gebhart/patrepeval huggingface dataset:
2-Phenylindoles. Relationship between structure, estrogen receptor affinity, and mammary tumor inhibiting activity in the rat (1984)

A number of 2-phenylindole derivatives with one hydroxy group in the meta or para position of the phenyl ring and a second one in position 5, 6, or 7 of the indole nucleus were synthesized. In addition, different alkyl groups were introduced into positions 1 and 3 of the heterocycle. The influence of these structural variations on the binding affinity for the calf uterine estrogen receptor was studied. A prerequisite for the binding is the presence of an alkyl group at the nitrogen. Favorable are a hydroxy group located in the para position of the phenyl ring and short alkyl chains both in position 1 and 3 of the indole. The highest relative binding affinity (RBA) values (e.g., 33 for 20b, 21 for 24b, 23 for 35b) are close to that of hexestrol (RBA = 25, estradiol = 100). Depending on the positions of the oxygen functions and size of the alkyl residues, the indole derivatives behaved as strong estrogens (20c, 24c, 35c) or impeded estrogens with antagonistic activity (23c, 29c, 30c, 31c, 40c, 44c) in the immature mouse. Some of these derivatives (20c, 23c, 24c, 29c, 30c, 31c) were tested for their inhibitory effect on dimethylbenzanthracene-induced hormone-dependent mammary tumors of the rat. Both types exhibited a strong growth inhibition with a reduction of the average tumor area at appropriate dosage. A mode of action involving the estrogen receptor system is assumed.
Operation direction to a mobile robot by projection lights (2006)

This paper describes the proposal of a novel concept for directing a mobile robot's motion by using human-operator lights. In addition, the construction of an experimental prototype, its operating system as well as results of some laboratory experiments are explained. Basically, the system architecture consists of a laser pointer and a flash light, whereby a target-object is brightened by a human-operator and an image is taken by an omni-directional camera. In such way that the position of the target object is showed to the mobile robot as for calculating its relative position by a vision system, and eventually the robot navigates towards the target-object direction.
Immunopharmacological and antitumor effects of second-generation immunomodulatory oligonucleotides containing synthetic CpR motifs (2004)

Bacterial and synthetic DNAs containing CpG dinucleotides in specific sequence contexts (CpG DNA) activate the vertebrate immune system and produce potent Th1 immune responses. Recently, we reported immunomodulatory oligonucleotides (IMOs) containing 3'-3'-attached novel structures (immunomers) and synthetic immunostimulatory CpR (R=2'-deoxy-7-deazguanosine) dinucleotides show potent stimulatory activity with distinct cytokine secretion profiles. In the present study, we evaluated in vivo immunopharmacological and antitumor properties of second-generation immunomodulatory oligonucleotides (IMOs) either alone or in combination with chemotherapeutic agents. Repeated peritumoral administration of IMOs at 1 mg/kg to mice bearing established subcutaneous CT26 colon tumor or B16.F0 melanoma resulted in complete regression or strong inhibition of tumor growth. Direct peritoneal injection of IMOs at 2.5 mg/kg to mice bearing peritoneally implanted ascites CT26 or B16.F0 tumors completely eradicated or inhibited tumor growth. Treatment of mice bearing beta-gal expressing CT26.CL25 tumor with IMOs resulted in a significant tumor-specific CTL responses compared with treatment with a control non-CpG DNA or PBS. These responses correlated with IFN-gamma, but not IL-4 secreted in IMO, treated mice. A 5-fold increase in beta-gal specific IgG2a antibodies was found in mice, significantly increasing the IgG2a/IgG1 ratio. IMOs showed similar antitumor activity in both wt and IL-6 knockout (ko) C57BL/6 mice but failed to elicit activity in IL-12 ko C57BL/6 mice. Tumor-free mice from the IMO treatment group rejected the same tumor cell rechallenge, suggesting an adaptive immune response against these cells. Moreover, naïve mice quickly developed specific antitumor response without IMO treatment following adoptive transfer of splenocytes obtained from tumor free mice from the IMO treated group. Additionally, the co-administration of IMOs with chemotherapeutic agents, docetaxel and doxorubicin, resulted in synergistic antitumor effects in both B16.F0 melanoma and 4T1 breast carcinoma models. These results demonstrate potent antitumor activity of second-generation IMO compounds containing a synthetic CpR stimulatory motif in a broad spectrum of tumor models through induction of strong Th1 immune responses. IMO treatment resulted in the development of tumor-specific memory immune responses. No treatment-related toxicity was observed in mice at the doses and treatment schedules studied.
IFN Regulatory Factor-4 and -8 Govern Dendritic Cell Subset Development and Their Functional Diversity (2005)

