gebhart/patrepeval huggingface dataset:
Substituting isoserine for serine in the thrombin receptor activation peptide SFLLRN confers resistance to aminopeptidase M-induced cleavage and inactivation. (1993)

Peptides containing sequences derived from the new NH2 terminus of the seven-transmembrane domain thrombin receptor after thrombin cleavage can activate platelets directly. We recently demonstrated that such peptides are readily cleaved and inactivated by plasma, serum, and endothelial cell-associated aminopeptidase M. The rapid degradation and inactivation of the peptides makes it difficult to assess dose-response relationships precisely or to conduct long term incubations with cells in the presence of plasma or serum. To overcome these problems, we first substituted D-serine for the NH2-terminal L-serine in an active peptide ligand (SFLLRNPNDKY). The D-serine derivative resisted degradation in plasma, but it is less than 1% as active as the L-serine peptide. Substituting a racemic mixture of the beta-amino acid isoserine for serine in a related peptide ligand (SFLLRN) produced an active peptide ((iso-S)FLLRN) that is approximately 15-20% as potent as SFLLRN as judged by platelet aggregation. To assess the stability of the peptides in plasma, SFLLRN (1 mM) was incubated with 50% plasma for various periods of time; after 15 min, 65% of the peptide remained intact, and after 2 h only 4% remained intact. Loss of aggregating activity paralleled the loss of intact peptide. In contrast, even after 2 h of incubation with plasma, 83% of the (iso-S)FLLRN remained intact and the aggregating activity was essentially unchanged. Qualitative differences in the patterns of platelet aggregation produced by the peptides were also observed. Thus, the distinct pattern of aggregation followed by rapid disaggregation observed with submaximal aggregating doses of SFLLRN was less evident with (iso-S)FLLRN, and inhibition of aminopeptidase M by amastatin enhanced aggregation in platelet-rich plasma induced by SFLLRN but not (iso-S)FLLRN. The (iso-S)FLLRN peptide should permit improved analysis of the effects of constant levels of peptide-induced thrombin receptor stimulation in the presence of plasma or serum, or when testing the effects of the peptide on cells that contain surface-associated aminopeptidase M.
Functional Characterization of Filamin A Interacting Protein 1–Like, a Novel Candidate for Antivascular Cancer Therapy (2008)

Inhibiting angiogenesis has become a major therapeutic strategy for cancer treatment. To identify common intracellular mediators, we previously analyzed gene expression profiles of endothelial cells after treatment with angiogenesis inhibitors. Filamin A interacting protein 1-like (FILIP1L; previously known as down-regulated in ovarian cancer 1) was identified as one of the genes up-regulated in endothelial cells in response to these inhibitors. However, the expression and function of FILIP1L protein is uncharacterized. Here, we provide the first description of the expression and specific subcellular localization of FILIP1L protein in human tissue. Overexpression of FILIP1L resulted in inhibition of cell proliferation and migration and increased apoptosis. In addition, overexpression of FILIP1L truncation mutants showed differential antiproliferative activity. A COOH terminal truncation mutant (FILIP1LDeltaC103) was more potent than wild-type FILIP1L in mediating this activity. Targeted expression of FILIP1LDeltaC103 in tumor vasculature inhibited tumor growth in vivo. Overall, these findings suggest that the novel protein FILIP1L may be an important mediator of the effects of angiogenesis inhibitors and that FILIP1L has the potential to be an antivascular reagent for cancer therapy.
Involvement of the Ca2+-dependent Phosphatase Calcineurin in Gene Transcription That Is Stimulated by cAMP through cAMP Response Elements (1995)

