gebhart/patrepeval huggingface dataset:
Interferon-dependent transcriptional activation: signal transduction without second messenger involvement? (1990)

Two specific macromolecular interactions are known to underlie the demonstrated transcriptional stimulation of different sets of genes incident to the binding of different polypeptide ligands to cells. The initial polypeptide-receptor interaction is widely recognized to be specific. It is also well established that the binding of specific transcription factors to well-defined DNA sites activates specific genes. In this paper, we suggest that a third, equally specific protein-protein interaction links the first two specific interactions and ensures the high specificity required in these pathways. We propose that a receptor-recognition protein is required to recognize the bound receptor. This receptor-recognition protein might itself be part of a transcription factor or might interact directly with a transcription factor that would thereby be activated and translocated to the nucleus to participate in gene activation. According to this hypothesis, no global changes in second messenger concentrations are necessary, and the enzymatic properties of the receptor-recognition protein(s) need not be specified. Phosphorylations of, or by, receptor-bound proteins would not, of course, be excluded. But such modifications during ligand-mediated signal transduction would not depend on global second messenger changes. This model is derived from studies of the proteins involved in interferon (IFN)-stimulated gene transcription. It is now established that interferon-alpha (IFN alpha) activates a multisubunit transcription factor in the cell cytoplasm, and that this factor then moves to the nucleus to activate a set of IFN-stimulated genes.(ABSTRACT TRUNCATED AT 250 WORDS)
Soluble CD26/Dipeptidyl Peptidase IV Induces T Cell Proliferation Through CD86 Up-Regulation on APCs (2001)

CD26 is a T cell costimulatory molecule with dipeptidyl peptidase IV enzyme activity in its extracellular region. We have previously reported that the addition of soluble CD26 (sCD26) resulted in enhanced proliferation of peripheral blood T lymphocytes induced by the recall Ag, tetanus toxoid (TT). However, the mechanism involved in this immune enhancement has not yet been elucidated. In this paper, we demonstrate that the enhancing effect of sCD26 on TT-induced T cell proliferation occurred in the early stages of immune response. The cells directly affected by exogenously added sCD26 are the CD14-positive monocytes in the peripheral blood. Mannose-6 phosphate interfered with the uptake of sCD26 into monocytes, suggesting that mannose-6 phosphate/insulin-like growth factor II receptor plays a role in the transportation of sCD26 into monocytes. When sCD26 was added after Ag presentation had taken place, enhancement in TT-induced T cell proliferation was not observed. In addition, enhancement of TT-mediated T cell proliferation by sCD26 does not result from trimming of the MHC-bound peptide on the surface of monocytes. Importantly, we also showed that exogenously added sCD26 up-regulated the expression of the costimulatory molecule CD86 on monocytes through its dipeptidyl peptidase IV activity, and that this increased expression of CD86 was observed at both protein and mRNA level. Therefore, our findings suggest that sCD26 enhances T cell immune response to recall Ag via its direct effect on APCs.
Lewis Acid-Promoted Reactions of Unsymmetrically Substituted Stilbenes with 2-Methoxy-1,4-benzoquinones: Stereoselective Synthesis of trans-2,3-Diaryl-2,3-dihydrobenzofurans (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLewis Acid-Promoted Reactions of Unsymmetrically Substituted Stilbenes with 2-Methoxy-1,4-benzoquinones: Stereoselective Synthesis of trans-2,3-Diaryl-2,3-dihydrobenzofuransThomas A. Engler, Gregory A. Gfesser, and Bill W. DraneyCite this: J. Org. Chem. 1995, 60, 12, 3700–3706Publication Date (Print):June 1, 1995Publication History Published online1 May 2002Published inissue 1 June 1995https://pubs.acs.org/doi/10.1021/jo00117a021https://doi.org/10.1021/jo00117a021research-articleACS PublicationsRequest reuse permissionsArticle Views349Altmetric-Citations33LEARN 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-AlertscloseSupporting Info (3)»Supporting Information Supporting Information Get e-Alerts
The Prioritization of Cancer Antigens: A National Cancer Institute Pilot Project for the Acceleration of Translational Research (2009)

