gebhart/patrepeval huggingface dataset:
Reaction of mast cell proteases tryptase and chymase with protease activated receptors (PARs) on keratinocytes and fibroblasts (1998)

Protease activated receptors (PARs) compose a family of G protein signal transduction receptors activated by proteolysis. In this study, the susceptibility of PARs expressed on human keratinocytes and dermal fibroblasts to the human mast cell proteases tryptase and chymase was evaluated. PAR activation was measured by monitoring cytosolic [Ca2+] in cells loaded with the fluorescent Ca2+ probe Fura-2. Tryptase produced transient cytosolic Ca2+ mobilization in keratinocytes, but not in fibroblasts. Ca2+ mobilization in keratinocytes required enzymatically active tryptase, demonstrated desensitization, and was blocked by pretreatment of cells with the PAR-2 peptide agonist SLIGKV, trypsin, or the phospholipase inhibitor U73122. Heparin, a GAG that binds to tryptase, stabilizing its functional form, also inhibited tryptase-induced Ca2+ mobilization. The maximal response elicited by tryptase was smaller than that observed upon treatment of keratinocytes with trypsin, a known activator of PAR-2, and keratinocytes made refractory to tryptase by pretreatment with the protease remained responsive to trypsin. Pretreatment of keratinocytes with thrombin, an activator of PAR-1 and -3 (thrombin receptors), had no detectable effect on the tryptase or trypsin responses. These data suggest that in keratinocytes tryptase may be activating a subpopulation of PAR-2 receptors. Treatment of keratinocytes or fibroblasts with human chymase did not produce Ca2+ mobilization, nor did it affect Ca2+ mobilization produced by trypsin. However, chymase pretreatment of fibroblasts rapidly inhibited the ability of these cells to respond to thrombin. Inhibition was dependent on chymase enzymatic activity and was not significantly affected by the presence of heparin. This finding is consistent with studies indicating that PAR-1 may be susceptible to proteases with chymotrypsin-like specificity. These results suggest that the proteases tryptase and chymase secreted from mast cells in skin may affect the behavior of surrounding cells by the hydrolysis of PARs expressed by these cells.
Performance of local power control in peer-to-peer impulse radio networks with bursty traffic (2002)

We present and investigate the performance of an impulse radio system with bursty traffic in a peer-to-peer network, with a combination of a bit rate variation scheme and a local power control algorithm. The peer-to-peer architecture considered is motivated by survivability, covertness, and the need for rapid deployment. Because the performance of a peer-to-peer architecture is topology dependent, we develop a model for generating random configurations of peer-to-peer links, and use the model to analyze the performance of the peer-to-peer network. Power control and bit rate variation techniques are developed to minimize the fraction of time that the aggregate transmitted power exceeds a given threshold. This fraction is further reduced by making initial power assignments based on local information available at connection set-up and by augmenting the closed loop power control scheme with an open loop power level adjustment. The amount of open loop power adjustment made depends on the change in processing gain due to bit rate variation. Simulation results are presented that show the performance of the peer-to-peer system with power control and bit rate variation schemes for different topologies.
Neutrophils express the high affinity receptor for IgG (Fc gamma RI, CD64) after in vivo application of recombinant human granulocyte colony- stimulating factor (1991)

Fc receptors are important effector molecules of neutrophilic granulocytes (polymorphonuclear neutrophils [PMN]), connecting phagocytic cells and the specific immune response. Neutrophils from healthy donors express the low-affinity receptors for IgG Fc gamma RII (CD32) and Fc gamma RIII (CD16), but not the high-affinity receptor Fc gamma RI (CD64). The latter has been found on neutrophils from patients with certain bacterial infections and can be induced in vitro after incubation with interferon-gamma. We show here that neutrophils strongly express Fc gamma RI after in vivo application of recombinant human granulocyte colony-stimulating factor (rhG-CSF). PMN from patients receiving rhG-CSF displayed higher cytotoxicity against Daudi lymphoma cells in vitro compared with control patients and with healthy donors. Fab fragments against Fc gamma RII (monoclonal antibody [MoAb] IV.3) inhibited neutrophil-mediated cytotoxicity of healthy donors but not of patients during rhG-CSF therapy. Therefore, expression of Fc receptors by PMN was investigated by flow cytometry and the mean fluorescence intensity (MFI) was compared. After staining with MoAb 32.2 against Fc gamma RL, the median MFI of neutrophils from G-CSF patients (median, 4.78; range, 2.40 to 8.50; n = 5) was significantly higher (P = .002 and P = .001, respectively) than the median MFI of patients not receiving G-CSF (median, 1.23; range, 1.01 to 1.58; n = 6) and the median MFI of healthy donors (median, 1.04; range, 0.67 to 1.12; n = 6). Fc gamma RI disappeared after the discontinuing of the G-CSF injections, but was reinduced during the next treatment cycle with rhG-CSF. The high expression of Fc gamma RI during rhG-CSF therapy correlated with enhanced cytotoxicity. In vitro incubation with rhG-CSF also enhances cytotoxicity, but only minor increments in Fc gamma RI expression were observed. Thus, during in vivo application of rhG-CSF neutrophils acquire an additional potent receptor for mediating tumor cell killing in vitro by induction of the high-affinity receptor for IgG (Fc gamma RI, CD64).
Use of a tomato mutant constructed with reverse genetics to study fruit ripening, a complex developmental process (1993)

