gebhart/patrepeval huggingface dataset:
Biosynthesis of heparin. Concerted action of late polymer-modification reactions. (1980)

The substrate specificity of O-sulfotransferases involved in the biosynthesis of heparin was studied by incubating exogenous polysaccharide acceptors with mouse mastocytoma microsomal fraction in the presence of phosphoadenylyl[35S]sulfate. Characterization of the labeled products showed that O-sulfation occurs preferentially in the vicinity of N-sulfate groups; that 2-O-sulfation of L-iduronic acid residues occurs preferentially or exclusively in the absence of a 6-O-sulfate group on adjacent D-glucosamine units; and that 6-O-sulfation of D-glucosamine residues occurs readily in the presence of 2-O-sulfate groups on adjacent L-iduronic acid units. Furthermore, structural analysis of microsomal heparin-precursor polysaccharides showed a distinct intermediate species that contained 2-O-sulfated L-iduronic acid units but essentially no 6-O-sulfate groups on the (N-sulfated) D-glucosamine residues. The results suggest that 2-O-sulfation of L-iduronic acid units is tightly coupled to the formation of these units (by 5-epimerization of D-glucuronic acid residues) and, furthermore, that both processes are completed before 6-O-sulfation of the polysaccharide molecule is initiated. D-Glucuronosyl 5-epimerization not accompanied by 2-O-sulfation occurs at a still earlier stage of polymer modification; the resulting L-iduronic acid units appear to remain nonsulfated throughout the subsequent modification reactions.
Single-feed small circularly polarised square microstripantenna (1997)

The design of a single-feed small microstrip antenna with circular polarisation (CP) radiation is described. This design is achieved by cutting slits in the square patch and, by adjusting the lengths of the slits, the microstrip antenna can perform CP radiation with a reduced patch size at a fixed operating frequency. This design also provides a wide CP bandwidth and relaxed fabrication tolerances.
Hsp60 Regulation of Tumor Cell Apoptosis (2007)

Molecular chaperones may promote cell survival, but how this process is regulated, especially in cancer, is not well understood. Using high throughput proteomics screening, we identified the cell cycle regulator and apoptosis inhibitor survivin as a novel protein associated with the molecular chaperone Hsp60. Acute ablation of Hsp60 by small interfering RNA destabilizes the mitochondrial pool of survivin, induces mitochondrial dysfunction, and activates caspase-dependent apoptosis. This response involves disruption of an Hsp60-p53 complex, which results in p53 stabilization, increased expression of pro-apoptotic Bax, and Bax-dependent apoptosis. In vivo, Hsp60 is abundantly expressed in primary human tumors, as compared with matched normal tissues, and small interfering RNA ablation of Hsp60 in normal cells is well tolerated and does not cause apoptosis. Therefore, Hsp60 orchestrates a broad cell survival program centered on stabilization of mitochondrial survivin and restraining of p53 function, and this process is selectively exploited in cancer. Hsp60 inhibitors may function as attractive anticancer agents by differentially inducing apoptosis in tumor cells.
Molecular cloning of cDNAs encoding a LD78 receptor and putative leukocyte chemotactic peptide receptors (1993)

Several cDNA clones encoding receptors for leukocyte chemoattractants, including IL-8, C5a, N-formyl peptides (FP), and platelet-activating factor, have been isolated in the past 3 years. The primary structure of these receptors revealed that they are members of the superfamily of G protein-coupled receptors containing seven transmembrane domains. In this study the polymerase chain reaction was carried out to isolate novel cDNA clones encoding human receptors of IL-8 related cytokines, chemokines, from a human monocyte cDNA library using degenerate oligonucleotide primers devised from conserved sequences among the cDNAs encoding the human receptors for IL-8, FP and C5a. Four novel cDNA clones (HM63, HM74, HM89, and HM145) in addition to cDNAs for FP and C5a receptors were isolated. All polypeptides encoded by the cloned cDNAs share common features with the G protein-coupled receptor superfamily, such as seven putative hydrophobic transmembrane domains and, except for HM74, N-linked glycosylation sites near the N-terminus. The amino acid sequence identities among HM63, HM89, HM145, IL-8 receptors, FP receptor, and C5a receptor are in the range of 24-68%, higher than those of other members of the G protein-coupled receptor superfamily. Moreover, the number of amino acids between the fifth and sixth transmembrane domains, which varies within this superfamily, is the same in these receptors. Thus, three of the newly identified proteins probably belong to a 'leukocyte chemotactic peptide receptor family'. HM74 differs from the other clones with respect to the amino acid homology, suggesting that this may be the receptor for a different type of ligand. Furthermore, it was confirmed that HM145 is a functional receptor for LD78, one of the C-C chemokines, as revealed by the measurement of decrease of cAMP accumulation as well as calcium influx using stable transfectants.
Plasmin‐activated doxorubicin prodrugs containing a spacer reduce tumor growth and angiogenesis without systemic toxicity (2004)