The purpose of the National Cancer Institute pilot project to prioritize cancer antigens was to develop a well-vetted, priority-ranked list of cancer vaccine target antigens based on predefined and preweighted objective criteria. An additional aim was for the National Cancer Institute to test a new approach for prioritizing translational research opportunities based on an analytic hierarchy process for dealing with complex decisions. Antigen prioritization involved developing a list of "ideal" cancer antigen criteria/characteristics, assigning relative weights to those criteria using pairwise comparisons, selecting 75 representative antigens for comparison and ranking, assembling information on the predefined criteria for the selected antigens, and ranking the antigens based on the predefined, preweighted criteria. Using the pairwise approach, the result of criteria weighting, in descending order, was as follows: (a) therapeutic function, (b) immunogenicity, (c) role of the antigen in oncogenicity, (d) specificity, (e) expression level and percent of antigen-positive cells, (f) stem cell expression, (g) number of patients with antigen-positive cancers, (h) number of antigenic epitopes, and (i) cellular location of antigen expression. None of the 75 antigens had all of the characteristics of the ideal cancer antigen. However, 46 were immunogenic in clinical trials and 20 of them had suggestive clinical efficacy in the "therapeutic function" category. These findings reflect the current status of the cancer vaccine field, highlight the possibility that additional organized efforts and funding would accelerate the development of therapeutically effective cancer vaccines, and accentuate the need for prioritization.
MobiDriveScore &#x2014; A system for mobile sensor based driving analysis: A risk assessment model for improving one's driving (2013)

Assessment of driving behavior and estimation of risk therein is an important use case for telematics and vehicular networking technology domain, which has gained interest in the fleet management and consumer verticals, but above all with the car insurance firms. These firms have started incorporating the results of such analysis to provide their customers with "pay as you drive" insurance plans, which decide the initial premium based on the driver's past history of crashes and violations. Then the parties enter into an evaluation period of about two months (say), at the end of which premium is recalculated based on analysis of accelerometer, GPS and on-board diagnostic (OBD II) data. However, the consumer has no knowledge of the progress of his or her evaluation due to lack of access to device data from insurance provider. One major criterion of such evaluation is based on the detection and aggregation of high-risk maneuvers by the driver, which typically constitutes of hard bump, sharp cornering, hard stop and speed limit violations. In this paper, we propose a novel method named MobiDriveScore for routine ventures using which the consumer can assess his/her own driving pattern. Thus the consumer can consciously reduce the risk associated with his/her driving by using MobiDriveScore. For MobiDriveScore, detection of maneuvers is done using accelerometer and GPS sensors only, which are integral part of modern day smartphones. Using MobiDriveScore, the user can choose an alternate route or choose to travel a little early to improve upon the premium rates and stay safe. It will also help aggressive drivers to become more passive. Experiments have been conducted and the initial results of MobiDriveScore are found to be encouraging.
Field effect in cancer-an update. (2009)

The concept "field effect in cancer" originated in 1953 from the histopathological observations of Slaughter and colleagues [1] regarding the occurrence of multiple primary oral squamous cell carcinomas and their local recurrences. The development of modern molecular technologies has extended the field effect concept by exploring the molecular abnormalities in tissues that appear histologically normal. To date, such field effect biomarkers have been reported in several sites and organs, eg, head and neck, colon and rectum, prostate, breast, lung, esophagus, stomach, and skin. Two popular hypotheses have been proposed. One hypothesis implicates genetic alterations that occur in a stepwise fashion (initiation, promotion, and progression); a clone gains growth advantage and acquires more genetic alterations, which eventually result in cancer. A second hypothesis focuses on epigenetic alterations, which include hypermethylation of the DNA promoter of certain tumor suppressor genes, leading to down-regulation of these genes. In this update, we discuss in detail the evidence that supports these two hypotheses. In addition, we attempt to provide a comprehensive overview of the field effect in carcinogenesis and its possible mechanisms in various organs. Moreover, we discuss the potential utilization of field effect biomarkers in cancer prevention, surgical considerations, and clinical prognosis.
Cell-Specific Aptamers as Emerging Therapeutics (2011)

