gebhart/patrepeval huggingface dataset:
Discovery of a New Class of Macrocyclic Antagonists to the Human Motilin Receptor (2006)

A novel class of macrocyclic peptidomimetics was identified and optimized as potent antagonists to the human motilin receptor (hMOT-R). Well-defined structure-activity relationships allowed for rapid optimization of potency that eventually led to high affinity antagonists to hMOT-R. Potency and antagonist functional activity were confirmed both in functional and cell-based assays, as well as on isolated rabbit intestinal smooth muscle strips. Rapid access to this novel class of macrocyclic target structures was made possible through two efficient and complementary solid-phase parallel synthetic approaches, both of which are reported herein.
Reverse Genetics System for Uukuniemi Virus ( Bunyaviridae ): RNA Polymerase I-Catalyzed Expression of Chimeric Viral RNAs (2001)

We describe here the development of a reverse genetics system for the phlebovirus Uukuniemi virus, a member of the Bunyaviridae family, by using RNA polymerase I (pol I)-mediated transcription. Complementary DNAs containing the coding sequence for either chloramphenicol acetyltransferase (CAT) or green fluorescent protein (GFP) (both in antisense orientation) were flanked by the 5'- and 3'-terminal untranslated regions of the Uukuniemi virus sense or complementary RNA derived from the medium-sized (M) RNA segment. This chimeric cDNA (pol I expression cassette) was cloned between the murine pol I promoter and terminator and the plasmid transfected into BHK-21 cells. When such cells were either superinfected with Uukuniemi virus or cotransfected with expression plasmids encoding the L (RNA polymerase), N (nucleoprotein), and NSs (nonstructural protein) viral proteins, strong CAT activity or GFP expression was observed. CAT activity was consistently stronger in cells expressing L plus N than following superinfection. No activity was seen without superinfection, nor was activity detected when either the L or N expression plasmid was omitted. Omitting NSs expression had no effect on CAT activity or GFP expression, indicating that this protein is not needed for viral RNA replication or transcription. CAT activity could be serially passaged to fresh cultures by transferring medium from CAT-expressing cells, indicating that recombinant virus containing the reporter construct had been produced. In summary, we demonstrate that the RNA pol I system, originally developed for influenza virus, which replicates in the nucleus, has strong potential for the development of an efficient reverse genetics system also for Bunyaviridae members, which replicate in the cytoplasm.
Nucleotide sequence of the coat protein genes of strawberry latent ringspot virus: lack of homology to the nepoviruses and comoviruses (1994)

The sequence of the 3'-terminal 2424 nucleotides of RNA-2 of the flowering cherry strain of strawberry latent ringspot virus (SLRV) was determined from cDNA clones. The sequence contains a reading frame in the virus-sense strand of 2070 nucleotides, a 3' untranslated region of 552 nucleotides and a 3'-terminal poly(A) tract. The positions of the two coat proteins of SLRV within the reading frame were determined from sequence data obtained by N-terminal sequencing using Edman degradation. The larger coat protein with an M(r) of 43K is located 5' of the smaller coat protein of 27K, and the two proteins are apparently cleaved at a Ser-Gly bond. Although there are numerous similarities between SLRV and the nepoviruses and comoviruses, there is no significant homology between the SLRV coat proteins and the coat proteins of either group. Furthermore, the hydropathy profiles of the SLRV coat proteins are unlike those of either group. No comparisons could be made with the fabaviruses owing to lack of sequencing information. This lack of homology suggests that SLRV is more distantly related to the nepoviruses and comoviruses than has been considered previously.
The cytolytic activity of pulmonary CD8+ lymphocytes, induced by infection with a vaccinia virus recombinant expressing the M2 protein of respiratory syncytial virus (RSV), correlates with resistance to RSV infection in mice (1993)

