gebhart/patrepeval huggingface dataset:
Autologous B lymphoblastoid cell lines and long-term cultured T cells as stimulators in the mixed lymphocyte reaction: analysis of the role of HLA class II antigens as stimulatory molecules. (1986)

Human activated T cells, long-term cultured in the presence of interleukin 2 (IL 2), were compared with autologous Epstein Barr virus-transformed B lymphoblastoid cell lines for expression of human leukocyte (HLA)-HLA-DR and -DQ antigens and for ability to induce proliferative responses in autologous and allogeneic lymphocytes. Immunofluorescence analysis performed with a panel of monoclonal antibodies (mAb) specific for HLA-DR or -DQ antigens did not reveal any significant difference in the expression of HLA-DR antigens but revealed reduced expression of HLA-DQ antigens on two out of four T cell lines tested. No obvious difference could be detected in the two-dimensional gel electrophoretic profile of HLA-DR and -DQ beta-chains synthesized by the autologous pairs of B and T cell lines. In contrast with previous reports, the IL 2-dependent cell lines consistently induced alloproliferative responses in standard 6-day mixed lymphocyte cultures; however, these responses were severalfold lower than those elicited by the autologous B lymphoid lines. Both anti-HLA-DR and anti-HLA-DQ mAb blocked the proliferative responses induced by the B cell lines but did not affect those generated by the T cell lines, suggesting that the latter cells induce T lymphocyte activation via a mechanism independent of HLA-DR or -DQ antigen expression on their surface. Addition of IL 2 to the mixed cultures with B cell lines as stimulators did not affect the outcome of the proliferative responses but partially or completely reversed the blocking activity of the mAb. In contrast, IL 2 significantly enhanced the alloproliferation induced by the T lymphoblastoid cell lines, and the anti-HLA class II mAb partially antagonized this effect. Taken together, these data suggest that unlike the HLA-DR and -DQ gene products on B cells, those on IL 2-dependent long-term cultured T cells do not play a direct or primary stimulatory role in the mixed lymphocyte reaction; the reduced levels of alloproliferation induced by the T cell lines are, at least in part, due to a defective production of endogenous IL 2 by the responder lymphocytes rather than to a defective expression of IL 2 receptors by the alloproliferative T cell subset; and the anti-HLA class II mAb in these cultures act only at the responder cell level, since they can efficiently block the enhancement of T cell proliferation triggered by exogenous IL 2, but not the proliferative responses induced by T cell lines in standard conditions.
LA FORMACIÓN PARA LA INVESTIGACIÓN DE LOS DOCENTES UNIVERSITARIOS COMO AGENTES DE CAMBIO ANTE LOS NUEVOS DESAFÍOS (2012)

Clear cell renal cell carcinoma (ccRCC) is an immunologically vulnerable tumor entity, and immune checkpoint inhibitors are now widely used to treat patients with advanced disease. Whether and to what extent immune responses in ccRCC are shaped by genetic alterations, however, is only beginning to emerge. In this proof-of-concept study, we performed a detailed correlative analysis of the mutational and immunological landscapes in a series of 23 consecutive kidney cancer patients. We discovered that a high infiltration with CD8 + T cells was not dependent on the number of driver mutations but rather on the presence of specific mutational events, namely pathogenic mutations in PTEN or BAP1. This observation encouraged us to compare mechanisms of T cell suppression in the context of four different genetic patterns, i.e., the presence of multiple drivers, a PTEN or BAP1 mutation, or the absence of detectable driver mutations. We found that ccRCCs harboring a PTEN or BAP1 mutation showed the lowest level of Granzyme B positive tumor-infiltrating lymphocytes (TILs). A multiplex immunofluorescence analysis revealed a significant number of CD8 + TILs in the vicinity of CD68 + macrophages/monocytes in the context of a BAP1 mutation but not in the context of a PTEN mutation. In line with this finding, direct interactions between CD8 + TILs and CD163 + M2-polarized macrophages were found in BAP1-mutated ccRCC but not in tumors with other mutational patterns. While an absence of driver mutations was associated with more CD8 + TILs in the vicinity of FOXP3 + Tregs and CD68 + monocytes/macrophages, the presence of multiple driver mutations was, to our surprise, not found to be strongly associated with immunosuppressive mechanisms. Our results highlight the role of genetic alterations in shaping the immunological landscape of ccRCC. We discovered a remarkable heterogeneity of mechanisms that can lead to T cell suppression, which supports the need for personalized immune oncological approaches.
Leukosialin (CD43) defines hematopoietic progenitors in human embryonic stem cell differentiation cultures (2006)