Gene transcription can be induced by cAMP and Ca2+ through distinct protein kinases phosphorylating the transcription factor CREB, which binds to cAMP response elements (CREs) in various genes. Induction of gene transcription by Ca2+ has been shown recently to depend on the Ca2+/calmodulin-dependent protein phosphatase calcineurin in pancreatic islet cells. This study investigates the role of calcineurin in CRE-directed gene transcription after stimulation by cAMP. Reporter fusion genes under the transcriptional control of CREs were transiently transfected into the cell line HIT. Pharmacological evidence suggests that cAMP stimulates CRE-mediated transcription through a Ca(2+)-dependent mechanism. The immunosuppressive drugs cyclosporin A and FK506 inhibited CRE-mediated transcription stimulated by cAMP. At the same concentrations they also inhibited calcineurin phosphatase activity. Reversal of calcineurin inhibition by rapamycin or overexpression of calcineurin led to disinhibition of CRE-mediated gene transcription. Immunoblots with a phosphoCREB-specific antibody showed that cyclosporin A and FK506 do not interfere with CREB phosphorylation at serine 119 stimulated with cAMP or membrane depolarization. These results indicate that in HIT cells stimulation of CRE-mediated transcription depends not only on the activity of protein kinases phosphorylating CREB but also on the Ca2+/calmodulin-dependent protein phosphatase calcineurin that is necessary for the transcriptional competence of phosphorylated CREB.
Scavenger Receptor BI Promotes High Density Lipoprotein-mediated Cellular Cholesterol Efflux (1997)

Scavenger receptor BI (SR-BI) binds high density lipoproteins (HDL) with high affinity and mediates the selective uptake of HDL cholesteryl ester. We examined the potential role of SR-BI in mediating cellular cholesterol efflux. In Chinese hamster ovary cells stably transfected with murine SR-BI, overexpression of SR-BI resulted in a 3-4-fold stimulation of initial cholesterol efflux rates. Efflux rates correlated with SR-BI expression in cells and HDL concentration in the medium. When incubated with synthetic cholesterol-free HDL, SR-BI-transfected cells showed approximately 3-fold increases in initial rates of efflux compared with control cells, indicating that SR-BI expression enhances net cholesterol efflux mediated by discoidal HDL. In six different cell types, including cultured macrophages, the rate of efflux of cholesterol mediated by HDL or serum was well correlated with cellular SR-BI expression level. In addition, in situ hybridization experiments revealed that SR-BI mRNA was expressed in the thickened intima of atheromatous aorta of apolipoprotein E knockout mice. Thus, SR-BI is an authentic HDL receptor mediating cellular cholesterol efflux. SR-BI may facilitate the initial steps of HDL-mediated cholesterol efflux in the arterial wall as well as later steps of reverse cholesterol transport involving uptake of HDL cholesterol in the liver.
Catalytic Activation of the Plant MAPK Phosphatase NtMKP1 by Its Physiological Substrate Salicylic Acid-induced Protein Kinase but Not by Calmodulins (2005)

MAPK phosphatases (MKPs) are negative regulators of MAPKs. Previously, we identified NtMKP1 as a novel calmodulin (CaM)-binding protein (Yamakawa, H., Katou, S., Seo, S., Mitsuhara, I., Kamada, H., and Ohashi, Y. (2004) J. Biol. Chem. 279, 928-936). In this study, we characterized the interaction of NtMKP1 with substrate MAPKs and CaM. NtMKP1 (produced by in vitro transcription/translation) inactivated salicylic acid-induced protein kinase (SIPK) through dephosphorylation of the TEY motif of SIPK. CaM bound but unexpectedly did not activate the phosphatase activity of NtMKP1. NtMKP1 has four characteristic domains, viz. a dual-specificity phosphatase catalytic domain, a gelsolin homology domain, a CaM-binding domain, and C-terminal domain. Deletion analysis revealed that the N-terminal non-catalytic region of NtMKP1 bound SIPK and was essential for inactivating SIPK, whereas the CaM-binding and C-terminal domains were dispensable. Moreover, the phosphatase activity of NtMKP1 was increased strongly by the binding of SIPK, but weakly by another MAPK, wound-induced protein kinase. Swapping and site-directed mutagenesis of SIPK and wound-induced protein kinase revealed that the strong activation of NtMKP1 phosphatase activity by SIPK partially depended on the putative common docking domain of SIPK. On the other hand, conversion of Lys(41) and Arg(43) of NtMKP1 to Ala (K41A/R43A) abolished the interaction with SIPK. Expression of constitutively active MAPK kinase in Nicotiana benthamiana induced activation of SIPK and cell death. Simultaneous expression of either NtMKP1 or NtMKP1 L443R, which was unable to bind CaM, compromised the constitutively active MAPK kinase-induced responses, whereas that of NtMKP1 K41A/R43A did not. These results indicate that the regulation of NtMKP1 activity by SIPK binding, but not by CaM binding, is important for the function of NtMKP1.
Diagnosis of graft coronary artery disease (2007)