Previous studies demonstrated that the pulmonary resistance to respiratory syncytial virus (RSV) challenge induced by immunization with a recombinant vaccinia virus expressing the M2 protein of RSV (vac-M2) was significantly greater 9 days after immunization than at 28 days and was mediated predominantly by CD8+ T cells. In this study, we have extended these findings and sought to determine whether the level of CD8+ cytotoxic T-lymphocyte (CTL) activity measured in vitro correlates with the resistance to RSV challenge in vivo. Three lines of evidence documented an association between the presence of pulmonary CTL activity and resistance to RSV challenge. First, vac-M2 immunization induced pulmonary CD8+ CTL activity and pulmonary resistance to RSV infection in BALB/c (H-2d) mice, whereas significant levels of pulmonary CTL activity and resistance to RSV infection were not seen in BALB.K (H-2k) or BALB.B (H-2b) mice. Second, pulmonary CD8+ CTL activity was not induced by infection with other vaccinia virus-RSV recombinants that did not induce resistance to RSV challenge. Third, the peak of pulmonary CTL activity correlated with the peak of resistance to RSV replication (day 6), with little resistance being observed 45 days after immunization. An accelerated clearance of virus was not observed when mice were challenged with RSV 45 days after immunization with vac-M2. The results indicate that resistance to RSV induced by immunization with vac-M2 is mainly mediated by primary pulmonary CTLs and that this resistance decreases to very low levels within 2 months following immunization. The implications for inclusion of CTL epitopes into RSV vaccines are discussed in the context of these observations.
VEGF is required for growth and survival in neonatal mice (1999)

We employed two independent approaches to inactivate the angiogenic protein VEGF in newborn mice: inducible, Cre-loxP- mediated gene targeting, or administration of mFlt(1-3)-IgG, a soluble VEGF receptor chimeric protein. Partial inhibition of VEGF achieved by inducible gene targeting resulted in increased mortality, stunted body growth and impaired organ development, most notably of the liver. Administration of mFlt(1-3)-IgG, which achieves a higher degree of VEGF inhibition, resulted in nearly complete growth arrest and lethality. Ultrastructural analysis documented alterations in endothelial and other cell types. Histological and biochemical changes consistent with liver and renal failure were observed. Endothelial cells isolated from the liver of mFlt(1-3)-IgG-treated neonates demonstrated an increased apoptotic index, indicating that VEGF is required not only for proliferation but also for survival of endothelial cells. However, such treatment resulted in less significant alterations as the animal matured, and the dependence on VEGF was eventually lost some time after the fourth postnatal week. Administration of mFlt(1-3)-IgG to juvenile mice failed to induce apoptosis in liver endothelial cells. Thus, VEGF is essential for growth and survival in early postnatal life. However, in the fully developed animal, VEGF is likely to be involved primarily in active angiogenesis processes such as corpus luteum development.
ING-1, a Monoclonal Antibody Targeting Ep-CAM in Patients with Advanced Adenocarcinomas (2004)

The recommended dose for ING-1 is 0.10 mg/kg by intravenous infusion weekly. The absence of severe toxicity at this dose, low immunogenicity, and preliminary evidence of ING-1 tumor localization and antitumor efficacy support the further clinical development of this antibody to treat Ep-CAM-positive malignant diseases.
Intravenous immunoglobulin suppresses NLRP1 and NLRP3 inflammasome-mediated neuronal death in ischemic stroke (2013)

Multi-protein complexes called inflammasomes have recently been identified and shown to contribute to cell death in tissue injury. Intravenous immunoglobulin (IVIg) is an FDA-approved therapeutic modality used for various inflammatory diseases. The objective of this study is to investigate dynamic responses of the NLRP1 and NLRP3 inflammasomes in stroke and to determine whether the NLRP1 and NLRP3 inflammasomes can be targeted with IVIg for therapeutic intervention. Primary cortical neurons were subjected to glucose deprivation (GD), oxygen-glucose deprivation (OGD) or simulated ischemia-reperfusion (I/R). Ischemic stroke was induced in C57BL/6J mice by middle cerebral artery occlusion, followed by reperfusion. Neurological assessment was performed, brain tissue damage was quantified, and NLRP1 and NLRP3 inflammasome protein levels were evaluated. NLRP1 and NLRP3 inflammasome components were also analyzed in postmortem brain tissue samples from stroke patients. Ischemia-like conditions increased the levels of NLRP1 and NLRP3 inflammasome proteins, and IL-1β and IL-18, in primary cortical neurons. Similarly, levels of NLRP1 and NLRP3 inflammasome proteins, IL-1β and IL-18 were elevated in ipsilateral brain tissues of cerebral I/R mice and stroke patients. Caspase-1 inhibitor treatment protected cultured cortical neurons and brain cells in vivo in experimental stroke models. IVIg treatment protected neurons in experimental stroke models by a mechanism involving suppression of NLRP1 and NLRP3 inflammasome activity. Our findings provide evidence that the NLRP1 and NLRP3 inflammasomes have a major role in neuronal cell death and behavioral deficits in stroke. We also identified NLRP1 and NLRP3 inflammasome inhibition as a novel mechanism by which IVIg can protect brain cells against ischemic damage, suggesting a potential clinical benefit of therapeutic interventions that target inflammasome assembly and activity.
New perspectives in the diagnosis of hepatitis C. (1999)