During hematopoietic differentiation of human embryonic stem cells (hESCs), early hematopoietic progenitors arise along with endothelial cells within the CD34(+) population. Although hESC-derived hematopoietic progenitors have been previously identified by functional assays, their phenotype has not been defined. Here, using hESC differentiation in coculture with OP9 stromal cells, we demonstrate that early progenitors committed to hematopoietic development could be identified by surface expression of leukosialin (CD43). CD43 was detected on all types of emerging clonogenic progenitors before expression of CD45, persisted on differentiating hematopoietic cells, and reliably separated the hematopoietic CD34(+) population from CD34(+)CD43(-)CD31(+)KDR(+) endothelial and CD34(+)CD43(-)CD31(-)KDR(-) mesenchymal cells. Furthermore, we demonstrated that the first-appearing CD34(+)CD43(+)CD235a(+)CD41a(+/-)CD45(-) cells represent precommitted erythro-megakaryocytic progenitors. Multipotent lymphohematopoietic progenitors were generated later as CD34(+)CD43(+)CD41a(-)CD235a(-)CD45(-) cells. These cells were negative for lineage-specific markers (Lin(-)), expressed KDR, VE-cadherin, and CD105 endothelial proteins, and expressed GATA-2, GATA-3, RUNX1, C-MYB transcription factors that typify initial stages of definitive hematopoiesis originating from endothelial-like precursors. Acquisition of CD45 expression by CD34(+)CD43(+)CD45(-)Lin(-) cells was associated with progressive myeloid commitment and a decrease of B-lymphoid potential. CD34(+)CD43(+)CD45(+)Lin(-) cells were largely devoid of VE-cadherin and KDR expression and had a distinct FLT3(high)GATA3(low)RUNX1(low)PU1(high)MPO(high)IL7RA(high) gene expression profile.
Manufacturing Recombinant Adeno-Associated Viral Vectors from Producer Cell Clones (2009)

A commercial rAAV manufacturing process needs to provide a safe product at high yield, be easily scalable, regulatory-compliant, and have reasonable cost of goods. Considerations for process development include not only product quantity and quality, but also ease of obtaining equipment, performing validation, and demonstrating control. In these regards, it is usually efficient to make use of proven technologies for more established areas of manufacturing, such as cell culture and purification methods used by the recombinant protein/monoclonal antibody industry. We have focused on stable mammalian producer cell lines with adenovirus type 5 helper virus as a means of achieving these goals. This review describes our current approach for generating producer cell clones and designing a scalable, regulatory-compliant vector production and purification process that addresses any product safety concerns relating to helper virus. To date, a producer cell line-based manufacturing process has been implemented at the 250-liter production scale, with no foreseeable impediments to scaling up to commercial vector manufacturing in 2000-liter bioreactors or larger.
Nucleotide sequence of cloned cDNAs encoding human preproparathyroid hormone. (1981)