There is no test sensitive and specific enough yet that can be confidently used to replace coronary angiography.
Luminescent Silole Nanoparticles as Chemoselective Sensors for Cr(VI) (2005)

Colloidal suspensions of 3-aminopropylmethyl(tetraphenyl)silole nanoparticles can be used as selective chemosensors for carcinogenic chromium(VI) analyte. Methylhydrosilole is functionalized by hydrosilation of allylamine, and the colloid is prepared by the rapid addition of water to a THF solution of the silole. The method of detection is through electron-transfer quenching of the fluorescence of the silole colloid (lambda(em) = 485 nm at 360 nm excitation) by the analytes, with hundred parts per billion detection limits. Stern-Volmer plots are linear up to 10 ppm in the case of chromium, but exhibit saturation behavior near 5-10 ppm for arsenic. Dynamic light scattering experiments and AFM measurements show the particle sizes to be around 100 nm in diameter and dependent on solvent composition, with a particle size dispersity of +/-25%. The fluorescence lifetimes of the silole in solution and colloid are approximately 31 ps and approximately 4.3 ns, respectively, while the silole has a lifetime of 6 ns in the bulk solid. A minimum volume fraction of 80% water is necessary to precipitate the colloid from THF, and the luminescence continues to rise with higher water fractions. Colloids in a pH 7 phosphate-buffered suspension show both higher sensitivity and greater selectivity (100-fold) for CrO4(2-) detection than for other oxoanion interferents, NO3-, NO2-, SO4(2-), and ClO4-.
Alphavbeta3 integrin antagonist S247 decreases colon cancer metastasis and angiogenesis and improves survival in mice. (2003)

Members of the integrin family influence several aspects of tumor progression and metastasis, including cell survival, proliferation, and angiogenesis. Specific integrins such as alpha(v)beta(3) and alpha(v)beta(5) are involved in regulating endothelial cell function, and thus angiogenesis. We evaluated the effect of the alpha(v)beta(3)/alpha(v)beta(5) integrin antagonist S247 on the growth and angiogenesis of colon cancer liver metastases in an orthotopic murine model. Murine colon cancer cells were injected into the spleens of BALB/c mice to produce liver metastases. On day 7, miniature osmotic pumps were implanted into the subcutis to continuously infuse either saline or 70 mg/kg/day S247. All mice were sacrificed when control mice became moribund. Mice that received S247 developed significantly fewer liver metastases than did controls (P < 0.05). Using the same model, a subsequent survival study was performed. Mice were sacrificed when moribund as determined by an observer blinded to the treatment given. Treatment with S247 significantly prolonged overall survival (P < 0.05). Interestingly, primary tumors in the spleen were the cause of death in the S247-treated group as S247 appeared to have little effect on these tumors. Immunohistochemical staining demonstrated a significant reduction of vessels in liver metastases of S247-treated mice (P < 0.001), a significant increase in endothelial cell apoptosis (P < 0.05), and a significant decrease in pericyte coverage (P < 0.0001). To determine the role of S247 on angiogenesis, we examined the effect of S247 in vitro on human umbilical vein endothelial cells (HUVECs) and human vascular smooth muscle cells (hVSMCs). The addition of S247 to HUVECs and hVSMCs growing on vitronectin-coated flasks and in Matrigel significantly impaired cell growth and colony formation, respectively (P < 0.05). Furthermore, S247 completely inhibited the attachment of HUVECs and hVSMCs and increased apoptosis by six- to 9fold compared with controls. In in vitro invasion assays, S247-treated cells demonstrated decreased migration (P < 0.05). In conclusion, S247 demonstrated significant antimetastatic and antiangiogenic activity and impaired both endothelial and hVSMC/pericyte function in vitro and in vivo. The use of agents such as integrin antagonists that target multiple cell types involved in angiogenesis may be a more effective method of inhibiting angiogenesis than agents targeting only the endothelial cells.
Haptoglobin-alpha subunit as potential serum biomarker in ovarian cancer: identification and characterization using proteomic profiling and mass spectrometry. (2003)

Haptoglobin-derived alpha subunit is a potential marker for ovarian cancer that is complementary to CA125. MS-based protein profiling is a valuable tool for screening protein markers and useful to detect post-translational modification of tumor-associated proteins or abnormal metabolic products. However, confirmation of protein identity with specific antibodies is crucial for clinical application and functional studies.
Colostrum and milk fatty acids of dairy cows as influenced by extruded linseed supplementation during the transition period (2009)