Dendritic cells (DCs) are bone marrow (BM)-derived APCs central to both innate and adaptive immunity. DCs are a heterogeneous cell population composed of multiple subsets with diverse functions. The mechanism governing the generation of multiple DC subsets is, however, poorly understood. In this study we investigated the roles of closely related transcription factors, IFN regulatory factor (IRF)-4 and IRF-8, in DC development by analyzing IRF-4(-/-), IRF-8(-/-), and IRF-4(-/-)IRF-8(-/-) (double-knockout) mice. We found that IRF-4 is required for the generation of CD4(+) DCs, whereas IRF-8 is, as reported previously, essential for CD8alpha(+) DCs. Both IRFs support the development of CD4(-)CD8alpha(-) DCs. IRF-8 and, to a lesser degree, IRF-4 contribute to plasmacytoid DC (PDC) development. Thus, the two IRFs together regulate the development of all conventional DCs as well as PDCs. Consistent with these findings, IRF-4, but not IRF-8, was expressed in CD4(+) DCs, whereas only IRF-8 was expressed in CD8alpha(+) DCs. CD4(-)CD8alpha(-) DCs and PDCs expressed both IRFs. We also demonstrate in vitro that GM-CSF-mediated DC differentiation depends on IRF-4, whereas Fms-like tyrosine kinase 3 ligand-mediated differentiation depends mainly on IRF-8. Gene transfer experiments with double-knockout BM cells showed that both IRFs have an overlapping activity and stimulate a common process of DC development. Nonetheless, each IRF also possesses a distinct activity to stimulate subset-specific gene expression, leading to the generation of functionally divergent DCs. Together, IRF-4 and IRF-8 serve as a backbone of the molecular program regulating DC subset development and their functional diversity.
Energy conservation law and its application for the direct energy method of power system stability (1999)

Many papers have contributed to the development of energy functions for power systems. However, there exists limitation in that the conventional energy functions cannot reflect the control effects of the speed governor and exciter efficiently. In this paper, two useful theorems are developed regarding the relationships of the energy integral of generator power versus its phasor current and voltage. With the use of the two theorems, the energy conservation law can be derived to reflect the resistance, flux-decaying effects, saliency with wide adaptability to various detailed generator models including the governor and exciter control loops. By the rigorous mathematical analysis and numerical tests with its application to sample systems, the proposed energy conservation law is proven to be very exact and valid for any kind of generator models including the speed governor and exciter controls.
Laser Ablation Electrospray Ionization for Atmospheric Pressure, in Vivo, and Imaging Mass Spectrometry (2007)

Mass spectrometric analysis of biomolecules under ambient conditions promises to enable the in vivo investigation of diverse biochemical changes in organisms with high specificity. Here we report on a novel combination of infrared laser ablation with electrospray ionization (LAESI) as an ambient ion source for mass spectrometry. As a result of the interactions between the ablation plume and the spray, LAESI accomplishes electrospray-like ionization. Without any sample preparation or pretreatment, this technique was capable of detecting a variety of molecular classes and size ranges (up to 66 kDa) with a detection limit of 8 and 25 fmol for verapamil and reserpine, respectively, and quantitation capabilities with a four-decade dynamic range. We demonstrated the utility of LAESI in a broad variety of applications ranging from plant biology to clinical analysis. Proteins, lipids, and metabolites were identified, and antihistamine excretion was followed via the direct analysis of bodily fluids (urine, blood, and serum). We also performed in vivo spatial profiling (on leaf, stem, and root) of metabolites in a French marigold (Tagetes patula) seedling.
Ischemia induced focal adhesion kinase cleavage in rat lung. (2004)