Since the identification and molecular characterization of the non-A, non-B hepatitis virus (HCV) in 1989, a variety of diagnostic tests based on the detection of hepatitis virus antibodies or HCV RNA in the serum have been developed and refined. The enzyme-linked immunosorbent assays (ELISAs) and the recombinant immunoblot assays (RIBAs) exhibit improved sensitivity and specificity for HCV antibodies compared with their predecessors, and the ELISA-3 is at the forefront of HCV screening. Furthermore, the advent of molecular assays that employ quantitative reverse-transcriptase polymerase chain reaction to detect HCV RNA has allowed clinicians to track the natural history of HCV and to monitor the progress of therapy. A role for further refinement of an HCV diagnosis using tests to determine genotype, subtype, and quasispecies is explored. In addition, the role of liver biopsy and non-invasive markers of histologic status are placed into the context of patient prognosis. This article reviews the state-of-the-art tests and assays developed for the diagnosis and management of HCV infection.
Combinatorial chemistry : a practical approach (2000)

Synthesis of combinatorial libraries using the portioning-mixing procedure One-bead-one-compound combinatorial library method Synthesis and screening of positional scanning synthetic combinatorial libraries High throughput combinatorial synthesis of discrete compounds in multimilligram quantities Positionally addressable parallel synthesis on membrane supports Resins and anchors for solid phase organic synthesis Organic reactions on solid support - an overview Analytical methods in combinatorial chemistry Multi-component reactions (mcrs) of isocyanides and their chemical libraries Multi-step solution phase combinatorial synthesis Experimental techniques in fluorous synthesis Dendrimer-supported combinatorial chemistry Automated solution phase synthesis and its application in combinatorial chemistry Combinatorial discovery and optimization of electrocatalysts Combinatorial library synthesis using polymer-supported catalysts Combinatorial Approaches to chiral catalysts discovery
Regulatory-B cell and regulatory-T cell collaborate to promote transplantation tolerance (126.2) (2012)

Abstract Backgrounds: The role of regulatory-B cells (Bregs) in transplant tolerance remains unclear. We found that the anti-CD45RB/anti-TIM1 induced tolerance depends on both Bregs and regulatory-T cells (Tregs). This finding offers a unique opportunity to explore the interplay of Bregs and Tregs in a transplant setting. Methods: Islet allograft were prepared from BALB/c donors and transplanted into B6. Recipients were treated with anti-CD45RB and anti-TIM1 antibodies for tolerance induction. Naive B cells or B cells isolated from mice that have been transplanted and treated in combination antibody therapy transferred into µMT-KO and assessed Treg expression by FACS. Anti-CD25 antibody, PC61, was used for Treg depletion. Anti-IL-10 or anti-TGF-β was used to neutralizing cytokine activity. Results: Treg numbers significantly increase following adoptive transfer of B cells purified from recipients bearing long-term surviving grafts (LTS). Moreover, adoptive transfer of LTS B cells suppressed allograft rejection upon transfer to untreated B cell-deficient secondary host, but this effect was not observed in Treg-deleted recipients. The absence of IL-10 by using anti-IL10 antibody did not affect on induction of long-term islet allograft by anti-CD45RB/anti-TIM1, however anti-TGF-β treatment abrogated the graft survival. Conclusions: B cell regulation induced by anti-CD45RB/anti-TIM1 is associated with Treg generation. This effect may be mediated by Treg promoting cytokines such as TGF-β.
Use of the two-hybrid system to identify the domain of p53 involved in oligomerization. (1993)