Aptamers are short nucleic acids that bind to defined targets with high affinity and specificity. The first aptamers have been selected about two decades ago by an in vitro process named SELEX (systematic evolution of ligands by exponential enrichment). Since then, numerous aptamers with specificities for a variety of targets from small molecules to proteins or even whole cells have been selected. Their applications range from biosensing and diagnostics to therapy and target-oriented drug delivery. More recently, selections using complex targets such as live cells have become feasible. This paper summarizes progress in cell-SELEX techniques and highlights recent developments, particularly in the field of medically relevant aptamers with a focus on therapeutic and drug-delivery applications.
High-Precision Dispensing of Nanoliter Biofluids on Glass Pedestal Arrays for Ultrasensitive Biomolecule Detection (2016)

Precise dispensing of nanoliter droplets is necessary for the development of sensitive and accurate assays, especially when the availability of the source solution is limited. Conventional approaches are limited by imprecise positioning, large shear forces, surface tension effects, and high costs. To address the need for precise and economical dispensing of nanoliter volumes, we developed a new approach where the dispensed volume is dependent on the size and shape of defined surface features, thus freeing the dispensing process from pumps and fine-gauge needles requiring accurate positioning. The surface we fabricated, called a nanoliter droplet virtual well microplate (nVWP), achieves high-precision dispensing (better than ±0.5 nL or ±1.6% at 32 nL) of 20-40 nL droplets using a small source drop (3-10 μL) on isolated hydrophilic glass pedestals (500 μm on a side) bonded to arrays of polydimethylsiloxane conical posts. The sharp 90° edge of the glass pedestal pins the solid-liquid-vapor triple contact line (TCL), averting the wetting of the glass sidewalls while the fluid is prevented from receding from the edge. This edge creates a sufficiently large energy barrier such that microliter water droplets can be poised on the glass pedestals, exhibiting contact angles greater >150°. This approach relieves the stringent mechanical alignment tolerances required for conventional dispensing techniques, shifting the control of dispensed volume to the area circumscribed by the glass edge. The effects of glass surface chemistry and dispense velocity on droplet volume were studied using optical microscopy and high-speed video. Functionalization of the glass pedestal surface enabled the selective adsorption of specific peptides and proteins from synthetic and natural biomolecule mixtures, such as venom. We further demonstrate how the nVWP dispensing platform can be used for a variety of assays, including sensitive detection of proteins and peptides by fluorescence microscopy or MALDI-TOF.
Overexpression of FK506-Binding Protein FKBP12.6 in Cardiomyocytes Reduces Ryanodine Receptor–Mediated Ca 2+ Leak From the Sarcoplasmic Reticulum and Increases Contractility (2001)

The FK506-binding protein FKBP12.6 is tightly associated with the cardiac sarcoplasmic reticulum (SR) Ca(2+)-release channel (ryanodine receptor type 2 [RyR2]), but the physiological function of FKBP12.6 is unclear. We used adenovirus (Ad)-mediated gene transfer to overexpress FKBP12.6 in adult rabbit cardiomyocytes. Western immunoblot and reverse transcriptase-polymerase chain reaction analysis revealed specific overexpression of FKBP12.6, with unchanged expression of endogenous FKBP12. FKBP12.6-transfected myocytes displayed a significantly higher (21%) fractional shortening (FS) at 48 hours after transfection compared with Ad-GFP-infected control cells (4.8+/-0.2% FS versus 4+/-0.2% FS, respectively; n=79 each; P:=0.001). SR-Ca(2+) uptake rates were monitored in beta-escin-permeabilized myocytes using Fura-2. Ad-FKBP12.6-infected cells showed a statistically significant higher rate of Ca(2+) uptake of 0.8+/-0.09 nmol/s(-)(1)/10(6) cells (n=8, P:<0.05) compared with 0.52+/-0.1 nmol/s(-)(1)/10(6) cells in sham-infected cells (n=8) at a [Ca(2+)] of 1 micromol/L. In the presence of 5 micromol/L ruthenium red to block Ca(2+) efflux via RyR2, SR-Ca(2+) uptake rates were not significantly different between groups. From these measurements, we calculate that SR-Ca(2+) leak through RyR2 is reduced by 53% in FKBP12.6-overexpressing cells. Caffeine-induced contractures were significantly larger in Ad-FKBP12.6-infected myocytes compared with Ad-GFP-infected control cells, indicating a higher SR-Ca(2+) load. Taken together, these data suggest that FKBP12.6 stabilizes the closed conformation state of RyR2. This may reduce diastolic SR-Ca(2+) leak and consequently increase SR-Ca(2+) release and myocyte shortening.
Molecular Cloning and Characterization of Endosialin, a C-type Lectin-like Cell Surface Receptor of Tumor Endothelium (2001)

