gebhart/patrepeval huggingface dataset:
Origin of CD4-CD8-B220+ T cells in MRL-lpr/lpr mice. Clues from a T cell receptor beta transgenic mouse (1993)

Abnormal development of T cells in the thymus is thought to be related to autoimmune disease and the expansion of the unusual CD4-CD8-B220+ peripheral T cel subset that results in lymphadenopathy in MRL-lpr/lpr mice. Although we and others have previously shown that rearranged TCR-transgenes alter T cell development in the thymus and abrogate lymphoproliferative disease in lpr mice, the origin and developmental pathway of the LN CD4-CD8-B220+ T cells has not been fully elucidated. We therefore undertook the systematic analysis of the effect of a TCR-beta transgene on the production and differentiation of (lymph node) LN T cells and the production, differentiation, and release of thymocyte T cell populations. In nontransgenic mice, there was increased proliferation of CD4-CD8-B220+ T cells in the LN of adult MRL-lpr/lpr mice compared to MRL(-)+/+ mice, as measured by in vivo BrdU labeling. These proliferating LN T cells were greatly reduced by thymectomy of adult MRL-lpr/lpr mice 1 wk before bromodeoxyuridine labeling, indicating that recent thymic emigrants or factors were required to sustain proliferation. In the thymus, there was increased production and accumulation of CD4+CD8+TCRdull thymocytes in nontransgenic MRL-lpr/lpr compared to MRL(-)+/+ mice. As the rate of maturation from CD4+CD8+TCRdull to CD4+CD8+TCRbright was the same (6%) in both MRL-lpr/lpr and MRL(-)+/+ mice, the accumulation of the immature population in the MRL-lpr/lpr mice could not be due to a maturation defect. However, there was a decrease in apoptosis and intrathymic death of CD4+CD8+TCRdull thymocytes in MRL-lpr/lpr compared to MRL(-)+/+ mice. Introduction of the TCR-beta transgene into lpr/lpr mice normalized the proliferation of T cells in the LN. In the thymus, the TCR-beta transgene resulted in a dramatic increase in maturation efficiency and a reduction in apoptosis in MRL(-)+/+ mice. These data suggest that the TCR transgene inhibits lymphoproliferation by reducing the production of "neglected" CD4+CD8+TCRdull thymocytes that will undergo Fas Ag-mediated apoptosis. They further suggest that in lpr mice, which express a mutated Fas Ag, the "neglected" thymocytes are able to continually escape to the periphery, where they proliferate.
Antibody-Enhanced Infection by HIV-1 Via Fc Receptor-Mediated Entry (1988)

Monocytes and macrophages, which may play a central role in the pathogenesis of infection with human immunodeficiency virus type 1 (HIV-1), express the CD4 molecule and Fc receptors (FcR) for immunoglobulin G (IgG). To explore the possibility that FcR mediate HIV-1 infection of monocytes, studies were conducted with the human monocytic cell line U937. These cells were exposed to HIV-1 complexed with various concentrations of serum from HIV-1 antibody-positive individuals and monitored for HIV-1 replication. Serum samples from antibody-negative normal individuals did not affect virus yields. High concentrations of antibody-positive sera showed virus-neutralizing activity; however, cells infected with HIV-1 in the presence of antibody-positive sera at subneutralizing concentrations significantly enhanced virus replication. This infection enhancement was blocked by heat-aggregated gamma-globulin. Moreover, the IgG fraction from an HIV-1 antibody-positive serum enhanced HIV-1 infection at the same serum dilution equivalents. In contrast, IgG-F(ab')2 did not enhance HIV-1 infection but showed neutralizing activity with HIV-1. These results are compatible with the concept of FcR-mediated infection enhancement and suggest that this immunological response to HIV-1, instead of protecting the host, potentially facilitates the infection.
plotROC: A Tool for Plotting ROC Curves (2017)

