gebhart/patrepeval huggingface dataset:
Design and Use of a Mammalian Protein-Protein Interaction Trap (MAPPIT) (2002)

Identifying the interaction partners of a protein is a straightforward way to gain insight into the protein's function and to position it in an interaction network such as a signal transduction pathway. Various techniques have been developed to serve this purpose, and some are specifically designed to study posttranslational modifications in mammalian proteins and to clarify their normal physiological context. However, several intrinsic constraints limit the use of these technologies, and most are not suitable for screening for new interacting partners. In the Mammalian Protein-Protein Interaction Trap (MAPPIT) Protocol described here, knowledge of cytokine receptor signaling has been used to design a versatile genetic tool that can be used analytically and for detection of new protein-protein interactions in mammalian cells.
Rokeya, painting (2011)

Click to increase image sizeClick to decrease image size Notes 1. Copyright permission to reprint this excerpt from Another Gulmohar Tree (2009) has been obtained from the author.
Power assist control for leg with HAL-3 based on virtual torque and impedance adjustment (2004)

This paper describes a method of power assist control for lower body based on neuromuscular signal, s-EMG (surface ElectroMyogram/Myoelectricity), and impedance adjustment around knee joint with the assist system, HAL (Hybrid Assistive Leg) -3 we have developed. Virtual Torque calculated by s-EMG enabled the HAL-3 to be operated as to intention of the experimental subject put on HAL, and assist the motion of lower body by predicting the moment around joints. Besides, the operator was able to swing the leg lighter by reducing the inertia and viscous friction around joint of the subject and HAL-3. In order to verify the proposed method, experiments for simple motion was performed with impedance values found by parameter identification with RLS (Recursive Least Square) method. The evaluation of assisted motion was done by Assist Efficiency (AE) calculated from s-EMG in nearly proportion to the operator's muscle force. The results showed the response of operational signal into actuator with impedance adjustment was improved dramatically, and the amplitudes of s-EMG were reduced significantly, then we could confirm the availability of impedance adjustment.
Histone Deacetylase-3 Activation Promotes Tumor Necrosis Factor-α (TNF-α) Expression in Cardiomyocytes during Lipopolysaccharide Stimulation (2010)

Lipopolysaccharides (LPS) induce tumor necrosis factor-alpha (TNF-alpha) production in cardiomyocytes, which contributes to myocardial depression during sepsis. However, the underlying mechanisms remain not fully understood. This study was undertaken to investigate the contribution of histone deacetylase (HDAC) to TNF-alpha expression in cardiomyocytes and the signaling mechanism of LPS-induced HDAC activation. Here, we show for the first time that LPS increases HDAC activity and that inhibition of HDAC decreases LPS-stimulated TNF-alpha expression via the accumulation of NF-kappaB/p65 at the TNF-alpha promoter in cardiomyocytes. Using a positive screen, we have further identified HDAC3 as a specific member of the HDAC family able to regulate TNF-alpha production. Furthermore, our data reveal that LPS-induced HDAC activity is mediated through reactive oxygen species from mitochondria and c-Src signaling. In summary, this study demonstrates a novel signaling mechanism by which LPS via mitochondrial reactive oxygen species/c-Src/HDAC3 pathways mediate TNF-alpha expression in cardiomyocytes.
Purification of Glycosaminoglycans from Bovine Follicular Fluid (1987)

The follicular glycosaminoglycans, dermatan sulfate and heparan sulfate, are not available in sufficient quantities for detailed analytical studies or to use as reagents in cell cultures. The purpose of this study was to purify follicular glycosaminoglycans simultaneously from bovine follicular fluid. The use of a chloroform:methanol extraction of 10 ml of fluid resulted in recoveries of at least 90% of the glycosaminoglycans, otherwise an insoluble product resulted. Heparan sulfate and dermatan sulfate eluted at .11 and .46 M NaCl, respectively, when subjected to HPLC with an anion exchange column. Fluid from small follicles allowed to "age" in the ovaries exhibited marked reductions in the concentrations of glycosaminoglycans. Aging of the fluid from large follicles resulted in greater glycosaminoglycan concentrations and appearance of glycosaminoglycans reflecting other charge distributions. Known amounts of purified follicular fluid heparan sulfate and dermatan sulfate were applied to a gel filtration HPLC column, and corresponding integrated peak areas were plotted in relation to the glycosaminoglycan concentrations. Slopes of the lines for commercial chondroitin sulfate and follicular dermatan sulfate were not significantly different, but the slope of the line for follicular heparan sulfate was 13.5-fold greater than the slope for commercial heparin.
XDMS-Network Address Book enabler (2007)