Fruit ripening is one of the most dramatic developmental transitions associated with extensive alteration in gene expression. The plant hormone ethylene is considered to be the causative ripening agent. Transgenic tomato plants were constructed expressing antisense or sense RNA to the key enzyme in the ethylene (C2H4) biosynthetic pathway, 1-aminocyclopropane-1-carboxylate (ACC) synthase using the constitutive CaMV 35S and fruit specific E8 promoters. Fruits expressing antisense LE-ACS2 RNA produce less ethylene and fail to ripen only when ethylene production is suppressed by more than 99% (> 0.1 nl/g fresh weight). Ethylene production is considerably inhibited (50%) in fruits expressing sense LE-ACS2 RNA. Antisense fruits accumulate normal levels of polygalacturonase (PG), ACC oxidase (pTOM13), E8, E17, J49, and phytoene desaturase (D2) mRNAs which were previously thought to be ethylene-inducible. E4 gene expression is inhibited in antisense fruits and its expression is not restored by treatment with exogenous propylene (C3H6). Antisense fruits accumulate PG mRNA, but it is not translated. Immunoblotting experiments indicate that the PG protein is not expressed in antisense fruits but its accumulation is restored by propylene (C3H6) treatment. The results suggest that at least two signal-transduction pathways are operating during tomato fruit ripening. The independent (developmental) pathway is responsible for the transcriptional activation of genes such as PG, ACC oxidase, E8, E17, D2, and J49. The ethylene-dependent pathway is responsible for the transcriptional and posttranscriptional regulation of genes involved in lycopene, aroma biosynthesis, and the translatability of developmentally regulated genes such as PG.
Effects of retinoic acid on proliferation, phenotype and expression of cyclin- dependent kinase inhibitors in TGF-β1-stimulated rat hepatic stellate cells (2000)

AIM:To study the molecular mechanisms of retinoic acid (RA)on prolix-feration and expression of cyclin-dependent kinase inhibitors (CKI), i.e.p16, p21 and p27 in cultured rat hepatic stellate cells (HSC) stimulated with transforming growth factor beta 1 (TGF-beta1).METHODS:HSC were isolated from healthy rat livers and cultured.After stimulated with 1mg/L TGF-beta1, subcultured HSC were treated with or without 1nmol/L RA. MTT assay, immunocytochemistry (ICC) for p16, p21, p27 and alpha-smooth muscle actin (alpha-SMA) protein, in situ hybridization (ISH) for retinoic acid receptor beta 2 (RAR-beta2) and p16, p21 and p27 mRNA and quantitative image analysis (partially) were performed.RESULTS:inhibited HSC proliferation (41.50%,P<0.05),decreased the protein level of alpha-SMA (55.09%, P<0.05), and induced HSC to express RAR-beta2 mRNA. In addition, RA increased the protein level of p16 (218.75%, P <0.05) and induced p21 protein expression; meanwhile, p27 was undetectable by ICC in both control and RA-treated HSC. However, RA had no influence on the mRNA levels of p16, p21 or p27 as determined by ISH.CONCLUSION:Up-regulation of p16 and p21 on post-transcriptional level may contribute, in part, to RA inhibition of TGF-beta 1-initiated rat HSC activation in vitro.
Characterization of the Optimal Culture Conditions for Clinical Scale Production of Human Mesenchymal Stem Cells (2005)