The effects of precalving fat sources on fatty acid (FA) profile of colostrum and milk and on metabolic parameters in early lactation were determined. Two fat supplements (target: 21% fat, DM basis) fed at 1.8 kg DM d -1 were compared: Control (C; containing fractionated palm oil rich in 16:0) and Linseed (L; containing extruded linseed, rich in 18:3n-3). Sixteen dry Holstein (n = 7) and Brown Swiss (n = 9) cows were assigned to four groups receiving the supplements from 5 wk pre- to 4 wk post-calving in different sequences: CC, CL, LC and LL. Treatments did not affect metabolic parameters, milk yield or composition. Linseed supplementation increased proportions of 18:0, 18:1, 18:2 and 18:3 in colostrum and milk (except 18:1 for colostrum). The highest n-3 FA proportion was observed in milk of LL cows. For most 16 and 18 FA, a fast response occurred within the first week of lactation for cows that switched treatments over calving. Carry-over to milk of 18:3 and its biohydrogenation products from linseed fed precalving was low. Pre-calving feeding strategies to favour incorporation of these FA into early lactation milk were not successful, but the reasons for this failure remain unclear.Key words: Linseed, omega-3 fatty acids, transition period, milk, colostrum, dairy cows
Merging Head and Tail Duplication for Convergent Hyperblock Formation (2006)

VLIW and EDGE (explicit data graph execution) architectures rely on compilers to form high-quality hyper-blocks for good performance. These compilers typically perform hyperblock formation, loop unrolling, and scalar optimizations in a fixed order. This approach limits the compiler's ability to exploit or correct interactions among these phases. EDGE architectures exacerbate this problem by imposing structural constraints on hyperblocks, such as instruction count and instruction composition. This paper presents convergent hyperblock formation, which iteratively applies if-conversion, peeling, unrolling, and scalar optimizations until converging on hyperblocks that are as close as possible to the structural constraints. To perform peeling and unrolling, convergent hyperblock formation generalizes tail duplication, which removes side entrances to acyclic traces, to remove back edges into cyclic traces using head duplication. Simulation results for an EDGE architecture show that convergent hyperblock formation improves code quality over discrete-phase approaches with heuristics for VLIW and EDGE. This algorithm offers a solution to hyperblock phase ordering problems and can be configured to implement a wide range of policies
Targeting the Primary Tumor to Generate CTL for the Effective Eradication of Spontaneous Metastases (2007)

Metastatic disease is the major cause of morbidity and mortality in cancer. Although surgery, chemotherapy, or radiation can often control primary tumor growth, successful eradication of disseminated metastases remains rare. We have now tested whether direct targeting tumor tissues to generate antitumor immune response before surgical excision produces sufficient CTL against micrometastases. One unsolved problem is whether such response allows coming CTL to be educated and then exit the tumor site. Another unsolved problem is whether these CTL can then patrol and effectively eliminate spontaneously metastasized tumor cells in the periphery. In this study, we have shown that adenovirus-expressing TNFSF14 [LIGHT (name derived from homologous to lymphotoxins, shows inducible expression, and competes with herpes simplex virus glycoprotein D for herpes virus entry mediator, a receptor expressed by T lymphocytes); Ad-LIGHT] inoculated directly into primary 4T1 tumor, a highly aggressive, spontaneously metastasizing mammary carcinoma, followed by surgical removal of the primary tumor can eradicate established and disseminated metastatic tumor cells in the peripheral tissues. Furthermore, we clearly show with a fibrosarcoma model Ag104L(d) that local treatment can generate plenty of tumor-specific CTL that exit the primary tumor and infiltrate distal tumors to completely eradicate distal tumors. Therefore, targeting the primary tumor with Ad-LIGHT before surgical excision is a new strategy to elicit better immune response for the eradication of spontaneous metastases.
High speed silicon modulators and detectors (2012)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text L. Vivien, D. Marris-Morini, M. Ziebell, G. Rasigade, L. Virot, J. Hartmann, E. Cassan, P. Crozat, D. Bouville, C. Baudot, F. Boeuf, and J. Fédéli, "High speed silicon modulators and detectors," in Asia Communications and Photonics Conference, OSA Technical Digest (online) (Optica Publishing Group, 2012), paper ATh4B.1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Endocrine fibroblast growth factors 15/19 and 21: from feast to famine (2012)