Plots of the receiver operating characteristic (ROC) curve are ubiquitous in medical research. Designed to simultaneously display the operating characteristics at every possible value of a continuous diagnostic test, ROC curves are used in oncology to evaluate screening, diagnostic, prognostic and predictive biomarkers. I reviewed a sample of ROC curve plots from the major oncology journals in order to assess current trends in usage and design elements. My review suggests that ROC curve plots are often ineffective as statistical charts and that poor design obscures the relevant information the chart is intended to display. I describe my new R package that was created to address the shortcomings of existing tools. The package has functions to create informative ROC curve plots, with sensible defaults and a simple interface, for use in print or as an interactive web-based plot. A web application was developed to reach a broader audience of scientists who do not use R.
Reversible axonal neuropathy from the treatment of AIDS and related disorders with 2′,3′‐dideoxycytidine (ddc) (1989)

A total of 20 patients with acquired immune deficiency syndrome (AIDS) or AIDS-related complex (ARC) received the anti-retroviral drug 2',3',dideoxycytidine in a phase I study at doses ranging from 0.03 mg/kg every 8 hours to 0.25 mg/kg every 8 hours. Of the 11 patients who participated in the study for more than 5 weeks, 9 developed symptoms and signs of a mainly sensory painful neuropathy that was confirmed by electromyography to be mixed sensory and motor neuropathy of axonal type. The neuropathy which developed on dideoxycytidine occurred between 9 and 12 weeks of treatment. One patient, who had the drug stopped at 3 weeks owing to thrombocytopenia, developed a similar clinical picture of a sensory peripheral neuropathy after 2 weeks off dideoxycytidine. However, he did not have electromyographic evidence of a neuropathy, and he subsequently returned to normal clinically while taking a lower dose of dideoxycytidine in an alternating regimen. Five patients were withdrawn from the study because of the neuropathy. The pattern of this neuropathy was different from that of the slowly progressive painful neuropathy of AIDS, in that there was (1) a sudden onset of intense burning discomfort in both feet sparing the hands at about the tenth week (mean 10.4 weeks) of treatment, (2) there was motor involvement in some patients without progression, and (3) onset of the neuropathy was temporally related to the administration of dideoxycytidine and began to resolve 3-5 weeks after its discontinuation. We believe that dideoxycytidine can be an axonal toxin, especially when given in high dose continuous regimens.(ABSTRACT TRUNCATED AT 250 WORDS)
Production of infectious human respiratory syncytial virus from cloned cDNA confirms an essential role for the transcription elongation factor from the 5' proximal open reading frame of the M2 mRNA in gene expression and provides a capability for vaccine development. (1995)

Infectious human respiratory syncytial virus (RSV) was produced by the intracellular coexpression of five plasmid-borne cDNAs. One cDNA encoded a complete positive-sense version of the RSV genome (corresponding to the replicative intermediate RNA or antigenome), and each of the other four encoded a separate RSV protein, namely, the major nucleocapsid N protein, the nucleocapsid P phosphoprotein, the major polymerase L protein, or the protein from the 5' proximal open reading frame of the M2 mRNA [M2(ORF1)]. RSV was not produced if any of the five plasmids was omitted. The requirement for the M2(ORF1) protein is consistent with its recent identification as a transcription elongation factor and confirms its importance for RSV gene expression. It should thus be possible to introduce defined changes into infectious RSV. This should be useful for basic studies of RSV molecular biology and pathogenesis; in addition, there are immediate applications to the development of live attenuated vaccine strains bearing predetermined defined attenuating mutations.
Epidermal growth factor receptor signaling intensity determines intracellular protein interactions, ubiquitination, and internalization (2003)