Various network functions such as, Presence, Push to Talk Over Cellular (PoC), Instant Messaging (IM), etc. need to access and manipulate personal, group and professional information owned by the end users from multiple places (home, work, travel, etc.) and devices (mobile phones, PDA, computers, network, etc.). These information (contacts, calendars, task list, notes or files) are not always composed of pure lists, but can be a combination of lists together with other properties define an end-userpsilas personalization of service behaviour. The XML Document Management Server -Network Address Book (NAB) enabler provides documents that can be shared by multiple enablers in real time and a common data synchronization framework for synchronizing data on network devices.
Boron acids as protective agents and catalysts in synthesis (2002)

Covering: 1978–2000. Previous review: R. J. Ferrier, Adv. Carbohydr. Chem. Biochem., 1978, 35, 31–80.
Quantitation of Membrane Type Serine Protease 1 (MT-SP1) in Transformed and Normal Cells (2003)

Membrane type serine protease 1 (MT-SP1) is a representative member of a large family of related enzymes known as type II transmembrane serine proteases or membrane type serine proteases. MT-SP1 has been implicated in the selective proteolysis of key extracellular substrates but its physiological role is still not fully understood. MT-SP1 expression at the protein and RNA level has been previously examined by nonquantitative methods such as in situ hybridization, Northern blotting and immunohistochemistry. To establish an introductory understanding of the quantitative mRNA expression of MT-SP1 and to correlate these levels with urokinase-type plasminogen activator receptor (uPAR), a key component of extracellular proteolysis, quantitative RT-PCR was carried out. RNA expression was analyzed in 34 human cancer cell lines, 26 human tissues and 18 primary human breast cancer tissue samples. MT-SP1 mRNA is highly expressed in many breast, ovarian, prostate and colon cancer cell lines and normal human tissues of endodermal origin. At the transcript level, MT-SP1 shows a highly statistically significant correlation (Pearson's product moment correlation r = 0.784, p < 0.001) with uPAR in human breast cancer tissue. The exact role of MT-SP1 in concert with proteins such as uPAR and other members of the plasminogen activator cascade has yet to be ascertained. However, the significant correlation between MT-SP1 and uPAR transcript levels in this initial study suggests further work to establish the role of MT-SP1 as a possible prognostic, diagnostic or therapeutic target for breast cancer.
Arabidopsis Basic Leucine Zipper Proteins That Mediate Stress-Responsive Abscisic Acid Signaling (2002)

The phytohormone abscisic acid (ABA) plays an essential role in adaptive stress responses. The hormone regulates, among others, the expression of numerous stress-responsive genes. From various promoter analyses, ABA-responsive elements (ABREs) have been determined and a number of ABRE binding factors have been isolated, although their in vivo roles are not known. Here we report that the ABRE binding factors ABF3 and ABF4 function in ABA signaling. The constitutive overexpression of ABF3 or ABF4 in Arabidopsis resulted in ABA hypersensitivity and other ABA-associated phenotypes. In addition, the transgenic plants exhibited reduced transpiration and enhanced drought tolerance. At the molecular level, altered expression of ABA/stress-regulated genes was observed. Furthermore, the temporal and spatial expression patterns of ABF3 and ABF4 were consistent with their suggested roles. Thus, our results provide strong in vivo evidence that ABF3 and ABF4 mediate stress-responsive ABA signaling.
Identification of novel transcripts in annotated genomes using RNA-Seq (2011)

Supplementary data are available at Bioinformatics online.
MAGED4 – expression in renal cell carcinoma and identification of an HLA-A*25-restricted MHC class I ligand from solid tumor tissue (2005)

MAGE derived HLA ligands have repeatedly been shown to elicit T-cell responses against tumor cells. In renal cell carcinoma (RCC), however, only few T-cell epitopes from cancer testis antigens have been described. To identify potential candidates, we applied a combined approach of microarray/qPCR expression analysis and sequencing of HLA ligands from RCC by mass spectrometry. We analyzed the expression of 21 MAGE genes in ten RCC samples and two glioblastoma samples and could identify the first MHC class I ligand NIGDEALIGRW from MAGED4 presented by HLA-A*25 on RCC solid tumor tissue. MAGED4 was expressed in 30% of RCC and both glioblastoma samples. Among the other MAGE family members only MAGEB2 and -C1 and the broadly expressed MAGED1, -D2, -F1 and -H1 were expressed in RCC. Ligands from MAGED4 could thus be interesting tumor-associated antigens in a subset of RCC, even though the identified ligand is presented by a rather rare allele.
Increased Expression of Interleukin-18 and its Receptor in Peripheral Blood of Patients with Chronic Obstructive Pulmonary Disease (2012)

