeneic tumor cells, we could distribute our clones in three groups that recognized three distinct Ags. We characterized one of these Ags by screening a cDNA library prepared with the RNA from this bladder tumor line. This new tumor Ag is a peptide presented by HLA-B4403 molecules. It is produced by a point mutation in a gene that is recorded in databases under the name KIAA0205, is ubiquitously expressed, and whose function is unknown. We also found this mutation in the tumor sample that was originally resected from this patient, but the mutation was not found in the 100 or more independent tumors of various histologic types that were tested. This report is the first to describe the isolation of CTL clones directed against human bladder cancer and the molecular characterization of a bladder tumor Ag.
Modulation of NifA activity by PII in Azospirillum brasilense: evidence for a regulatory role of the NifA N-terminal domain (1996)

Azospirillum brasilense NifA, which is synthesized under all physiological conditions, exists in an active or inactive from depending on the availability of ammonia. The activity also depends on the presence of PII, as NifA is inactive in a glnB mutant. To investigate further the mechanism that regulates NifA activity, several deletions of the nifA coding sequence covering the amino-terminal domain of NifA were constructed. The ability of these truncated NifA proteins to activate the nifH promoter in the absence or presence of ammonia was assayed in A. brasilense wild-type and mutant strains. Our results suggest that the N-terminal domain is not essential for NifA activity. This domain plays an inhibitory role which prevents NifA activity in the presence of ammonia. The truncated proteins were also able to restore nif gene expression to a glnB mutant, suggesting that PII is required to activate NifA by preventing the inhibitory effect of its N-terminal domain under conditions of nitrogen fixation. Low levels of nitrogenase activity in the presence of ammonia were also observed when the truncated gene was introduced into a strain devoid of the ADP-ribosylation control of nitrogenase. We propose a model for the regulation of NifA activity in A. brasilense.
Synthesis, Pharmacology, and Cell Biology of sn-2-Aminooxy Analogues of Lysophosphatidic Acid (2008)

An efficient enantioselective synthesis of sn-2-aminooxy (AO) analogues of lysophosphatidic acid (LPA) that possess palmitoyl and oleoyl acyl chains is presented. Both sn-2-AO LPA analogues are agonists for the LPA1, LPA2, and LPA4 G-protein-coupled receptors, but antagonists for the LPA3 receptor and inhibitors of autotaxin (ATX). Moreover, both analogues stimulate migration of intestinal epithelial cells in a scratch wound assay.
The template update problem (2004)

Template tracking dates back to the 1981 Lucas-Kanade algorithm. One question that has received very little attention, however, is how to update the template so that it remains a good model of the tracked object. We propose a template update algorithm that avoids the "drifting" inherent in the naive algorithm.
Detection by GenoType MTBDR sl Test of Complex Mechanisms of Resistance to Second-Line Drugs and Ethambutol in Multidrug-Resistant Mycobacterium tuberculosis Complex Isolates (2010)

The GenoType MTBDRsl test rapidly detects resistance to ethambutol, fluoroquinolones, and second-line aminoglycosides (amikacin and kanamycin) and cyclic peptide (capreomycin) in Mycobacterium tuberculosis. A set of 41 multidrug-resistant (MDR) M. tuberculosis strains, 8 extensively drug-resistant (XDR) M. tuberculosis strains, and 3 non-MDR M. tuberculosis strains were tested by the MTBDRsl test and by DNA sequencing of the resistance-determining regions in gyrA and gyrB (fluoroquinolones [FQ]), rpsL (streptomycin), rrs and tlyA (aminoglycosides and/or cyclic peptide), and embB (ethambutol). The sensitivity and specificity of the MTBDRsl test were as follows: 87% and 96%, respectively, for fluoroquinolones; 100% for both for amikacin; 77% and 100%, respectively, for kanamycin, 80% and 98%, respectively, for capreomycin; and 57% and 92%, respectively, for ethambutol. Analysis of the discrepant results indicated that three FQ-resistant strains (including one XDR strain) with mutations in gyrB were missed by the MTBDRsl test and that one FQ-susceptible strain, identified as resistant by the MTBDRsl test, had a double mutation (T80A-A90G) in GyrA that did not confer resistance to FQ. Five strains (including two XDR strains) without mutations in rrs were monoresistant to aminoglycosides or cyclic peptide and were missed by the MTBDRsl test. Finally, 12/28 ethambutol-resistant strains had no mutation at codon 306 in embB, while 2/24 ethambutol-susceptible strains had such a mutation. In conclusion, the MTBDRsl test efficiently detects the most common mutations involved in resistance to fluoroquinolones, aminoglycosides/cyclic peptide, and ethambutol and accurately assesses susceptibility to amikacin. However, due to mutations not included in the test (particularly in gyrB) or resistance mechanisms not yet characterized (particularly those related to ethambutol resistance and to monoresistance to aminoglycosides or cyclic peptide), the wild-type results yielded by the MTBDRsl test should be confirmed by drug susceptibility testing.
Antiarthritic activity of an orally active C5a receptor antagonist against antigen‐induced monarticular arthritis in the rat (2002)