Ligand activation of the epidermal growth factor receptor (EGFR) causes the binding of Cbls, which leads to EGFR polyubiquitination and internalization through endophilin complexes that contain the adaptor protein SH3-domain encoding, expressed in tumorigenic astrocytes/Cbl-interacting protein of 85 kDa/regulator of ubiquitous kinase (SETA/CIN85/Ruk). In cells grown at high density, high levels of SETA interfered in the recruitment of Casitas B-lineage (Cbl) proteins to the EGFR and reduced its polyubiquitination, suggesting that SETA has a regulatory function in the formation of the EGFR-Cbl-endophilin complex and in EGFR down-regulation. In a situation where there is EGFR signaling but no internalization or down-regulation, as is the case with the EGFR with exons 2-7 deleted (DeltaEGFR) oncogene, these proteins were absent altogether. By using mAb 806, which recognizes an EGFR-activation state and preferentially immunoprecipitates DeltaEGFR, we show that DeltaEGFR did not interact with Cbls, SETA, or endophilin A1, providing a mechanistic explanation for its lack of internalization. As would be expected by the absence of Cbl proteins in the DeltaEGFR complex, the mutant receptor was also not polyubiquitinated. The intracellular C terminus and tyrosine autophosphorylation pattern of DeltaEGFR are similar to wild-type EGFR, but it signals at a lower intensity as determined by levels of EGFR phosphotyrosine. To test the implication that the lack of interaction with the Cbl-SETA-endophilin complex is because of differences in signal intensity, EGFR-expressing cells were treated with tyrphostin AG1478 EGFR inhibitor. Attenuation of wild-type EGFR signal to levels similar to that found in DeltaEGFR resulted in the dissociation of SETA and Cbl proteins and a concomitant attenuation of receptor internalization.
Early diagnosis of acute myocardial infarction by myoglobin latex agglutination test. (1988)

Early elevation of the serum myoglobin level in acute myocardial infarction (AMI) has been noted for years. In this study, 39 patients admitted to the Coronary Care Unit with acute chest pain within 72 hours (mean 12 +/- 15 hours) or electrocardiographic changes suspected of acute myocardial infarction had a serum myoglobin latex agglutination test to evaluate its diagnostic accuracy in acute myocardial infarction. Of these 39 patients, 24 had documented acute myocardial infarction as their final diagnosis. By the time of admission, 18 of the 24 cases with infarction had positive myoglobin tests (sensitivity 75%). Of those 15 cases without myocardial infarction, 13 had negative myoglobin tests (specificity 87%). If only those 17 cases admitted within 5 hours of the onset of chest pain were analyzed, the serum myoglobin test became positive in 8 of 10 cases with documented AMI but the 2 cases with negative results turned positive 2 hours later (sensitivity 80% to 100%). Due to the fact that myoglobin tests were negative in all other 7 cases without infarction, the specificity was 7/7 (100%). In contrast, the creatine phosphokinase isoenzyme study was positive only in 3 of these 10 patients with documented AMI in the first blood sample taken during admission. In conclusion, the serum myoglobin latex agglutination test is a quick and reliable method that helps in the early diagnosis of acute myocardial infarction.
PLASMA PROTEIN TURNOVER AND TISSUE EXCHANGE (1959)

The rate of plasma protein turnover is more rapid in dogs receiving adequate dietary protein than when a diet devoid of protein is fed. Both albumin and combined globulins are involved in this change. The difference in turnover is reflected in a total protein half-life of 4.8 days with protein feeding versus 7.8 days without protein in the diet and in the metabolism of 1.0 and 0.65 gm. per kilogram of body weight per day on the respective diets. Additions of dietary protein from 10 to 30 per cent caused no further increase in the rate of plasma protein turnover. With protein depletion due to plasmapheresis and a very low protein diet there is evidence of reduced protein metabolism as indicated by nitrogen retention as well as a reduction in total plasma protein breakdown and interchange of isotope between plasma and tissue proteins. Following introduction of labeled plasma protein into the circulation the net amount of isotope transferred to tissues has been computed from the difference between total plasma protein breakdown and combined C(14) excretion in urine and expired air. In animals receiving adequate dietary protein, tissue transfer amounts to 70 per cent of the total lost from the plasma proteins each day while the percentage rises to 85 in depleted dogs deprived of protein. In dogs with both plasma and tissue proteins labeled it can be estimated that, under conditions of protein feeding, an amount of C(14) approximately equal to that lost from the plasma must recycle to account for the observed decrease in Apparent plasma protein turnover rate, (t(1/2) of 15 versus 5 days). Without protein in the diet the isotope contribution of the tissues to the maintenance of plasma protein levels must be as great as or greater than that transferred in the opposite direction.
A Polymorphism in the CDKN1B Gene Is Associated with Increased Risk of Hereditary Prostate Cancer (2004)