We have cloned cDNA copies of human preproparathyroid hormone in Escherichia coli after insertion of double-stranded DNA into the Pst I site of plasmid pBR322 using the poly(dG) . poly(dC) homopolymer extension technique. Recombinant plasmids coding for preproparathyroid hormone were identified by filter hybridization assay using as a probe 32P-labeled bovine preproparathyroid cDNA. Nucleotide sequence analysis of five recombinant plasmids permitted the assignment of 74 nucleotides of the 5' noncoding region, the entire coding region of 345 nucleotides, and the entire 3' noncoding region of 348 nucleotides of the mRNA. The coding sequence predicts the previously unknown "pre" amino acid sequence and clarifies the hormone's amino acid sequence, which has been disrupted. The 5' noncoding region contains an AUG codon followed by a UGA stop codon before the authentic initiator codon. The 3' noncoding region is 120 nucleotides longer than in bovine preproparathyroid mRNA and contains two A-A-U-A-A-A sequences, potential signals for polyadenylation.
Comparison of DNA Quantification Methods for Next Generation Sequencing (2016)

Next Generation Sequencing (NGS) is a powerful tool that depends on loading a precise amount of DNA onto a flowcell. NGS strategies have expanded our ability to investigate genomic phenomena by referencing mutations in cancer and diseases through large-scale genotyping, developing methods to map rare chromatin interactions (4C; 5C and Hi-C) and identifying chromatin features associated with regulatory elements (ChIP-seq, Bis-Seq, ChiA-PET). While many methods are available for DNA library quantification, there is no unambiguous gold standard. Most techniques use PCR to amplify DNA libraries to obtain sufficient quantities for optical density measurement. However, increased PCR cycles can distort the library's heterogeneity and prevent the detection of rare variants. In this analysis, we compared new digital PCR technologies (droplet digital PCR; ddPCR, ddPCR-Tail) with standard methods for the titration of NGS libraries. DdPCR-Tail is comparable to qPCR and fluorometry (QuBit) and allows sensitive quantification by analysis of barcode repartition after sequencing of multiplexed samples. This study provides a direct comparison between quantification methods throughout a complete sequencing experiment and provides the impetus to use ddPCR-based quantification for improvement of NGS quality.
Resistivity Imaging by Time Domain Electromagnetic Migration (TDEMM) (1995)

One of the most challenging problems of electrical geophysical methods is the interpretation of time domain electromagnetic (TDEM) sounding data in the areas with the horizontally inhomogeneous geoelectrical structures. This problem is of utmost importance in mining exploration and environmental study, in particular, in the case of sounding conducted in the transmitter offset or slingram mode. The conventional 1D EM inversion technique cannot solve this problem, because the observed data are strongly distorted by horizontal conductivity inhomogeneities. The multidimensional EM inversion techniques existing today can handle only simple models, require repetitive forward modeling solutions, and therefore are very time consuming.We developed a new approach to the interpretation of TDEM data over inhomogeneous structures based on downward extrapolation of the observed electromagnetic field in reverse time (the time domain electromagnetic migration). Numerical solution of this problem is provided by an electromagnetic analog of the Rayleigh integral. TDEM migration transforms EM data, observed on the surface of the Earth, into immediate geoelectrical images of geological cross sections. This transformation is very fast (requiring only a few seconds of CPU time on PC) and stable to the random noise in the data.The numerical results of rapid inversion based on the time domain electromagnetic migration illustrate the property of migration described above. This method has also been applied to waste site characterisation. We have analysed the data obtained as a result of high density TDEM profiling survey with the Geonics EM47 along the set of profiles, intersecting Cold Test Pit waste site within the Radioactive Waste Management Complex (RWMC) at the Idaho National Engineering Laboratory (INEL). Time domain electromagnetic migration and resistivity imaging made it possible to outline the conductive sections of the pit filled with the waste.
Targeted disruption ofSHIPleads to hemopoietic perturbations, lung pathology, and a shortened life span (1998)