Focal adhesion kinase (FAK), a 125 kDa protein, is located at the focal adhesion sites that stabilize endothelial cells on the matrix. Ischemic stimuli cause FAK cleavage and FAK depletion from focal adhesion sites. To test this hypothesis under ischemic conditions, we established an isolated rat lung that we ventilated at 40 inflations/min at inspiratory and expiratory pressures of 10 and 3 cm H2O, respectively. After 5 min of blood perfusion at pulmonary arterial and left atrial pressures of 13 and 3 cm H2O respectively, we either stopped (ischemic group, n=10) or continued (perfused group, n=10) perfusion for 2 hr. We then recovered endothelial cells from each lung, using our previously reported magnetic cell separation method. The endothelial lysates were separated into cytosol and membrane fractions, then immunoprecipitated and blotted with anti-FAK, and anti-phospho-FAK antibody. In ischemic as compared to perfused lungs, immunoblotting with anti-FAK antibody revealed a greater prominence of bands at 125 kDa as well as at cleavage products 80, 70 and 44 kDa in the cytosol fraction. Immuno-blotting with anti-phosphotyrosine antibody revealed decreased enhancement of bands at 80, 70 and 44 kDa, also at 125 kDa in the cytosol fraction. We propose that during lung ischemia, FAK is dephosphorylated, cleaved and translocated to the cytosol. This first evidence of the involvement of FAK in lung ischemia suggests that destabilization of focal adhesions may underlie endothelial barrier deterioration, contributing to increased vascular permeability in ischemic lung injury.
Not Just an Adhesion Molecule: LFA-1 Contact Tunes the T Lymphocyte Program (2017)

The α<sub>L</sub>β<sub>2</sub> integrin LFA-1 is known to play a key role in T lymphocyte migration, which is necessary to mount a local immune response, and is also the main driver of autoimmune diseases. This migration-triggering signaling process in T cells is tightly regulated to permit an immune response that is appropriate to the local trigger, as well as to prevent deleterious tissue-damaging bystander effects. Emerging evidence shows that, in addition to prompting a diverse range of downstream signaling cascades, LFA-1 stimulation in T lymphocytes modulates gene-transcription programs, including genetic signatures of TGF-β and Notch pathways, with multifactorial biological outcomes. This review highlights recent findings and discusses molecular mechanisms by which LFA-1 signaling influence T lymphocyte differentiation into the effector subsets Th1, Th17, and induced regulatory T cells. We argue that LFA-1 contact with a cognate ligand, such as ICAM-1, independent of the immune synapse activates a late divergence in T cells' effector phenotypes, hence fine-tuning their functioning.
Insulin-like growth factor 1 treatment via hydrogels rescues cochlear hair cells from ischemic injury (2008)

This study was designed to investigate the protective effects of recombinant human insulin-like growth factor 1 (rhIGF1), applied locally via a hydrogel, against ischemic damage of the cochleae in gerbils. A hydrogel was immersed in rhIGF1 or saline and was applied on the round window membrane 30 min after the ischemia. Local rhIGF1 treatment significantly reduced the elevation of auditory brain responses thresholds at a frequency of 8 kHz on days 1, 4, and 7 after ischemia. A histological analysis revealed increased survival of inner hair cells in the animals treated with rhIGF1 via the hydrogel 7 days after ischemia. These findings showed that local rhIGF1 application using a hydrogel has the potential to protect the cochleae from ischemic injury.
Damage-induced neuronal endopeptidase (DINE) is a unique metallopeptidase expressed in response to neuronal damage and activates superoxide scavengers (2000)

We isolated a membrane-bound metallopeptidase, DINE (damage-induced neuronal endopeptidase), by differential display PCR using rat normal and axotomized hypoglossal nuclei. The most marked properties of DINE were neuron-specific expression and a striking response to axonal injury in both the central nervous system and peripheral nervous system. For instance, cranial and spinal nerve transection, ischemia, corpus callosum transection, and colchicine treatment increased DINE mRNA expression in the injured neurons, whereas kainate-induced hyperexcitation, immobilization, and osmotic stress failed to up-regulate DINE mRNA. Expression of DINE in COS cells partially inhibited C2-ceramide-induced apoptosis, probably because of the activation of antioxidant enzymes such as Cu/Zn-superoxide dismutase, Mn-superoxide dismutase, and glutathione peroxidase through the proteolytic activity of DINE. These data provide insight into the mechanism of how injured neurons protect themselves against neuronal death.
Chemical Cytometry: Fluorescence-Based Single-Cell Analysis (2008)

Cytometry deals with the analysis of the composition of single cells. Flow and image cytometry employ antibody-based stains to characterize a handful of components in single cells. Chemical cytometry, in contrast, employs a suite of powerful analytical tools to characterize a large number of components. Tools have been developed to characterize nucleic acids, proteins, and metabolites in single cells. Whereas nucleic acid analysis employs powerful polymerase chain reaction-based amplification techniques, protein and metabolite analysis tends to employ capillary electrophoresis separation and ultrasensitive laser-induced fluorescence detection. It is now possible to detect yoctomole amounts of many analytes in single cells.
Nuclear Activity of MLA Immune Receptors Links Isolate-Specific and Basal Disease-Resistance Responses (2006)