The loss of cell cycle control is believed to be an important mechanism in the promotion of carcinogenesis. CDKN1B (p27) belongs to the Cip/Kip family and functions as an important cell cycle gatekeeper. Several lines of evidence from clinical studies and laboratory experiments demonstrate that CDKN1B is an important tumor suppressor gene in prostate cancer etiology. In addition, a case-control study has shown that the 326T/G (V109G) polymorphism in CDKN1B is associated with advanced prostate cancer. In light of the evidence for linkage between the chromosomal location of the CDKN1B gene (12p13) and prostate cancer susceptibility in several hereditary prostate cancer (HPC) populations, we hypothesized that sequence variants of CDKN1B play a role in HPC. To test this hypothesis, we first resequenced this gene in 96 HPC probands to identify germ-line mutations and sequence variants. We then genotyped the identified sequence variants among all family members of 188 HPC families and tested for their cosegregation with prostate cancer. In total, 10 sequence variants were identified, including three nonsynonymous changes. A family-based test, which is free from the effects of population stratification, revealed a significant association between single nucleotide polymorphism (SNP) -79C/T and prostate cancer (with a nominal P of 0.0005). The C allele of -79C/T was overtransmitted from parents to their affected offspring. Evidence for this association was primarily contributed by affected offspring whose age at diagnosis was <65 years. Together with the previous association study in a sporadic prostate cancer population, our new findings additionally suggest that germ-line variants of this gene play a role in prostate cancer susceptibility.
Renal Effects of DPP-4 Inhibitors: A Focus on Microalbuminuria (2013)

Incretin-based therapies represent one of the most promising options in type 2 diabetes treatment owing to their good effectiveness with low risk of hypoglycemia and no weight gain. Other numerous potential beneficial effects of incretin-based therapies have been suggested based mostly on experimental and small clinical studies including its beta-cell- and vasculo-protective actions. One of the recently emerged interesting features of dipeptidyl peptidase-4 (DPP-4) inhibitors is its possible protective effect on the diabetic kidney disease. Here, we review the renal effects of DPP-4 inhibitors with special focus on its influence on the onset and progression of microalbuminuria, as presence of microalbuminuria represents an important early sign of kidney damage and is also associated with increased risk of hypoglycemia and cardiovascular complications. Mechanisms underlying possible nephroprotective properties of DPP-4 inhibitors include reduction of oxidative stress and inflammation and improvement of endothelial dysfunction. Effects of DPP-4 inhibitors may be both glucagon-like peptide-1 (GLP-1) dependent and independent. Ongoing prospective studies focused on the nephroprotective effects of DPP-4 inhibitors will further clarify its possible role in the prevention/attenuation of diabetic kidney disease beyond its glucose lowering properties.
The Cellular src Gene Product Regulates Junctional Cell-to-Cell Communication (1988)

Overexpression of the cellular src gene in NIH 3T3 cells causes reduction of cell-to-cell transmission of molecules in the 400- to 700-dalton range. This down-regulation of gap junctional communication correlates with the activity of the gene product, the protein tyrosine kinase pp60c-src. The down-regulation was enhanced by point mutation of Tyr527 (a site that is phosphorylated in pp60c-src and that inhibits kinase activity) or by substitution of the viral-src for the cellular-src carboxyl-terminal coding region. Mutation of Tyr416 (a site phosphorylated upon Tyr527 mutation) suppresses both the down-regulation of communication by Tyr527 mutation and that by gene overexpression. The regulation of communication by src may be important in the control of embryonic development and cellular growth.
A new drug-delivery-system of anticancer agents: activated carbon particles adsorbing anticancer agents. (1992)

A new drug delivery system comprizing activated carbon particles adsorbing anticancer agents has been developed in order to enhance anticancer efficacy on local lesions and to reduce systemic toxicity. The system is designed to release the adsorbed anticancer agent slowly at a designated concentration level at the local site, and to allow the agent to remain for a long time at the local site, with affinity for the lymphatic system and the surface of cancer cells. Through this process, anticancer efficacy is enhanced at the local lesion and systemic toxicity decreases. Because the size of the particles influences the distribution of the agent, size is selected according to both targeted organs, i.e. lymphatic metastases, carcinomatous peritonitis, and administration methods, i.e. intramural, intracavitary, intrabronchial, or intratumoral administration.
Reduced‐bond tight‐binding inhibitors of HIV‐1 protease Fine tuning of the enzyme subsite specificity (1992)