To generate doxorubicin (Dox) specifically at the tumor site, the chemotherapeutic agent was incorporated into a prodrug by linkage to a peptide specifically recognized by plasmin, which is overproduced in many cancers. ST-9905, which contains an elongated self-elimination spacer, is activated more rapidly in vitro by plasmin than is ST-9802. Prodrug activation in vitro depended on the level of urokinase produced by tumor cells and was inhibited by aprotinin, a plasmin inhibitor. Comparison of equimolar concentrations of ST-9905, ST-9802, and Dox in EF43.fgf-4 and MCF7 models revealed that both prodrugs, in sharp contrast to Dox, displayed antiproliferative and antiangiogenic activities without discernible toxicity. Although MCF7 cells are poor urokinase producers in vitro, prodrug efficacy in this model may be explained by production of plasmin by tumor-infiltrating host cells. Mice treated with equitoxic concentrations (maximum tolerated doses) of prodrugs showed 100% survival and negligible body weight loss, in contrast to results after Dox treatment. ST-9905 was substantially more effective than ST-9802 and induced similar tumor growth inhibition as Dox but without apparent toxicity. This finding may be explained by the elongated spacer, which facilitates enzymatic prodrug activation. These data validate both the use of elongated spacers in vivo and the concept of targeting anticancer prodrugs to tumor-associated plasmin.
Video Object Segmentation Using Bayes-Based Temporal Tracking and Trajectory-Based Region Merging (2004)

A novel unsupervised video object segmentation algorithm is presented, aiming to segment a video sequence to objects: spatiotemporal regions representing a meaningful part of the sequence. The proposed algorithm consists of three stages: initial segmentation of the first frame using color, motion, and position information, based on a variant of the K-means-with-connectivity-constraint algorithm; a temporal tracking algorithm, using a Bayes classifier and rule-based processing to reassign changed pixels to existing regions and to efficiently handle the introduction of new regions; and a trajectory-based region merging procedure that employs the long-term trajectory of regions, rather than the motion at the frame level, so as to group them to objects with different motion. As shown by experimental evaluation, this scheme can efficiently segment video sequences with fast moving or newly appearing objects. A comparison with other methods shows segmentation results corresponding more accurately to the real objects appearing on the image sequence.
Animal Models as the Basis of Pharmacologic Intervention in Trauma and Sepsis Patients (1996)

With limited resources and the current concerns about using animals for research purposes, the needs must be clear when setting up trauma and sepsis experiments for pharmacologic interventions. Such interventions are performed typically for four reasons: (1) to study the pathophysiologic role of certain mediators (which can be influenced by pharmacologic agents); (2) to study the therapeutic efficacy of treatment strategies; (3) to study the overall safety of new drugs under trauma/sepsis conditions, which are adjunct studies to standard toxicology; (4) to test new diagnostic procedures in a defined trauma or sepsis setting. Intervention in the inflammatory response may be performed at several levels: (1) at the primary induction site (e.g., by antilipopolysaccharide or by preventing complement activation); (2) at the intermediate mediator level (e.g., by antitumor necrosis factor); (3) at the final mediator level (e.g. , by block of polymorphonuclear neutrophil elastase, and (4) at the target (e.g., by membrane stabilization or enhanced antioxidant defense).
Heterologous expression of genes in filamentous fungi. (1999)

Isolation of some biologically important proteins from natural sources was found to be too expensive or scarcely possible (human proteins). The problem could be solved by expression of heterologous genes. Many biologically active proteins have been successfully expressed in filamentous fungi, some of them, however, at a low level. Thus, improvement of this technique appears to be a very important task. The process comprises several steps. Some of them, such as efficient transformation, vector construction, processing of signal sequences, post-translational modifications and secretion of the expressed proteins, have been intensively investigated. This review presents obstacles and problems encountered in expression of heterologous genes and discusses strategies of development in this area.
Targeted cell killing by reconstituted caspases (2007)