We used a yeast-based genetic assay, the two-hybrid system, to characterize the domain of the tumor-suppressor p53 involved in oligomerization. This assay relies on the reconstitution of the function of a transcriptional activator, the yeast GAL4 protein, via the interaction of a protein fused to the DNA-binding domain of GAL4 with a protein fused to the transcriptional activation domain of GAL4. We show by a reconstruction experiment that this approach could detect the interaction of p53 deleted for its N-terminal activation domain with SV40 large T antigen. We then searched a library of human proteins present as activation domain hybrids for proteins that can interact with the hybrid of p53 with the DNA-binding domain. This search identified 36 plasmids containing the p53 gene, representing 10 different classes. These results provide an additional in vivo demonstration of p53 oligomerization. The smallest p53 fragment identified from screening the library contained only amino acids 331-393, indicating that this small C-terminal fragment is sufficient to mediate oligomerization. In addition, a mutant p53 protein could bind to the wild-type protein in this assay, providing support for the idea that mutant forms of p53 act in a dominant-negative manner through C-terminal oligomerization with the wild type.
Graph-based clustering for finding distant relationships in a large set of protein sequences (2004)

The complete result of our algorithm for all the human proteins in SWISS-PROT and TrEMBL, and other supplementary information are available at http://motif.ics.es.osaka-u.ac.jp/Ncut-KL/
Ornithine decarboxylase: an unreliable marker for the identification of population groups at risk for colonic neoplasia. (1990)

Ornithine decarboxylase (ODC) is the first and rate-limiting enzyme in the polyamine biosynthetic pathway. Polyamines have been studied as potential markers of neoplastic diseases, including colonic cancer. Previous studies have pointed out the possible value of this enzyme as a biochemical marker of colonic neoplasia, we studied 100 patients undergoing diagnostic total colonoscopy. There were 40 normal controls and 20 patients in each of the following groups: 1) family members of patients diagnosed as having colonic tumors, 2) patients with adenomas, and 3) patients with colonic adenocarcinoma. Six forceps biopsies were obtained from the normal-appearing sigmoid mucosa for the analysis of ODC. No difference was found among the four groups studied. We therefore conclude that ODC is unreliable for clinical use as a biochemical marker for the identification of population groups at risk for colonic neoplasia.
Vesicular stomatitis virus phenotypically mixed with retroviruses: an efficient detection method. (1983)

Two methods of assaying vesicular stomatitis virus (VSV) particles phenotypically mixed with retrovirus-coded antigens were compared. Each of them detected phenotypically mixed particles with different minimum proportion of surface glycoprotein molecules of the donor virus, and consequently also profoundly different proportions of VSV virions containing retrovirus antigens. Only a low proportion (10(-4) of VSV virions grown in XMuLV-infected rabbit SIRC cells behaved as pseudotypes, resistant to anti-VSV serum and neutralized by anti-XMuLV serum. VSV produced in mouse L cells did not contain significant titre of pseudotype particles in the neutralization test. However, when immunoprecipitation was used with corresponding antibody and Staphylococcus aureus cells, almost 100% of the VSV virions produced in L cells and in XMuLV-preinfected SIRC cells were found to contain MuLV-related antigen molecules.
Liver sinusoidal endothelial cells are responsible for nitric oxide modulation of resistance in the hepatic sinusoids. (1997)

The mechanisms that regulate vascular resistance in the liver are an area of active investigation. Previously, we have shown that nitric oxide (NO) modulates hepatic vascular tone in the normal rat liver. In this study, the production of NO is examined in further detail by isolating sinusoidal endothelial cells (SEC) from the rat liver. Endothelial NO synthase (eNOS) was present in SEC based on Western blotting and confocal immunofluorescence microscopy. Exposure of SEC to flow increased the release of NO. To investigate the relevance of these in vitro findings to the intact liver, we modified an in situ perfusion system to allow for direct measurement of NO release from the hepatic vasculature. NO was released from the hepatic vasculature in a time-dependent manner, and administration of N-monomethyl-L-arginine reduced NO release and increased portal pressure. Immunostaining of intact liver demonstrated eNOS localization to endothelial cells lining the hepatic sinusoids. These findings demonstrate that SEC in vitro and in vivo express eNOS and produce NO basally, and increase their production in response to flow. Additionally, an increase in portal pressure concomitant with the blockade of NO release directly demonstrates that endogenous endothelial-derived NO modulates portal pressure.
In vivo clearance of ethoxycoumarin and its prediction from In vitro systems. Use Of drug depletion and metabolite formation methods in hepatic microsomes and isolated hepatocytes. (1998)