Chronic obstructive pulmonary disease (COPD) is a complex systemic disorder characterized by both local pulmonary and systemic inflammation. Many studies suggested that activation of circulating inflammatory cells and increased circulating levels of inflammatory cytokines occur in COPD. Interleukin (IL)-18 is a unique proinflammatory cytokine that mediates its effects by binding to the IL-18 receptor (IL-18R). In the present study, the expression of IL-18 in serum and IL-18R on peripheral blood T lymphocytes was analyzed. Enzyme-linked immunosorbent assay (ELISA) was used to determine the serum levels of IL-18 and interferon (IFN)-γ, and high sensitivity C-reactive protein (hsCRP) were measured by chemiluminiscent immunoassay. Expression of IL-18R was examined using a three-color flow cytometry method. In total, 120 subjects were recruited including 32 nonsmokers, 30 current smokers and 58 stable COPD patients. Serum levels of IL-18 and hsCRP were significantly higher in stable COPD patients than those in nonsmokers and current smokers. A significant negative correlation existed between pulmonary function and serum level of IL-18 rather than hsCRP in stable COPD patients. The proportions of IL-18Rα-expressing T lymphocytes and CD8(+) T lymphocytes were significantly higher in stable COPD patients than in nonsmokers and current smokers. The current study extended prior analyses by examining IL-18R expression in peripheral blood. The results suggested that IL-18/IL-18R system was active in peripheral blood of COPD patients.
Use of thoracoscopy and a minimal thoracotomy, in mammary-coronary bypass to left anterior descending artery, without extracorporeal circulation. Experience in 2 cases. (1995)

A new surgical approach to mammary-coronary bypasses, to the left anterior descending artery, without the use of extracorporeal circulation, is described here. A minimal left anterior thoracotomy and the use of thoracoscopy are combined in this procedure performed in two patients (54-year-old male and 56-year-old male). Results were excellent: both patients were soon discharged from hospital (3 days patient 1 and 36 hours patient 2). Neither blood nor inotropic drugs were required. New angiographies previous to discharge were done, showing 100% patency of the mammary grafts. Both patients are angina-free. Due to its simplicity, and with more experience, this technique could be a good alternative for patients with severe lesions of the left anterior descending artery.
Syntheses of (S,S)-Reboxetine via a Catalytic Stereospecific Rearrangement of β-Amino Alcohols (2007)

The formal total synthesis of (S,S)-reboxetine has been realized by two different approaches using a stereospecific rearrangement of beta-amino alcohols catalyzed by (CF3CO)2O.
DC and microwave performance of high-current AlGaN/GaN heterostructure field effect transistors grown on p-type SiC substrates (1998)

The fabrication and characterization of high performance AlGaN/GaN heterostructure field effect transistors (HFETs) grown on p-type SiC substrates are reported for the first time. The HFETs were fabricated with gate lengths of 0.25, 0.5, and 1 μm. These devices exhibited simultaneously high drain currents, high extrinsic transconductances, and excellent frequency response. The 0.25-μm gate-length devices produced a peak drain current of 1.43 A/mm, a transconductance of 229 mS/mm, a unity current-gain cutoff frequency of 53 GHz, and a maximum frequency of oscillation of 58 GHz. The unity current-gain cutoff frequency also exhibited little degradation as the drain-source bias was swept up to 20 V. These results represent a significant improvement over similar HFETs grown on sapphire substrates and are attributed to the higher thermal conductivity and reduced lattice mismatch associated with SiC substrates.
Detection of β 2 -adrenergic receptor dimerization in living cells using bioluminescence resonance energy transfer (BRET) (2000)