We have developed a two-component system involving reconstituted caspase (recCaspase) for selective and/or conditional ablation of targeted cells. Caspases, the executioners of programmed cell death, are normally synthesized as inactive zymogens and are activated by proteolytic processing of their subunits. We show here, using two different caspases, Caenorhabditis elegans CED-3 and human Caspase-3, that coexpression of the subunits generates constitutively active caspase activity that leads to cell death. This recCaspase activity, however, occurred only when the subunits associated through binding of linked antiparallel leucine-zipper domains. We exploited the dual-component nature of recCaspases by expressing the individual subunits from combinations of promoters either to target selectively the subset of cells for apoptosis or induce cell death in specific cells at specific times during development. The high degree of target specificity and tight regulation of induction of recCaspase would be advantageous in creating animal models that are ablated for specific cells and in other targeted cell killings.
Functional Significance of Tie2 Signaling in the Adult Vasculature (2004)

Abundant data now demonstrate that the growth of new blood vessels, termed angiogenesis, plays both pathological and beneficial roles in human disease. Based on these data, a tremendous effort has been undertaken to understand the molecular mechanisms that drive blood vessel growth in adult tissues. Tie2 recently was identified as a receptor tyrosine kinase expressed principally on vascular endothelium. Disrupting Tie2 function in mice resulted in embryonic lethality with defects in embryonic vasculature, suggesting a role in blood vessel maturation and maintenance. Based on these studies, we undertook a series of studies to probe the function of Tie2 in adult vasculature that will form the focus of this chapter. Consistent with a role in blood vessel growth in adult vasculature, Tie2 was upregulated and activated in the endothelium of rat ovary and in healing rat skin wounds, both areas of active angiogenesis. Moreover, Tie2 was upregulated in the endothelium of vascular "hot spots" in human breast cancer specimens. Surprisingly, Tie2 also was expressed and activated in the endothelium of all normal rat tissues examined, suggesting a role in maintenance of adult vasculature. To determine the functional role of Tie2 in tumor vasculature, a soluble Tie2 extracellular domain (ExTek) was designed that blocked the activation of Tie2 by its activating ligand, angiopoietin 1 (Ang1). Administration of recombinant ExTek protein or an ExTek adenovirus inhibited tumor growth and metastasis in rodent tumor models, demonstrating a functional role for Tie2 in pathological angiogenesis in adult tissues. To begin to understand the endothelial signaling pathways and cellular responses that mediate Tie2 function, we identified signaling molecules that are recruited to the activated, autophosphorylated Tie2 kinase domain. Two of these molecules, SHP2 and GRB2, are part of the pathway upstream of mitogen-activated protein kinase (MAPK) activation, a pathway that may be responsible for morphogenetic effects of Tie2 on endothelial cells. Another signaling molecule, p85, is responsible for recruitment of phosphatidylinositol 3 kinase (PI3-K) and activation of the Akt/PI3-K pathway. Akt/PI3-K has emerged as a critical pathway downstream of Tie2 that is necessary for cell survival effects as well as for chemotaxis, activation of endothelial nitric oxide synthase, and perhaps for anti-inflammatory effects of Tie2 activation. Taken together, these studies and many others demonstrate that the Tie2 pathway has important functions in adult tissues, in both quiescent vasculature and during angiogenesis, and help to validate the Tie2 pathway as a therapeutic target.
Synergistic effects of various Her inhibitors in combination with IGF-1R, C-MET and Src targeting agents in breast cancer cell lines (2017)