An agent that inhibits the action of C5a in this model significantly reduced joint pathology, while ibuprofen was not effective. C5a antagonists could therefore have broader therapeutic benefits than nonsteroidal antiinflammatory drugs as antiarthritic agents for rheumatoid arthritis.
Enhancement of albumin expression in bone tissues with healing rat fractures (2003)

The characterization of 66 kDa protein molecule, a major protein component which is produced from femoral-diaphyseal tissues with fracture healing (Igarashi and Yamaguchi [2002] Int. J. Mol. Med. 9:503-508), was investigated. Weaning rats were killed at 7 and 14 days after femoral fracture. When the femoral-diaphyseal tissues with fracture healing were cultured for 48 h in a serum-free medium, many proteins in the bone tissues were released into the medium. Analysis with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed that a protein molecule of approximately 66 kDa was markedly increased in culture medium from bone tissues with fracture healing. N-terminal sequencing of 66 kDa protein indicated that its N-terminus was identical to that of rat albumin. Western blot analysis of medium 66 kDa protein showed expression of albumin. This expression was significantly enhanced by fracture healing. The expression of albumin was seen in the diaphyseal (cortical bone) and metaphyseal (trabecular bone) tissues of rat femur. When the femoral-diaphyseal tissues obtained at 7 days after femoral fracture were cultured in a serum-free medium containing either vehicle, parathyroid hormone (1-34) (10(-7) M), insulin-like growth factor-I (10(-8) M) or zinc acexamate (10(-4) M), medium albumin was significantly increased in the presence of those bone-stimulating factors. The addition of albumin (0.5 or 1.0 mg/ml of medium) caused a significant increase in calcium and deoxyribonucleic acid contents in the femoral-diaphyseal and -metaphyseal tissues obtained from normal rats in vitro. The present study demonstrates that fracture healing induces a remarkable production of albumin which is a major protein component produced from femoral-diaphyseal tissues of rats, and that albumin has an anabolic effect on bone components.
Stereochemical Dichotomy in the Stevens Rearrangement of Axially Twisted Dihydroazepinium and Dihydrothiepinium Salts. A Novel Enantioselective Synthesis of Pentahelicene (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemical Dichotomy in the Stevens Rearrangement of Axially Twisted Dihydroazepinium and Dihydrothiepinium Salts. A Novel Enantioselective Synthesis of PentaheliceneIrena G. Stara, Ivo Stary, Milos Tichy, Jiri Zavada, and Vladimir HanusCite this: J. Am. Chem. Soc. 1994, 116, 12, 5084–5088Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/ja00091a009https://doi.org/10.1021/ja00091a009research-articleACS PublicationsRequest reuse permissionsArticle Views708Altmetric-Citations60LEARN 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
Quantitative differential phase measurement and imaging in transparent and turbid media by optical coherence tomography (2001)

Differential phase-contrast optical coherence tomography allows one to measure the path-length differences of two transversally separated beams in the nanometer range. We calculate these path-length differences from the phase functions of the interferometric signals. Pure phase objects consisting of chromium layers containing steps of approximately 100-200-nm height were imaged. Phase differences can be measured with a precision of +/-2 degrees , corresponding to a path-difference resolution of 2-3 nm. To investigate the influence of scattering, we imaged the phase objects through scattering layers with increasing scattering coefficients. The limit of phase imaging through these layers was at approximately 8-9 mean free path lengths thick (single pass).
Genome-wide mapping of imprinted differentially methylated regions by DNA methylation profiling of human placentas from triploidies (2011)