Endosialin, the antigen identified with monoclonal antibody FB5, is a highly restricted 165-kDa cell surface glycoprotein expressed by tumor blood vessel endothelium in a broad range of human cancers but not detected in blood vessels or other cell types in many normal tissues. Functional analysis of endosialin has been hampered by a lack of information about its molecular structure. In this study, we describe the purification and partial amino acid sequencing of endosialin, leading to the cloning of a full-length cDNA with an open reading frame of 2274 base pairs. The endosialin cDNA encodes a type I membrane protein of 757 amino acids with a predicted molecular mass of 80.9 kDa. The sequence matches with an expressed sequence tag of unknown function in public data bases, named TEM1, which was independently linked to tumor endothelium by serial analysis of gene expression profiling. Bioinformatic evaluation classifies endosialin as a C-type lectin-like protein, composed of a signal leader peptide, five globular extracellular domains (including a C-type lectin domain, one domain with similarity to the Sushi/ccp/scr pattern, and three EGF repeats), followed by a mucin-like region, a transmembrane segment, and a short cytoplasmic tail. Carbohydrate analysis shows that the endosialin core protein carries abundantly sialylated, O-linked oligosaccharides and is sensitive to O-sialoglycoprotein endopeptidase, placing it in the group of sialomucin-like molecules. The N-terminal 360 amino acids of endosialin show homology to thrombomodulin, a receptor involved in regulating blood coagulation, and to complement receptor C1qRp. This structural kinship may indicate a function for endosialin as a tumor endothelial receptor for as yet unknown ligands, a notion now amenable to molecular investigation.
Three new monoclonal antibodies that define a unique antigen associated with prolymphocytic leukemia/non-Hodgkin‧s lymphoma and are effectively internalized after binding to the cell surface antigen (1993)

Prolymphocytic leukemia (PLL) is closely related to chronic lymphocytic leukemia (CLL), but present with distinctive clinical/laboratory features and associated with much worse prognosis. In this study, we generated three new IgG1-kappa monoclonal antibodies (MoAbs), termed SN8, SN8a and SN8b, by use of an unconventional approach, ie, by using an isolated B PLL antigen preparation to immunize mice. These MoAbs, particularly SN8, showed a highly selective reactivity to B PLL and B non-Hodgkin's lymphoma (NHL) among various human leukemia-lymphoma specimens tested; eg, SN8 was capable of effectively distinguishing B PLL from B CLL as well as from hairy cell leukemia (HCL) cell specimens. The cell surface antigen defined by the three MoAbs was determined to be a covalently linked heterodimeric glycoprotein complex (gp49/40) consisting of a 49,000 dalton (alpha-chain) and a 40,000- dalton component (beta-chain). Epitope comparison showed that the epitope defined by SN8 (SN8 epitope) is in close proximity to SN8a epitope but in a distant position from SN8b epitope. Western blot analysis showed that both SN8 and SN8a epitopes are on the beta-chain, but SN8b epitope was not detected on either the alpha- or the beta- chain of the reduced antigen in the same analysis. Binding of either SN8 or SN8b to the cell surface gp49/40 did not cause significant downregulation of the antigen expression whereas binding of SN8a to the antigen caused small (approximately 20%) decrease in the antigen expression. Among the various normal peripheral blood cells, only a subpopulation (6.0% to 24.2% among different specimens derived from different donors) of B cells reacted with the SN8 series MoAbs; these MoAbs showed no significant reactivity against T cells, granulocytes, monocytes, erythrocytes, and platelets. Minimal or no significant reactivity (0 to 2.6% among different specimens) was detected against normal bone marrow cells. Ricin A-chain conjugates of the three MoAbs are all strongly effective for specific killing of SN8 antigen- expressing leukemia cells in the absence of any potentiators; furthermore, the addition of 10 mmol/L NH4Cl, a potentiator, enhanced strongly the cytotoxic activities of the SN8, SN8a, and SN8b conjugates. Thus, each of the three MoAbs was effectively internalized after binding to the cell surface antigen.
CTLA-4 Control over Foxp3 + Regulatory T Cell Function (2008)