Overexpression of HER2 has been reported in around 25% of human breast cancers. Despite recent advances in HER2 targeted therapy, many patients still experience primary and secondary resistance to such treatments, the mechanisms for which are poorly understood. Here, we investigated the sensitivity of a panel of breast cancer cell lines to treatment with various types of HER-family inhibitors alone or in combination with other tyrosine kinase inhibitors or chemotherapeutic agents. We found that treatment with the second-generation irreversible HER-family inhibitors, particularly afatinib and neratinib, were more effective than treatment with the first-generation reversible inhibitors in inhibiting growth, migration and downstream cell signalling in breast cancer cells. Of the three HER2 overexpressing cell lines in this panel, SKBr3 and BT474 were highly sensitive to treatment with HER-family inhibitors, while MDA-MB-453 was comparatively resistant. Combinations of HER-family inhibitors with NVP-AEW541, dasatinib or crizotinib (inhibitors of IGF-1R, Src and c-Met/ALK, respectively) led to synergistic effects in some of the cell lines examined. In particular, treatment with a combination of Src and HER-family member inhibitors resulted in synergistic growth inhibition of MDA-MB453 cells, implicating Src as a mediator of resistance to HER2-targeting agents. Our results suggest that combining HER-family inhibitors with other TKIs such as dasatinib may have therapeutic advantages in certain breast cancer subtypes and warrants further investigation.
Dual Targeting of CDK and Tropomyosin Receptor Kinase Families by the Oral Inhibitor PHA-848125, an Agent with Broad-Spectrum Antitumor Efficacy (2010)

Altered expression and activity of cyclin-dependent kinase (CDK) and tropomyosin receptor kinase (TRK) families are observed in a wide variety of tumors. In those malignancies with aberrant CDK activation, the retinoblastoma protein (pRb) pathway is deregulated, leading to uncontrolled cell proliferation. Constitutive activation of TRKs is instead linked to cancer cell survival and dissemination. Here, we show that the novel small-molecule PHA-848125, a potent dual inhibitor of CDKs and TRKs, possesses significant antitumor activity. The compound inhibits cell proliferation of a wide panel of tumoral cell lines with submicromolar IC(50). PHA-848125-treated cells show cell cycle arrest in G(1) and reduced DNA synthesis, accompanied by inhibition of pRb phosphorylation and modulation of other CDK-dependent markers. The compound additionally inhibits phosphorylation of TRKA and its substrates in cells, which functionally express this receptor. Following oral administration, PHA-848125 has significant antitumor activity in various human xenografts and carcinogen-induced tumors as well as in disseminated primary leukemia models, with plasma concentrations in rodents in the same range as those found active in inhibiting cancer cell proliferation. Mechanism of action was also confirmed in vivo as assessed in tumor biopsies from treated mice. These results show that the dual CDK-TRK inhibitor PHA-848125 has the potential for being a novel and efficacious targeted drug for cancer treatment.
Cellular immune response to human sarcomas: cytotoxic T cell clones reactive with autologous sarcomas. I. Development, phenotype, and specificity. (1986)

Human T cell clones cytotoxic for autologous sarcoma cell lines have been developed from patient JM with an osteogenic sarcoma, and from patients EG and RM with malignant fibrohistiocytoma. These clones were derived from the cocultivation of peripheral blood lymphocytes (PBL) with the respective patient's autologous irradiated established tumor cell lines (AIT). After two cycles of stimulation for 5 days in bulk culture, these "educated" lymphocytes were seeded at a density of 1 X 10(6) cells/well in 24-well plates and were cultured in the presence of highly purified natural IL 2 and AIT, the latter serving as a feeder layer. Cell numbers were reduced from the initial seeding density by one log each week until reaching a density of 10(2) cells. These cells were found to be stable in viability and cytotoxic activity, after which limiting dilution was then performed. Within 4 to 6 wk, clones were isolated with unique specificities. These clones were capable of proliferating to a total density of 10(9) cells/ml and maintained their specific cytotoxicity for more than 6 mo. Testing with a panel of target cells of various histotypes, cold-target inhibition assays, and blocking of cytotoxicity with anti-HLA monoclonal antibodies showed that the T cell clones recognize a common sarcoma-associated antigen and that the lysis is HLA restricted. Phenotypically, cytotoxic clones derived from JM were Leu-1+, Leu-2+, and Leu-3-, whereas those derived from EG exhibited either Leu-24 or Leu-3+ markers, the latter phenotype lacking cytotoxicity. RM exhibited mainly Leu-3+ clones with strong cytotoxicity. All were HNK-1- and HLA class II+, with less than 1% of cells of each clone stained by anti-TAC monoclonal antibody. The clones from each patient did not lyse autologous or allogeneic PBL, mitogen-induced T lymphoblasts, normal fibroblasts, cells isolated from benign neoplasms, carcinoma cells, Daudi B lymphoid cells, or K562 cells. With the exception of EG, all clones produced immune interferon in a range from 12 to 50 U/ml. The generation of long-term specific T cell clones can be used to further dissect the cellular immune response to sarcomas. Cytotoxic T cell clones have potential application for tumor immunotherapy.
Expression of phosphorylated histone H2AX as a surrogate of cell killing by drugs that create DNA double-strand breaks. (2003)