Plant immune responses are triggered by pattern recognition receptors that detect conserved pathogen-associated molecular patterns (PAMPs) or by resistance (R) proteins recognizing isolate-specific pathogen effectors. We show that in barley, intracellular mildew A (MLA) R proteins function in the nucleus to confer resistance against the powdery mildew fungus. Recognition of the fungal avirulence A10 effector by MLA10 induces nuclear associations between receptor and WRKY transcription factors. The identified WRKY proteins act as repressors of PAMP-triggered basal defense. MLA appears to interfere with the WRKY repressor function, thereby de-repressing PAMP-triggered basal defense. Our findings reveal a mechanism by which these polymorphic immune receptors integrate distinct pathogen signals.
Identification of immunodominant T cell epitopes of human glutamic acid decarboxylase 65 by using HLA-DR(α1*0101,β1*0401) transgenic mice (1997)

Glutamic acid decarboxylase isoform 2 (GAD65; EC 4.1.1.15) has been identified as a key target autoantigen of insulin-dependent diabetes mellitus (IDDM). IDDM is genetically associated with the major histocompatibility complex (MHC), and particular alleles from the HLA-DQ and HLA-DR loci contribute to disease. Among DR4 subtypes, HLA-DRB1*0401, HLA-DRB1*0402, and HLA-DRB1*0405 alleles lend susceptibility, while HLA-DRB1*0403 confers protection. We have utilized HLA-DR(alpha1*0101,beta1*0401) (hereafter referred to as DR0401), human CD4, murine class II null triple transgenic mice and recombinant GAD65 to generate T cell hybridomas, and we have used overlapping sets of peptides to map the immunodominant epitopes of this autoantigen. We have identified 10 immunogenic regions for GAD65, of which 6 are recognized by multiple hybridomas. These epitopes are also generated by human antigen-presenting cells and their presentation is DR0401 restricted, as shown by the use of typed human lymphoblastoid cell lines and antibody blocking experiments. Immunodominant GAD65 epitopes defined in transgenic mice correspond to GAD65 regions previously shown to elicit T cell responses specifically in DR0401 IDDM patients, underscoring the validity of this approach. Interestingly, although the major epitopes contain DR0401 binding motifs, one of the epitopes contains a DR0405 motif.
Engineering of an artificial glycosylation pathway blocked in core oligosaccharide assembly in the yeast Pichia pastoris: production of complex humanized glycoproteins with terminal galactose (2004)

A significant percentage of eukaryotic proteins contain posttranslational modifications, including glycosylation, which are required for biological function. However, the understanding of the structure-function relationships of N-glycans has lagged significantly due to the microheterogeneity of glycosylation in mammalian produced proteins. Recently we reported on the cellular engineering of yeast to replicate human N-glycosylation for the production of glycoproteins. Here we report the engineering of an artificial glycosylation pathway in Pichia pastoris blocked in dolichol oligosaccharide assembly. The PpALG3 gene encoding Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol mannosyltransferase was deleted in a strain that was previously engineered to produce hybrid GlcNAcMan(5)GlcNAc(2) human N-glycans. Employing this approach, combined with the use of combinatorial genetic libraries, we engineered P. pastoris strains that synthesize complex GlcNAc(2)Man(3)GlcNAc(2) N-glycans with striking homogeneity. Furthermore, through expression of a Golgi-localized fusion protein comprising UDP-glucose 4-epimerase and beta-1,4-galactosyl transferase activities we demonstrate that this structure is a substrate for highly efficient in vivo galactose addition. Taken together, these data demonstrate that the artificial in vivo glycoengineering of yeast represents a major advance in the production of glycoproteins and will emerge as a practical tool to systematically elucidate the structure-function relationship of N-glycans.
Scintigraphic imaging of the hypoxia marker (99m)technetium-labeled 2,2'-(1,4-diaminobutane)bis(2-methyl-3-butanone) dioxime (99mTc-labeled HL-91; prognox): noninvasive detection of tumor response to the antivascular agent 5,6-dimethylxanthenone-4-acetic acid. (2000)