SHIP is a 145-kD SH2-containing inositol-5-phosphatase widely expressed in hemopoietic cells. It was first identified as a tyrosine phosphoprotein associated with Shc in response to numerous cytokines. SHIP has been implicated in FcgammaRIIB receptor-mediated negative signaling in B cells and mast cells and is postulated to down-regulate cytokine signal transduction in myeloid cells. To define further its role in the proliferation and differentiation of hemopoietic progenitors, as well as its function in mature cells, we have generated embryonic stem cells and mice bearing a targeted disruption of both SHIP alleles. Here we show that although SHIP null mice are viable and fertile, they fail to thrive and survival is only 40% by 14 weeks of age. Mortality is associated with extensive consolidation of the lungs resulting from infiltration by myeloid cells. Increased numbers of granulocyte-macrophage progenitors are observed in both the bone marrow and spleen of SHIP-/- mice, perhaps as a consequence of hyper-responsiveness to stimulation by macrophage-colony stimulating factor, granulocyte-macrophage colony stimulating factor, interleukin-3, or Steel factor as observed in vitro. In contrast, numbers of bone marrow lymphoid and late erythroid progenitors (CFU-E) are reduced. Thus, homozygous disruption of SHIP establishes the crucial role of this molecule in modulating cytokine signaling within the hemopoietic system and provides a powerful model for further delineating its function.
Insulin-like growth factor receptor cooperates with integrin alpha v beta 5 to promote tumor cell dissemination in vivo. (1997)

Tumor cell interactions with adhesion proteins and growth factors likely contribute to the metastatic cascade. Evidence is provided that insulin or insulin-like growth factor-mediated signals cooperate with the commonly expressed integrin alpha v beta 5 to promote spontaneous pulmonary metastasis of multiple tumor cell types in both the chick embryo and severe combined immune deficiency mouse/human chimeric models. Expression of alpha v beta 5 in tumor cells promoted their adhesion to vitronectin in vitro. However, cell motility required cytokine stimulation, which caused redistribution of alpha-actinin to membrane-adhesive sites containing alpha v beta 5. Significantly, ligation of alpha v beta 5 and cytokine receptors were both required for spontaneous pulmonary metastasis of multiple tumor types even though it was not necessary for primary tumor growth. Thus, tumor cell metastasis can be regulated by a functional cooperation between cytokine signaling events and the adhesion receptor alpha v beta 5 in a manner independent of tumor cell growth. These findings provide evidence that integrin ligation, in conjunction with cytokine activation, plays an important role in the dissemination of malignant tumor cells.
Information Technology in the Major International Financial Markets (1993)

Financial markets perform a seemingly simple function: facilitating the transfer of securities into cash, or cash into securities. Closer inspection of the activities and the information intensity of a trading floor or a dealing room reveals great complexity. Information technology (IT) plays a crucial role in supporting maker activities, and no trader today could operate without real-time data services, and computer-based analytical tools. Market information - about prices, interest rates, transactions, investor supply and demand, and company and economic news - is at the heart of any trading operation. Consequently, the major international markets from Tokyo to Zurich are making increased use of information technology. While IT is capable of making physical marketplaces and trading floors obsolete, no consensus is emerging on the design of an integrated global financial market, and many technological and regulatory issues remain unsolved. Multiple, fragmented markets may be a consequence of the lack of coordination. This chapter highlights the technologies that are revolutionizing international financial markets. The future direction of financial markets will be charted by automation and systems, and IT'S influence on banks, securities firms, and the markets themselves will continue to be a subject of debate and controversy.
A Laboratory Approach to the Evaluation of Hereditary Hypercoagulability (1997)

The concept of hypercoagulability and especially its evaluation in the clinical laboratory has changed dramatically during the last few years. The genetic basis and the mechanisms of the various factors responsible for hypercoagulability are briefly reviewed with emphasis on the most common genetic deficiencies. The major thrust of this review centers on the cost-effective approach to examining patients with a personal or family history of venous thrombosis. Several new concepts dealing with thrombotic risk are presented with a focus on the theory that multiple factors cause thrombosis in affected patients. A proposal for a cost-effective sequential testing scheme for the accurate diagnosis of hereditary hypercoagulability is discussed. The knowledge of thrombotic risk factors is evolving rapidly, requiring the clinical laboratory to remain flexible. Ultimately, the clinical laboratory must take a leading role in the diagnosis of hereditary thrombotic disease by serving as the consultant to the primary caregiver by providing an up-to-date and cost-effective evaluation.
Prospective study comparing hyoscyamine, doxazosin, and combination therapy for the treatment of urgency and frequency in women (1998)