The pharmacokinetics of ethoxycoumarin have been characterized using steady-state plasma concentrations achieved after administration of this compound, at a series of infusion rates, into the hepatic portal vein of rats. The clearance of ethoxycoumarin could be described by a one-site Michaelis-Menten kinetic model with Vmax and unbound KM values of 495 nmol/min/standard rat weight (SRW) and 3.6 microM, respectively, and an intrinsic clearance (CLint, Vmax/KM ratio) of 137 ml/min/SRW (where SRW is 250 g). Urinary excretion experiments, using both ethoxycoumarin and hydroxycoumarin, demonstrated that 7-hydroxycoumarin, the metabolite frequently measured in in vitro studies, accounted for 26% of the metabolism of ethoxycoumarin. In vitro studies with hepatic microsomes and isolated hepatocytes were undertaken to characterize the kinetics of both hydroxycoumarin formation and ethoxycoumarin depletion and to compare the utility of these methods for predicting in vivo clearance. In both in vitro systems, hydroxycoumarin formation displayed biphasic kinetics, with a high-affinity/low-capacity component (with Vmax, KM, and CL1 terms) and a low-affinity/high-capacity component (with a CL2 term) that was not saturated over the substrate concentration range studied (0.5-100 microM). The use of scaling factors to relate in vitro and in vivo data showed that, although microsomal and hepatocyte Vmax values were comparable (26 and 17 nmol/min/SRW, respectively), both were substantially lower than the in vivo value. However, scaling of the in vitro CLint values, by taking into account the fraction of ethoxycoumarin metabolized to hydroxycoumarin, yielded in vivo predictions of 127 and 122 ml/min/SRW (representing 93 and 89% of the observed CLint value) for microsomes and hepatocytes, respectively. The depletion of ethoxycoumarin (1-1.5 microM) with time in both microsomes and hepatocytes displayed a monoexponential decline and predicted in vivo CLint values of 53 and 117 ml/min/SRW (representing 39 and 85% of the observed value), respectively. Therefore, both in vitro systems can accurately predict ethoxycoumarin CLint values using hydroxycoumarin formation rates, providing the importance of this pathway in total clearance is taken into account. Moreover, these results demonstrate that, even when the complete metabolic fate of the compound under investigation is unknown, isolated hepatocytes can be successfully used to predict in vivo CLint values by measurement of substrate depletion with time.
Polymers with controlled molecular architecture: control of surface functionality in the synthesis of dendritic hyperbranched macromolecules using the convergent approach (1991)

The synthesis of unsymmetrically or non-uniformly surface-functionalized dendritic macromolecules using a stepwise convergent-growth approach is described. By stepwise alkylation of the monomer unit, 3,5-dihydroxybenzyl alcohol, with unsubstituted and substituted benzylic bromides, followed by activation of the group located at the focal point, dendritic ‘wedges’ can be obtained in which there is only a single substituent such as a cyano group at the periphery. Use of only substituted benzylic bromides in the first step of growth allows fully functionalized dendritic wedges to be obtained. Coupling to a polyfunctional core such as 1,1,1-tris-(4′-hydroxyphenyl)ethane can also be done in a stepwise manner with both mono or fully substituted and unsubstituted ‘wedges’ to give dendritic macromolecules containing one, two, or three cyano groups or sixteen or thirty-two bromine atoms at the periphery of the macromolecule. These hyperbranched dendritic polymers were purified by normal flash chromatography and fully characterized by a combination of spectroscopic and chromatographic techniques. By using variations of this general scheme both the number and placement of the functional groups at the periphery of the dendritic macromolecule can be accurately controlled to afford a large variety of functionalized hyperbranched moieties.
A Scientific Overview of the Development of AIDS Vaccines (2000)

This article explores the development of AIDS vaccines. It briefly describes the differences between cellular and humoral immune systems and their role in HIV disease. It also considers the use of animal models in vaccine research to simulate human immune system responses to HIV. In addition, various vaccine strategies are explained. These strategies include live attenuated vaccines, subunit vaccines, live vector-based vaccines, DNA vaccines, pseudovirions, whole inactivated virus, and combination products. Advantages and disadvantages for each strategy will be described as well as the current state of progress in vaccine development. The purpose of this article is to educate nurses and other health care providers about the recent developments in vaccine technology as well as to encourage all health care providers to advocate for increased research and development of HIV-1 vaccines.