Heptahelical receptors that interact with heterotrimeric G proteins represent the largest family of proteins involved in signal transduction across biological membranes. Although these receptors generally were believed to be monomeric entities, a growing body of evidence suggests that they may form functionally relevant dimers. However, a definitive demonstration of the existence of G protein-coupled receptor (GPCR) dimers at the surface of living cells is still lacking. Here, using bioluminescence resonance energy transfer (BRET), as a protein-protein interaction assay in whole cells, we unambiguously demonstrate that the human beta(2)-adrenergic receptor (beta(2)AR) forms constitutive homodimers when expressed in HEK-293 cells. Receptor stimulation with the hydrophilic agonist isoproterenol led to an increase in the transfer of energy between beta(2)AR molecules genetically fused to the BRET donor (Renilla luciferase) and acceptor (green fluorescent protein), respectively, indicating that the agonist interacts with receptor dimers at the cell surface. Inhibition of receptor internalization did not prevent agonist-promoted BRET, demonstrating that it did not result from clustering of receptors within endosomes. The notion that receptor dimers exist at the cell surface was confirmed further by the observation that BS3, a cell-impermeable cross-linking agent, increased BRET between beta(2)AR molecules. The selectivity of the constitutive interaction was documented by demonstrating that no BRET occurred between the beta(2)AR and two other unrelated GPCR. In contrast, the well characterized agonist-dependent interaction between the beta(2)AR and the regulatory protein beta-arrestin could be monitored by BRET. Taken together, the data demonstrate that GPCR exist as functional dimers in vivo and that BRET-based assays can be used to study both constitutive and hormone-promoted selective protein-protein interactions.
Hypoxia-Activated Prodrugs: Substituent Effects on the Properties of Nitro seco-1,2,9,9a-Tetrahydrocyclopropa[c]benz[e]indol-4-one (nitroCBI) Prodrugs of DNA Minor Groove Alkylating Agents (2009)

Nitrochloromethylbenzindolines (nitroCBIs) are a new class of hypoxia-activated prodrugs for antitumor therapy. The recently reported prototypes undergo hypoxia-selective metabolism to form potent DNA minor groove alkylating agents and are selectively toxic to some but not all hypoxic tumor cell lines. Here we report a series of 31 analogues that bear an extra electron-withdrawing substituent that serves to raise the one-electron reduction potential of the nitroCBI. We identify a subset of compounds, those with a basic side chain and sulfonamide or carboxamide substituent, that have consistently high hypoxic selectivity. The best of these, with a 7-sulfonamide substituent, displays hypoxic cytotoxicity ratios of 275 and 330 in Skov3 and HT29 human tumor cell lines, respectively. This compound (28) is efficiently and selectively metabolized to the corresponding aminoCBI, is selectively cytotoxic under hypoxia in all 11 cell lines examined, and demonstrates activity against hypoxic tumor cells in a human tumor xenograft in vivo.
Recombinant Vitronectin Is a Functionally Defined Substrate That Supports Human Embryonic Stem Cell Self-Renewal via αVβ5 Integrin (2008)

Defined growth conditions are essential for many applications of human embryonic stem cells (hESC). Most defined media are presently used in combination with Matrigel, a partially defined extracellular matrix (ECM) extract from mouse sarcoma. Here, we defined ECM requirements of hESC by analyzing integrin expression and ECM production and determined integrin function using blocking antibodies. hESC expressed all major ECM proteins and corresponding integrins. We then systematically replaced Matrigel with defined medium supplements and ECM proteins. Cells attached efficiently to natural human vitronectin, fibronectin, and Matrigel but poorly to laminin + entactin and collagen IV. Integrin-blocking antibodies demonstrated that alphaVbeta5 integrins mediated adhesion to vitronectin, alpha5beta1 mediated adhesion to fibronectin, and alpha6beta1 mediated adhesion to laminin + entactin. Fibronectin in feeder cell-conditioned medium partially supported growth on all natural matrices, but in defined, nonconditioned medium only Matrigel or (natural and recombinant) vitronectin was effective. Recombinant vitronectin was the only defined functional alternative to Matrigel, supporting sustained self-renewal and pluripotency in three independent hESC lines.
Vaccination with Plasmid DNA Encoding Mycobacterial Antigen 85A Stimulates a CD4+and CD8+T-Cell Epitopic Repertoire Broader than That Stimulated byMycobacterium tuberculosisH37Rv Infection (1998)