We review the physiology and pharmacology of two atypical fibroblast growth factors (FGFs)-FGF15/19 and FGF21-that can function as hormones. Both FGF15/19 and FGF21 act on multiple tissues to coordinate carbohydrate and lipid metabolism in response to nutritional status. Whereas FGF15/19 is secreted from the small intestine in response to feeding and has insulin-like actions, FGF21 is secreted from the liver in response to extended fasting and has glucagon-like effects. FGF21 also acts in an autocrine fashion in several tissues, including adipose. The pharmacological actions of FGF15/19 and FGF21 make them attractive drug candidates for treating metabolic disease.
Structural basis for KIT receptor tyrosine kinase inhibition by antibodies targeting the D4 membrane-proximal region (2013)

Somatic oncogenic mutations in the receptor tyrosine kinase KIT function as major drivers of gastrointestinal stromal tumors and a subset of acute myeloid leukemia, melanoma, and other cancers. Although treatment of these cancers with tyrosine kinase inhibitors shows dramatic responses and durable disease control, drug resistance followed by clinical progression of disease eventually occurs in virtually all patients. In this report, we describe inhibitory KIT antibodies that bind to the membrane-proximal Ig-like D4 of KIT with significant overlap with an epitope in D4 that mediates homotypic interactions essential for KIT activation. Crystal structures of the anti-KIT antibody in complex with KIT D4 and D5 allowed design of affinity-matured libraries that were used to isolate variants with increased affinity and efficacy. Isolated antibodies showed KIT inhibition together with suppression of cell proliferation driven by ligand-stimulated WT or constitutively activated oncogenic KIT mutant. These antibodies represent a unique therapeutic approach and a step toward the development of "naked" or toxin-conjugated KIT antibodies for the treatment of KIT-driven cancers.
President's letter (1996)

</br>![][1]</img> Spring has finally arrived! Your society has been working diligently throughout the last two months to solidify the didactic and social programs for our upcoming Nashville conference. I specifically commend the tireless efforts of Dr. Russell Knudsen and Carol Rosanelli in
Current State of Intellectual Property in Microfluidic Nucleic Acid Analysis (2007)

The development of novel fabrication methods, materials and surface chemistries to implement nucleic acid analysis brings reduced cost, reduced reagent consumption, increased analysis efficiency, portability, ease of use and reliability to todays genomic approach. This trend, as evident by the exponential growth in the number of patent applications, granted patents and commercialized systems, is motivated by the promise for significant breakthroughs and benefits of nucleic acid analysis to drug discovery and point-of-care diagnosis. This review paper aims at identifying the enabling technologies and key patents in microfluidics for nucleic acid analysis. In particular, it seeks to identify granted and pending patents for cell sorting and lysis, nucleic acid extraction and purification, followed by nucleic acid amplification, separation and detection. Additionally, it presents an overview of the current intellectual property environment and seeks to identify trends for the future development. Much of this development is geared increasingly toward fully integrated systems. The convergence of technology and interdisciplinary interests is expected to foster further breakthroughs and commercialization. Keywords: Microfluidic nucleic acid analysis, cell sorting, cell lysis, nucleic acid extraction, nucleic acid separation, polymerase chain reaction, electrophoresis, integrated systems, Lab-on-a-Chip
Unique Glycan Signatures Regulate Adeno-Associated Virus Tropism in the Developing Brain (2015)

Viruses invade the CNS through various mechanisms. In the current study, we utilized AAV as a model to study the dynamics of virus-carbohydrate interactions in the developing brain and their impact on viral tropism. Our findings suggest that carbohydrate content can be exploited to regulate viral transport and tropism in the brain.
New approaches for preventing and treating chronic graft-versus-host disease (2005)

Despite improvements in the practice of allogeneic hematopoietic stem cell transplantation (HCT) over the last 25 years, chronic graft-versus-host disease (GVHD) remains a substantial problem with little change in the incidence, morbidity, and mortality of this complication. In fact, with increased use of peripheral blood, transplantation of older patients, and less immediate transplantation-related mortality, the prevalence of chronic GVHD may increase. One of the difficulties in combating chronic GVHD is a lack of understanding about the pathophysiology of the syndrome. Inherent difficulties in conducting human clinical trials also contribute to the lack of meaningful progress. This review covers potential new approaches to the prevention and treatment of chronic GVHD.