5,6-Dimethylxanthenone-4-acetic acid (DMXAA) and combretastatin A4 phosphate (CA-4-P) markedly inhibit tumor blood flow in mice and are both currently in clinical trial. One of the challenges in clinical evaluation of antivascular agents is the monitoring of tumor blood flow inhibition in individual patients. This study investigates, using mouse models, whether a new marker for tissue hypoxia, (99m)technetium-labeled 2,2'-(1,4-diaminobutane)bis(2-methyl-3-butanone) dioxime (99mTc-labeled HL-91; Prognox)] has potential for the scintigraphic monitoring of tumor response to antivascular agents. Determination of radioactivity in dissected tissues 3 h after DMXAA (80 micromol/kg) or CA-4-P (227 micromol/kg) was injected indicated that both drugs inhibited blood flow (86RbCl uptake; 84 and 87%, respectively) and increased 99mTc-labeled HL-91 levels (350 and 300%, respectively) selectively in murine RIF-1 tumors. Planar imaging of 99mTc-labeled HL-91 3 h after DMXAA injection showed a dose-dependent increase in tumor levels above a threshold of 50 micromol/kg; this same threshold was observed for the inhibition of tumor blood flow (determined using Hoechst 33342). DMXAA also inhibited blood flow--and increased 99mTc-labeled HL-91 uptake--in MDAH-MCa-4 mouse mammary carcinomas and in NZMN10 human melanoma xenografts. Whether 99mTc-labeled HL-91 might also be useful as a biomarker for tumor cell killing was investigated by clonogenic assay of surviving cells 15 h after imaging 99mTc-labeled HL-91 in RIF-1 tumors. Log cell kill in individual tumors showed a statistically significant linear correlation (P < 0.001) with 99mTc-labeled HL-91 uptake after 60 micromol/kg (r2 = 0.79) and 70 micromol/kg (r2 = 0.44) but not at 80 micromol/kg DMXAA. The lack of correlation at high doses presumably reflects the insensitivity of the tumor-averaged 99mTc-labeled HL-91 signal to small regions in which tumor blood flow is preserved (which will limit log cell kill). The results indicate the potential of 99mTc-labeled HL-91 for the noninvasive imaging of tumor blood flow inhibition by antivascular drugs in humans.
Quantitative PCR Reveals Increased Levels of Tumor Necrosis Factor-alpha mRNA in Peripheral Blood Mononuclear Cells of Multiple Sclerosis Patients During Relapses (1999)

Quantification of tumor necrosis factor-alpha (TNF-alpha) mRNA in peripheral blood mononuclear cells (PBMC) could provide information about disease activity in multiple sclerosis (MS); however, specific competitive methods must be utilized. A competitor cDNA, having the same sequence of the target TNF-alpha cDNA, a part from an internal 49-bp deletion, was generated and used to set-up a quantitative polymerase chain reaction (PCR) to quantify mRNA of TNF-alpha. Competitor and target were co-amplified using the same primers. The rates of generation of competitor and target TNF-alpha conformed closely to the prediction of the mathematical model, and a high level of accuracy and reproducibility was achieved. The method was applied to quantify TNF-alpha mRNA in PBMC of normal subjects and multiple sclerosis (MS) patients both during clinical relapses and remissions. A statistically significant higher level of TNF-alpha mRNA was detected during relapses than during remissions. High levels of TNF-alpha mRNA were found in 44% of relapses and 12% of samples during remissions, suggesting that TNF-alpha mRNA synthesis is abnormal in MS.
Cutting Edge: Administration of Anti-CD40 Ligand and Donor Bone Marrow Leads to Hemopoietic Chimerism and Donor-Specific Tolerance Without Cytoreductive Conditioning (2000)

Transplantation tolerance, defined as allograft acceptance by an immunocompetent recipient in the absence of long-term immunosuppression, has remained an elusive goal in clinical transplantation. Robust experimental tolerance induction strategies have in common methods to induce mixed hemopoietic chimerism. To date, however, chimerism induction across allogeneic barriers has required recipient conditioning with irradiation or cytoablative agents. In this paper we show that B6 recipients of fully allogeneic BALB/c skin grafts treated with repeated doses of donor bone marrow and anti-CD40 ligand (CD40L) develop durable (>300 days), readily detectable (6-12%) multilineage hemopoietic chimerism, indefinite allograft acceptance (>300 days), and donor-specific tolerance to secondary skin grafts. Analysis of the TCR repertoire of treated mice indicates that the underlying mechanisms of tolerance are in part mediated by deletion of donor-reactive T cells. These data demonstrate that durable hemopoietic chimerism and robust transplantation tolerance can be achieved without cytotoxic conditioning using a potentially clinically applicable regimen.