Phosphorylation of histone H2AX on serine 139 (gammaH2AX) occurs at sites flanking DNA double-strand breaks and can provide a measure of both number and location of these breaks within the nucleus. Because double-strand breaks are often lethal and are produced by several chemotherapeutic agents, we examined the possibility that expression of gammaH2AX after treatment might be useful as a surrogate indicator of clonogenic cell kill. Chinese hamster V79 cells were exposed for 30 min to drugs known to produce DNA double-stand breaks with different efficiencies: bleomycin, tirapazamine, doxorubicin, etoposide, 4-nitro-quinoline-N-oxide, and hydrogen peroxide. Cells were then allowed 1 h to develop foci before fixation or were plated to measure colony formation ability. Anti-gammaH2AX antibody staining was measured using flow cytometry. Flow histograms were analyzed for the percentage of cells that showed gammaH2AX levels greater than untreated cells, and this percentage was compared with the clonogenic surviving fraction. H2AX expression measured 1 h after treatment predicted cell killing for all of the drugs examined over two logs of cell kill. Moreover, predictive ability was largely independent of drug type in this cell line, and gammaH2AX levels five times background resulted in 50-90% cell kill. This method seems to provide a useful indicator of clonogenic response to treatment with selected chemotherapeutic drugs.
Muscle precursor cells injected into irradiated mdx mouse muscle persist after serial injury (1999)

Muscle of donor origin was formed after implantation of H-2Kb-tsA58 muscle precursor cells (mpc) into irradiated mdx nu/nu mouse muscles. A series of injections of the myotoxin, notexin, which destroys mature muscle fibers but spares muscle precursor cells and other tissues, was made into the mpc-injected muscles, leaving time for regeneration to occur between each injection. New muscle fibers of donor origin were formed after up to four notexin treatments, providing evidence that some of the implanted mpc reentered an undifferentiated, quiescent, stem cell-like state and were capable of myogenesis after further injuries to the muscle. A similar model could be used to assay whether preparations of human mpc contain long-lasting precursor cells, prior to their implantation into patients. In control mdx muscles, which had been irradiated, injected with tissue culture medium, and given three notexin injections, regeneration also occurred, indicating that radiation-resistant mpc were present, presumably within the treated muscle. © 1999 John Wiley & Sons, Inc. Muscle Nerve 22: 174–185, 1999
Optical coherent broad-band transmission for long-haul and distribution systems using subcarrier multiplexing (1993)

The system configuration and future possibility of a coherent optical transmission system using subcarrier multiplexing (SCM) techniques are described. First, signal multiplexing techniques for coherent optical transmission are compared, and appropriate application for coherent SCM system is discussed. By comparing optical modulation methods, optical frequency modulation (FM) using direct modulation of a DFB-LD and a heterodyne detection is shown to be feasible. lkansmission system using a configuration with a local laser in the transmitter is unaffected by polarization and is cost-effective. Phase noise can be suppressed by a phase-noise-canceling circuit (PNC) in a heterodyne receiver. This circuit is also effective for compensating for the frequency instability of light sources. A theoretical simulation of a coherent SCM system showed that a 100 channel of 30-MHz FM signal or a 15 channel of 155-Mb/s signal can be distributed to 10 000 subscribers using single stage or double stage optical amplifiers. To confirm the feasibility of coherent SCM transmission, preliminary experiments have been performed with optical FM by 2-channels 560-Mb/s ASK-SCM signal and a heterodyne detection using 3-electrode DFB-LD's. With a local LD setting at the transmitter, a span-loss margin of 40.7 dB was obtained using single stage Er3+-doped fiber amplifier (EDFA), and the system was insensitive to the state of polarization in the transmission fiber. In a subcarrier transmission of 560 Mb/s DPSK signal, the PNC effectively suppressed phase noise and the influence of IF frequency deviation. Finally, application of coherent SCM combined with optical frequency division multiplexing (OFDM) is discussed. A model allocation of optical carriers is proposed and possible receiving channel number is estimated.