Truncation of a peptide substrate in the N-terminus and replacement of its scissile amide bond with a non-cleavable reduced bond results in a potent inhibitor of HIV-1 protease. A series of such inhibitors has been synthesized, and S2-S3' subsites of the protease binding cleft mapped. The S2 pocket requires bulky Boc or PIV groups, large aromatic Phe residues are preferred in P1 and P1' and Glu in P2'. The S3' pocket prefers Phe over small Ala or Val. Introduction of a Glu residue into the P2' position yields a tight-binding inhibitor of HIV-1 protease, Boc-Phe-[CH2-NH]-Phe-Glu-Phe-OMe, with a subnanomolar inhibition constant. The relevant peptide derived from the same amino acid sequence binds to the protease with a Ki of 110 nM, thus still demonstrating a good fit of the amino acid residues into the protease binding pockets and also the importance of the flexibility of P1-P1' linkage for proper binding. A new type of peptide bond mimetic, N-hydroxylamine -CH2-N(OH)-, has been synthesized. Binding of hydroxylamino inhibitor of HIV-1 protease is further improved with respect to reduced-bond inhibitor.
Autologous tumor-lysate pulsed dendritic cell vaccination, together with the TLR-7 agonist 5% imiquimod, and serum pro- inflammatory cytokine levels in glioblastoma patients (2008)

11021 Background: Standard therapy for glioblastoma, which includes surgery followed by radiation and concurrent chemotherapy, creates a low tumor burden environment that could be ideal for immunotherapeutic approaches. We conducted a Phase I study to assess the safety and immunologic responses of tumor lysate-pulsed dendritic cell (DC) therapy plus topical imiquimod, in combination with standard radio-chemotherapy. Methods: Thirteen patients with newly diagnosed glioblastoma were immunized using autologous tumor lysate-pulsed DC at 2-week intervals, following completion of radio-chemotherapy. The primary clinical endpoint was 2-year survival. Patients without tumor progression subsequently received booster vaccinations combined with topical administration of the TLR-7 agonist, imiquimod. Immunologic responses to tumor antigens were monitored by tetramer staining and intracellular cytokine staining. Measurement of serum cytokine levels (TH1/TH2: IFN-γ, TNF-α, IL-2, IL-4, IL-6, IL-10) was performed using cytometric bead arrays (CBA). Global gene expression profiling was also performed on pre-treatment tumor samples. Results: All immunizations were well tolerated, with only mild side effects attributable to the DC vaccination and imiquimod adjuvant. Increased levels of CD8+ T cells reactive against tumor antigens, (e.g., gp100, TRP-2, her-2, survivin, and CMV antigens), were detected in 5 patients. CBA measurement of serum cytokine levels revealed small, but detectable levels of TNF-α following the initial DC vaccination. Robust increases in serum TNF-α and IL-6 were observed after booster vaccinations, temporally correlating with imiquimod administration. Clinically, 8 of the 13 patients have progressed, and 6 of those have died. The median PFS to date is 13.9 mos. and median OS is 33.8 mos. This compares favorably to the published literature, with a median PFS of 6.9 mos and OS of 14.6 mos. Conclusions: This study demonstrates the safety and clinical/immunologic effects of an autologous tumor lysate-pulsed DC vaccine for patients with newly diagnosed glioblastoma. Serum TNFα responses may portend therapeutic anti-tumor immune responses to DC vaccination. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Northwest Biotherapeutics, Inc. Northwest Biotherapeutics, Inc. Northwest Biotherapeutics, Inc.
Baculoviruses as vectors for foreign gene expression in insect cells (1990)

Abstract Recombinant DNA technology has enabled the expression of a large number of eukaryotic genes in vitro. There has been growing interest in recent years in the development of baculovirus expression vectors as an easily manipulated gene expression system. Both virus and insect cell culture are relatively easy to handle, and biologically active proteins have been produced abundantly from a variety of eukaryotic, prokaryotic and viral genes. This review describes the molecular biology of baculoviruses and some of the current applications of the baculovirus expression system in insect cells. Specific emphasis is placed on those features relevant to the use of this system in pesticide research .