Vaccination of mice with plasmid DNA carrying the gene for the major secreted mycobacterial antigen 85A (Ag85A) from Mycobacterium tuberculosis is a powerful technique for generating robust specific Thl helper T-cell responses, CD8+-mediated cytotoxicity, and protection against M. tuberculosis challenge (K. Huygen et al., Nat. Med. 2:893-898, 1996). We have now analyzed in more detail the antigen-specific immune CD4+- and CD8+-T-cell responses induced in BALB/c mice vaccinated with Ag85A DNA and have compared these responses to those generated by intravenous infection with M. tuberculosis. T-cell-epitope mapping, as measured by interleukin-2 and gamma interferon secretion from splenic T cells restimulated in vitro with synthetic 20-mer peptides spanning the complete mature sequence of Ag85A, demonstrated that DNA vaccination stimulated a stronger and broader T-cell response than did M. tuberculosis infection. Moreover, elevated cytotoxic T lymphocyte (CTL) activity against Ag85A-transfected and peptide-pulsed P815 target cells could be generated exclusively by vaccination with plasmid DNA, not following M. tuberculosis infection. By using DNA vaccination, three Ag85A CTL epitopes with predicted major histocompatibility complex class I binding motifs were defined. One of them was previously reported as a dominant, promiscuously recognized T-cell epitope in healthy humans with primary infections. These data strengthen the potential of DNA vaccination with respect to inducing antituberculous immunity in humans.
Interstitial MR lymphography using Gd-carrying liposomes. (1997)

The detection of metastasis in lymph nodes is greatly enhanced by the use of contrast media. Interstitial injection of lymphography contrast agents requires only injection of a low dose of the agent, and leads to high accumulation in regional lymph nodes with only minor side effects. We were able to show the suitability of liposome-encapsulated gadobutrol as an interstitially injectable lymphography contrast agent in an experimental animal model. For screening of possible lymphotrophic compounds a guinea pig model was used. Accumulation of the contrast agent in 3 successive lymph node groups was determined 4 h after subcutaneous injection of the contrast agent (about 0.1 ml of a 30 mmol Gd/l solution resulting in a total dose of 10 mumol/kg) into the interdigital skin fold of a hind limb. The Gd concentration in the first lymph node group (popliteal) was 540 mumol/l (16% dose/g tissue), in the second group (inguinal): 260 mumol/l (8% dose/g tissue), and in the third group (iliac): 910 mumol/l (27% dose/g tissue). Moreover, this compound was completely eliminated and well tolerated.
Enzymes in Organic Synthesis VII—Enzymatic Activity of Hrp After Chemical Modification of the Carbohydrate Moiety (1990)

The carbohydrate moiety of horseradish peroxidase was conjugated with hexadecylamine or octylamine in a micellar medium. Recovery and purification of these conjugates was facilitated by the short length of the added spacers. The modification increased the liposolubility of the enzyme without detracting from its catalytic activity. For the hexadecylamine conjugate, the optimum reaction temperature was increased by 10d`C. In addition, activity in organic solvents, such as toluene or chloroform, remained high, even at 70d`C.
Drug-Encoded Biomarkers for Monitoring Biological Therapies (2015)

Blood tests are necessary, easy-to-perform and low-cost alternatives for monitoring of oncolytic virotherapy and other biological therapies in translational research. Here we assessed three candidate proteins with the potential to be used as biomarkers in biological fluids: two glucuronidases from E. coli (GusA) and Staphylococcus sp. RLH1 (GusPlus), and the luciferase from Gaussia princeps (GLuc). The three genes encoding these proteins were inserted individually into vaccinia virus GLV-1h68 genome under the control of an identical promoter. The three resulting recombinant viruses were used to infect tumor cells in cultures and human tumor xenografts in nude mice. In contrast to the actively secreted GLuc, the cytoplasmic glucuronidases GusA and GusPlus were released into the supernatants only as a result of virus-mediated oncolysis. GusPlus resulted in the most sensitive detection of enzyme activity under controlled assay conditions in samples containing as little as 1 pg/ml of GusPlus, followed by GusA (25 pg/ml) and GLuc (≥375 pg/ml). Unexpectedly, even though GusA had a lower specific activity compared to GusPlus, the substrate conversion in the serum of tumor-bearing mice injected with the GusA-encoding virus strains was substantially higher than that of GusPlus. This was attributed to a 3.2 fold and 16.2 fold longer half-life of GusA in the blood stream compared to GusPlus and GLuc respectively, thus a more sensitive monitor of virus replication than the other two enzymes. Due to the good correlation between enzymatic activity of expressed marker gene and virus titer, we conclude that the amount of the biomarker protein in the body fluid semiquantitatively represents the amount of virus in the infected tumors which was confirmed by low light imaging. We found GusA to be the most reliable biomarker for monitoring oncolytic virotherapy among the three tested markers.