Mesenchymal stem cells (MSCs) are multipotent cells defined by multilineage potential, ease to gene modification, and immunosuppressive ability, thus holding promise for tissue engineering, gene therapy, and immunotherapy. They exhibit a unique in vitro expansion capacity, which, however, does not compensate for the very low percentage in their niches given the vast numbers of cells required for the relative studies. Taking into consideration the lack of a uniform approach for MSC isolation and expansion, we attempted in this study, by comparing various culture conditions, to identify the optimal protocol for the large-scale production of MSCs while maintaining their multilineage and immunosuppressive capacities. Our data indicate that, apart from the quality of fetal calf serum, other culture parameters, including basal medium, glucose concentration, stable glutamine, bone marrow mononuclear cell plating density, MSC passaging density, and plastic surface quality, affect the final outcome. Furthermore, the use of basic fibroblast growth factor (bFGF), the most common growth supplement in MSC culture media, greatly increases the proliferation rate but also upregulates HLA-class I and induces low HLA-DR expression. However, not only does this upregulation not elicit significant in vitro allogeneic T cell responses, but also bFGF-cultured MSCs exhibit enhanced in vivo immunosuppressive potential. Besides, addition of bFGF affects MSC multilineage differentiation capacity, favoring differentiation toward the osteogenic lineage and limiting neurogenic potential. In conclusion, in this report we define the optimal culture conditions for the successful isolation and expansion of human MSCs in high numbers for subsequent cellular therapeutic approaches.
Stereochemistry of Internucleotide Bond Formation by the H-Phosphonate Method. 1. Synthesis and 31P Nmr Analysis of 16 Diribonulceoside (3′-5′)-H-Phosphonates and the Corresponding Phosphorothioates (2005)

Sixteen diribonucleoside (3'-5')-H-phosphonates were synthesized via condensation of the protected ribonucleoside 3'-H-phosphonates with nucleosides, and the influence of a nucleoside sequence on the observed stereoselectivity was analyzed. 31P NMR spectroscopy was used to evaluate a relationship between chemical shift and absolute configuration at the phosphorous center of the H-phosphonate diesters as well as of the corresponding phosphorothioate diesters. Although for the most cases such correlation was found, there was however several exceptions to the rule where the relative positions of resonances arisingfrom Rp and Sp diastereomers were reversed.
Establishment of HLA-DR4 Transgenic Mice for the Identification of CD4+ T Cell Epitopes of Tumor-Associated Antigens (2013)

Reports have shown that activation of tumor-specific CD4(+) helper T (Th) cells is crucial for effective anti-tumor immunity and identification of Th-cell epitopes is critical for peptide vaccine-based cancer immunotherapy. Although computer algorithms are available to predict peptides with high binding affinity to a specific HLA class II molecule, the ability of those peptides to induce Th-cell responses must be evaluated. We have established HLA-DR4 (HLA-DRA*01:01/HLA-DRB1*04:05) transgenic mice (Tgm), since this HLA-DR allele is most frequent (13.6%) in Japanese population, to evaluate HLA-DR4-restricted Th-cell responses to tumor-associated antigen (TAA)-derived peptides predicted to bind to HLA-DR4. To avoid weak binding between mouse CD4 and HLA-DR4, Tgm were designed to express chimeric HLA-DR4/I-E(d), where I-E(d) α1 and β1 domains were replaced with those from HLA-DR4. Th cells isolated from Tgm immunized with adjuvant and HLA-DR4-binding cytomegalovirus-derived peptide proliferated when stimulated with peptide-pulsed HLA-DR4-transduced mouse L cells, indicating chimeric HLA-DR4/I-E(d) has equivalent antigen presenting capacity to HLA-DR4. Immunization with CDCA155-78 peptide, a computer algorithm-predicted HLA-DR4-binding peptide derived from TAA CDCA1, successfully induced Th-cell responses in Tgm, while immunization of HLA-DR4-binding Wilms' tumor 1 antigen-derived peptide with identical amino acid sequence to mouse ortholog failed. This was overcome by using peptide-pulsed syngeneic bone marrow-derived dendritic cells (BM-DC) followed by immunization with peptide/CFA booster. BM-DC-based immunization of KIF20A494-517 peptide from another TAA KIF20A, with an almost identical HLA-binding core amino acid sequence to mouse ortholog, successfully induced Th-cell responses in Tgm. Notably, both CDCA155-78 and KIF20A494-517 peptides induced human Th-cell responses in PBMCs from HLA-DR4-positive donors. Finally, an HLA-DR4 binding DEPDC1191-213 peptide from a new TAA DEPDC1 overexpressed in bladder cancer induced strong Th-cell responses both in Tgm and in PBMCs from an HLA-DR4-positive donor. Thus, the HLA-DR4 Tgm combined with computer algorithm was useful for preliminary screening of candidate peptides for vaccination.
Lithium niobate-based transparent ultrasound transducers for photoacoustic imaging (2019)