DNA methylation profiling of triploidies in different tissues and developmental ages can be a powerful and effective way to map and characterize imprinted regions in the genome.
Changes in the expression of Sialyl-Lewisx, a hepatic necroinflammation-associated carbohydrate neoantigen, in human hepatocellular carcinomas (1994)

SLEX, a NICA, showed HCC-associated changes that were dependent on the levels of HCC cell differentiation. Suppression and reactivation of alpha 1-3fucosyl-transferase was a possible enzymatic basis for the observed changes.
Role of Src Kinases in the ADAM-mediated Release of L1 Adhesion Molecule from Human Tumor Cells (2000)

The ectodomain of certain transmembrane molecules can be released by proteolysis, and the solubilized antigens often exert important biological functions. We demonstrated before that the L1 adhesion molecule is shed from the cell surface. Here we show that L1 release in AR breast carcinoma cells is mediated by a member of the disintegrin metalloproteinase (ADAM) family of proteinases. Up-regulation of L1 shedding by phorbol ester or pervanadate involved distinct mechanisms. Pervanadate induced shedding and rounding-up of cells from the substrate, which was blocked by the Src kinase inhibitor PP2. Tyr phosphorylation of the L1 cytoplasmic tail and the Src kinase Fyn was observed following pervanadate treatment. Up-regulation of L1 release and activation of Fyn occurred also when cells were detached by EDTA suggesting that the regulation of L1 shedding by this pathway was linked to cell morphology and adhesion. The phorbol 12-myristate 13-acetate-induced shedding was inhibited by the protein kinase C inhibitor bisindolylmaleimide I and by PD98059, a specific inhibitor of the mitogen-activated protein kinase pathway. Soluble L1 binds to the proteoglycan neurocan and in bound form could support integrin-mediated cell adhesion and migration. We propose that the release of cell-associated adhesion molecules such as L1 may be relevant to promote cell migration.
Interleukin-8: An Important Neutrophil Chemotaxin in Some Cases of Exudative Pleural Effusions (1993)

It was hypothesized that IL-8, a neutrophil chemotaxin, contributes to the influx of neutrophils into the pleural cavity of patients with pleural effusions. Pleural fluids were collected from 57 patients including 13 with effusions due to congestive heart failure, 28 with pleural involvement by carcinoma, 5 with empyema, 4 with parapneumonic effusions complicating bacterial pneumonia, 3 with hemothorax, 3 with tuberculosis, and 1 with rheumatoid arthritis. All exudate groups had significantly higher IL-8 concentrations than the CHF group (p < .001). In 18 of the exudate fluids, the concentrations of IL-8 was equal to or in excess of the optimal concentration of IL-8 which causes neutrophil chemotaxis in vitro. Between 20 and 90% of the chemotactic activity in the fluids was removed by absorbing the IL-8 with an IL-8 affinity column. These data showed that IL-8 is a major chemotaxin in the fluid. The percentage of neutrophils in the fluids was not correlated with the IL-8 concentration. Although TNF alpha, a potent stimulator of IL-8 production, is present in some pleural effusions, no correlation was found between the concentrations of IL-8 and TNF alpha in the fluids. The data suggest that IL-8 contributes to the neutrophil influx into the pleural space of patients with pleural exudates in conjunction with other chemoattractants. It is unlikely that TNF alpha is the sole stimulus for the IL-8 production in pleural disease states.
A Pyrazolo[3,4-d]pyrimidin-4-amine Derivative Containing an Isoxazole Moiety Is a Selective and Potent Inhibitor of RET Gatekeeper Mutants (2015)

Aberrant RET kinase signaling plays critical roles in several human cancers such as thyroid carcinoma. The gatekeeper mutants (V804L or V804M) of RET are resistant to currently approved RET inhibitors such as cabozantinib and vandetanib. We, for the first time, report a highly selective and extremely potent RET inhibitor, 6i rationally designed. Compound 6i inhibits strongly RET gatekeeper mutants and other clinically relevant RET mutants as well as wt-RET. This substance also significantly suppresses growth of thyroid cancer-derived TT cell lines and Ba/F3 cells transformed with various RET mutants. Docking studies reveal that the isoxazole moiety in 6i is responsible for binding affinity improvement by providing additional site for H-bonding with Lys758. Also, 6i not only substantially blocks cellular RET autophosphorylation and its downstream pathway, it markedly induces apoptosis and anchorage-independent growth inhibition in TT cell lines while having no effect on normal thyroid Nthy ori-3-1 cells.