Anticholinergics are commonly used for the treatment of frequency, urgency, and urge incontinence in women. Alpha-blockers have been shown to have a modulating effect on bladder smooth muscle but are not commonly used clinically for this indication. To evaluate the clinical effectiveness of each treatment as well as the combination therapy, we performed an open prospective study comparing these agents. Between September 1994 and October 1995, 34 women aged 28-91 (mean age, 62) received either 0.375 mg of sustained-release hyoscyamine twice a day or 2 mg doxazosin QHS prior to being crossed over to the other drug and/or the combination. Symptoms were assessed using an expanded American Urological Association (AUA) symptoms score, which included questions regarding incontinence at completion of each therapeutic phase. Evaluation included 6-channel urodynamics. All three therapies were noted to be effective in reducing AUA symptom scores. By urodynamic evaluation, a greater percentage of patients with increased voiding pressures or decreased compliance responded to doxazosin than hyoscyamine. Side effects were noted to be less prevalent with doxazosin than with the other therapies. There appears to be a significant role for alpha-blockers in the treatment of voiding symptoms in women.
Phage Display (1997)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhage DisplayGeorge P. Smith and Valery A. PetrenkoView Author Information Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 Cite this: Chem. Rev. 1997, 97, 2, 391–410Publication Date (Web):April 1, 1997Publication History Received2 January 1997Revised23 January 1997Published online1 April 1997Published inissue 1 April 1997https://pubs.acs.org/doi/10.1021/cr960065dhttps://doi.org/10.1021/cr960065dresearch-articleACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views19658Altmetric-Citations1355LEARN 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 SUBJECTS:Genetics,Monomers,Peptides and proteins,Receptors,Viruses Get e-Alerts
PKC δ-isoform translocation and enhancement of tonic contractions of gastrointestinal smooth muscle (2006)

PKC is involved in mediating the tonic component of gastrointestinal smooth muscle contraction in response to stimulation by agonists for G protein-coupled receptors. Here, we present pharmacological and immunohistochemical evidence indicating that a member of the novel PKC isoforms, PKC-delta, is involved in maintaining muscarinic receptor-coupled tonic contractions of the guinea pig ileum. The tonic component of carbachol-evoked contractions was enhanced by an activator of conventional and novel PKCs, phorbol 12,13-dibutyrate (PDBu; 200 nM or 1 microM), and by an activator of novel PKCs, ingenol 3,20-dibenzoate (IDB; 100 or 500 nM). Enhancement was unaffected by concentrations of bisindolylmaleimide I (BIM-I; 22 nM) that block conventional PKCs or by a PKC-epsilon-specific inhibitor peptide but was attenuated by higher doses of BIM-I (2.2 microM). Relevant proteins were localized at a cellular and subcellular level using confocal analysis. Immunohistochemical staining of the ileum showed that PKC-delta was exclusively expressed in smooth muscles distributed throughout the layers of the gut wall. PKC-epsilon immunoreactivity was prominent in enteric neurons but was largely absent from smooth muscle of the muscularis externa. Treatment with PDBu, IDB, or carbachol resulted in a time- and concentration-dependent translocation of PKC-delta from the cytoplasm to filamentous structures within smooth muscle cells. These were parallel to, but distinct from, actin filaments. The translocation of PKC-delta in response to carbachol was significantly reduced by scopolamine or calphostin C. The present study indicates that the tonic carbachol-induced contraction of the guinea pig ileum is mediated through a novel PKC, probably PKC-delta.