This Letter demonstrates lithium niobate (LiNbO<sub>3</sub>)-based transparent ultrasound transducers (TUTs) for photoacoustic imaging applications. The TUTs were fabricated by coating the top and bottom surfaces of a 0.25 mm thick LiNbO<sub>3</sub>wafer with transparent indium-tin-oxide (ITO) electrodes. The resulting transducers showed ∼80% optical transparency in the wavelength range of 690-970 nm. The TUTs had a resonant frequency of 14.5 MHz and ∼70% photoacoustic bandwidth. The versatility of the TUT approach is demonstrated by introducing two different transparent photoacoustic imaging (PAI) geometries. In one method, which suits endoscopy applications, an optical fiber of a laser diode is directly fixed on the backside of a 2.5 mm diameter TUT, and the fiber-TUT device is raster scanned to form 3D photoacoustic images. In the second method, which suits high-throughput applications, a free-space optical-only raster scanning of the laser fiber across a 1 cm×1 cm planar TUT yielded 3D photoacoustic images. The proposed TUT approach is low in cost, easy to manufacture, compatible with conventional clinical ultrasound electronics, and scalable for different configurations, including 2D TUT arrays to achieve real-time 3D high-throughput PAI.
Joule heating effects on particle immobilization in insulator‐based dielectrophoretic devices (2013)

In this work, the temperature effects due to Joule heating obtained by application of a direct current electric potential were investigated for a microchannel with cylindrical insulating posts employed for insulator-based dielectrophoresis. The conductivity of the suspending medium, the local electric field, and the gradient of the squared electric field, which directly affect the magnitude of the dielectrophoretic force exerted on particles, were computationally simulated employing COMSOL Multiphysics. It was observed that a temperature gradient is formed along the microchannel, which redistributes the conductivity of the suspending medium leading to an increase of the dielectrophoretic force toward the inlet of the channel while decreasing toward the outlet. Experimental results are in good agreement with simulations on the particle-trapping zones anticipated. This study demonstrates the importance of considering Joule heating effects when designing insulator-based dielectrophoresis systems.
An Overview of Phenylcyclopropylamine Derivatives: Biochemical and Biological Significance and Recent Developments (2012)

trans-2-Phencylcyclopropylamine (2-PCPA), a potent, clinically used antidepressant, affects monoamine neurotransmitter levels by inhibiting the main metabolizing enzymes, monoamine oxidases (MAOs). However, the antidepressant action of this compound was not fully explained by its effects on MAOs due to its wide variety of biological effects. 2-PCPA also affects depression-associated pathophysiological pathways, and linked with increased levels of trace amines in brain, upregulation of GABAB receptors (where GABA is gamma amino butyric acid), modulation of phospholipid metabolism, and interference with various cytochrome P450 (CYP) enzymes. Consequently, despite its adverse effects and limited clinical applicability, 2-PCPA has attracted interest as a structural scaffold for the development of mechanism-based inhibitors of various enzymes, including lysine-specific demethylase 1 (LSD1), which is a possible target for cancer chemotherapy. In the recent years, many reports have appeared in the literature based on 2-PCPA scaffold and their potential medicinal implications. This review mainly focuses on the medicinal chemistry aspects including drug design, structure-activity relationships (SAR), biological and biochemical properties, and mechanism of actions of 2-PCPA and its derivatives. Furthermore, we also highlight recent advance in this area and discuss their future applications for beneficial therapeutic effects.
Expression of Human Interleukin-2 in Recombinant Baby Hamster Kidney, Ltk−, and Chinese Hamster Ovary Cells (1989)

The similarity or identity of O-glycosylation in glycoproteins from natural sources or produced in heterologous cell lines, a central problem for the development of many biotechnologically relevant production processes, was examined using interleukin-2 (IL-2) as a model. Human interleukin-2 was constitutively expressed in several mammalian cell lines in high amounts. The recombinant proteins were purified to homogeneity and their carbohydrate structures were analyzed. Only the NeuAc alpha 2-3Gal beta 1-3[NeuAc alpha 2-6]GalNAc oligosaccharide structure or the NeuAc alpha 2-3Gal beta 1-3GalNAc were found in all IL-2 preparations secreted from recombinant Ltk-, Chinese hamster ovary, and baby hamster kidney cell lines. The O-linked chains were exclusively linked to Thr in position 3 of the polypeptide chain which is the carbohydrate attachment site in natural human IL-2. The proportions of O-glycosylated versus nonglycosylated forms of the protein secreted by each recombinant cell line were independent of productivity or of cell culture conditions. Our results show that O-glycosylated human IL-2 can be produced by applying recombinant DNA technology in heterologous cell lines with the same type of post-translational modification that is observed for the protein secreted from natural T lymphocytes.
Cytotoxic T cell response against the chimeric p210 BCR-ABL protein in patients with chronic myelogenous leukemia. (1998)