Naturally occurring Foxp3+CD4+ regulatory T cells (Tregs) are essential for maintaining immunological self-tolerance and immune homeostasis. Here, we show that a specific deficiency of cytotoxic T lymphocyte antigen 4 (CTLA-4) in Tregs results in spontaneous development of systemic lymphoproliferation, fatal T cell-mediated autoimmune disease, and hyperproduction of immunoglobulin E in mice, and it also produces potent tumor immunity. Treg-specific CTLA-4 deficiency impairs in vivo and in vitro suppressive function of Tregs-in particular, Treg-mediated down-regulation of CD80 and CD86 expression on dendritic cells. Thus, natural Tregs may critically require CTLA-4 to suppress immune responses by affecting the potency of antigen-presenting cells to activate other T cells.
Expression of the types A and B tumor necrosis factor (TNF) receptors is independently regulated, and both receptors mediate activation of the transcription factor NF-kappa B. TNF alpha is not needed for induction of a biological effect via TNF receptors. (1990)

The expression and biological function of the types A and B tumor necrosis factor (TNF) receptors were studied using three cell types. SW480T, HEp2, and HL60 cells had, respectively, mainly the type A, only the type B, and roughly similar amounts of both receptors. Dibutyric cAMP treatment induced a 3-6-fold increase in the amount of the type A receptor in HL60 cells without affecting the amount of the type B receptor. Expression of both receptors can thus be regulated independently. HEp2 and human umbilical vein endothelial cells only showed the type B receptor, and expression of the type A receptor could not be induced in these cells. HL60 cells showed, upon Scatchard analysis, a single binding site for TNF alpha, and its Kd may correspond to that of the type A receptor. The approximately 7-fold lower affinity of TNF alpha binding to the type B receptor of HL60 cells was only detected after blocking all TNF alpha binding to the type A receptor. Both the types A and B receptors mediated TNF alpha-induced activation of the transcription factor NF-kappa B. The agonistic antibody htr9 to the type B receptor also activated NF-kappa B. Thus, signal transduction via the type B receptor may only require interaction with the receptor's extracellular domain.
Vascular Endothelial Growth Factor (VEGF), VEGF Receptors and Their Inhibitors for Antiangiogenic Tumor Therapy (2011)

Vascular endothelial growth factor (VEGF) and its receptors (VEGFRs) have crucial roles in both physiological and pathological angiogenesis. The VEGF family consists of VEGF-A (generally called VEGF), VEGF-B, VEGF-C, VEGF-D, and placental growth factor (PlGF). These peptides show different affinities for VEGFR subtypes. VEGFR exists as three subtypes, VEGFR-1, VEGFR-2, and VEGFR-3, and is structurally related to platelet-derived growth factor receptors. All subtypes possess seven immunoglobulin-like domains in the extracellular region and a tyrosine kinase domain in the intracellular region. VEGF-A activates VEGFR-1 and VEGFR-2, whereas VEGF-B and PlGF bind to only VEFGR-1. VEGF-C and VEGF-D only bind to VEGFR-3. VEGFR-1 (fms-like tyrosine kinase-1, Flt-1) negatively regulates embryonic vasculogenesis and is involved in tumor angiogenesis via activation of monocytes and macrophages. VEGFR-2 (KDR in humans or Flk-1 in mice) is predominantly responsible for both embryonic vasculogenesis and tumor angiogenesis. In contrast, VEGFR-3 (Flt-4) regulates lymphangiogenesis. Consequently, VEGF-A and VEGFR-2 are currently the main targets for antiangiogenic therapy. Bevacizumab is a humanized monoclonal antibody against VEGF-A, and aflibercept (VEGF-Trap) is a soluble fusion protein of the extracelluar domain of VEGFR-1 and VEGFR-2 and the Fc region of immunoglobulin G (IgG). They neutralize VEGF-A, resulting in prevention of tumor angiogenesis. VEGFR tyrosine kinase inhibitors such as sunitinib and sorafenib are also effective in antiangiogenic tumor therapy by inhibiting VEGFR signaling. Anti-VEGF drugs are a promising therapy for cancer patients.