Human chronic myelogenous leukemia (CML) is characterized by a translocation between chromosomes 9 and 22 that results in a BCR-ABL fusion gene coding for chimeric proteins. The junctional region of the BCR-ABLb3a2 molecule represents a potential leukemia-specific antigen which could be recognized by cytotoxic T lymphocytes (CTL). In fact, we identified a junctional nonapeptide (SSKALQRPV) which binds to HLA-A2.1 molecules. This peptide, as well as those binding to HLA-A3, -A11, and -B8 molecules (previously identified by others), elicits primary CTL responses in vitro from PBLs of both healthy donors and CML patients. Such CTL recognize HLA-matched, BCR-ABL-positive leukemic cells, implying efficient natural processing and presentation of these junctional peptides. Specific CTL were found at high frequency in 5 of 21 CML patients, suggesting that these epitopes are, to some extent, immunogenic in vivo during the course of the disease. These peptides could be useful for the development of specific immunotherapy in CML patients.
P2X7Receptor Blockade Prevents ATP Excitotoxicity in Oligodendrocytes and Ameliorates Experimental Autoimmune Encephalomyelitis (2007)

Oligodendrocyte death and demyelination are hallmarks of multiple sclerosis (MS). Here we show that ATP signaling can trigger oligodendrocyte excitotoxicity via activation of calcium-permeable P2X(7) purinergic receptors expressed by these cells. Sustained activation of P2X(7) receptors in vivo causes lesions that are reminiscent of the major features of MS plaques, i.e., demyelination, oligodendrocyte death, and axonal damage. In addition, treatment with P2X(7) antagonists of chronic experimental autoimmune encephalomyelitis (EAE), a model of MS, reduces demyelination and ameliorates the associated neurological symptoms. Together, these results indicate that ATP can kill oligodendrocytes via P2X(7) activation and that this cell death process contributes to EAE. Importantly, P2X(7) expression is elevated in normal-appearing axon tracts in MS patients, suggesting that signaling through this receptor in oligodendrocytes may be enhanced in this disease. Thus, P2X(7) receptor antagonists may be beneficial for the treatment of MS.
Normal gut microbiota modulates brain development and behavior (2011)

Microbial colonization of mammals is an evolution-driven process that modulate host physiology, many of which are associated with immunity and nutrient intake. Here, we report that colonization by gut microbiota impacts mammalian brain development and subsequent adult behavior. Using measures of motor activity and anxiety-like behavior, we demonstrate that germ free (GF) mice display increased motor activity and reduced anxiety, compared with specific pathogen free (SPF) mice with a normal gut microbiota. This behavioral phenotype is associated with altered expression of genes known to be involved in second messenger pathways and synaptic long-term potentiation in brain regions implicated in motor control and anxiety-like behavior. GF mice exposed to gut microbiota early in life display similar characteristics as SPF mice, including reduced expression of PSD-95 and synaptophysin in the striatum. Hence, our results suggest that the microbial colonization process initiates signaling mechanisms that affect neuronal circuits involved in motor control and anxiety behavior.
Development of an orientation-dependent anisotropic etching simulation system MICROCAD (2000)

As a tool to support the fabrication process design of micromachine devices with complicated three-dimensional (3D) configurations, a crystal orientation-dependent aniso-tropic etching analysis system called MICROCAD has been developed. This system has the capability to analyze the time variations of the 3D etching profile for an arbitrary mask pattern, by preparing the etching rate of the single-crystal silicon to be processed in all directions as a database. The measurement method of the etching rate in all directions, the configuration of the analysis system, and the computational method for the 3D etching profile are described. As examples of the applications of this system, a design of a compensation mask pattern, an analysis of the etching shape while still in progress after etching through of the wafer, and the process design of a multistage etching process are presented so that the effectiveness of this system for the process design is discussed. © 2000 Scripta Technica, Electron Comm Jpn Pt 2, 83(4): 13–22, 2000