gebhart/patrepeval huggingface dataset:
Expression pattern of the neu (NGL) gene-encoded growth factor receptor protein (p185neu) in normal and transformed epithelial tissues of the digestive tract. (1989)

The neu gene (also called NGL, erbB-2, and HER-2) encodes a 185-190 kDa transmembrane glycoprotein, p185neu, which has tyrosine-specific kinase activity and is homologous to but distinct from the epidermal growth factor receptor. The normal expression of neu mRNA and protein has been demonstrated in epithelial tissues of adult animals. Also, activation of the neu oncogene has been implicated in a variety of human adenocarcinomas. In the present study, we examined the expression of the p185neu protein in normal and transformed digestive tract tissues and in a panel of digestive tract-derived cell lines. By immunohistochemistry, strong reactivity was observed in the mucosal epithelium of the stomach, small intestine, and colon of both rodents and humans. In the small intestine, there was prominent p185neu expression by mucosal epithelium of the villus, with little or no staining in the crypts. Prominent expression was observed in the liver parenchyma, the endocrine and exocrine portions of the pancreas, and in the salivary gland. Immunoreactive p185neu was also demonstrated in fetal human intestinal epithelium. Tissue sections of selected benign and malignant colonic neoplasms were also examined. Immunoreactivity was consistently greater in adenomatous polyps than in adjacent normal colonic epithelium or areas showing malignant degeneration. By radioimmunoprecipitation, there was decreased expression in cell lines derived from more anaplastic colonic tumors. The p185neu protein is expressed widely in normal and transformed epithelial tissues of the digestive tract of the adult rat and human. This finding suggests that p185neu, a putative growth factor receptor, may play a role in the regulation of normal growth and function or in the malignant transformation of these cells.
Effect of methanol on soybean photosynthesis and chlorophyll (1995)

Abstract Recently, an increase in the growth and yield of C3 plants in arid environments due to foliar application of methanol has been reported. The mechanism for these changes is not clear as little information is available on the changes in photosynthesis and chlorophyll content of plants caused by methanol application. The objective of this study was to measure the net photosynthesis (PN) and chlorophyll (CHL‐a, b) formation in soybean [Glycine max (L.) Merr] by foliar applications of methanol at the pod‐filling R5) stage. No changes were found in PN or CHL content with 0, 25, or 50% (v/v) methanol during 1, 2 or 3 weekly applications. Seed weight, seed yield, and pod number (per plant) were significantly higher for plants treated with methanol. A single application of methanol (25%) resulted in the highest increase in soybean growth and yield.
Compact system of wavelength-tunable femtosecond soliton pulse generation using optical fibers (1999)

Using passively mode-locked femtosecond (fs) fiber laser and polarization maintaining fibers, the compact system of wavelength-tunable femtosecond (fs) fundamental soliton pulse generation is realized. The monocolored soliton pulse, not multicolored ones, with the ideal sech <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> shape is generated, and its wavelength can be linearly shifted by varying merely the fiber-input power in the wide wavelength region of 1.56-1.78 μm for a 75-m fiber. The soliton pulses of less than 200 fs are generated with the high conversion efficiency of 75%-85%. This system can be widely used as a portable and practical wavelength-tunable fs optical pulse sources.
Auralization of a virtual orchestra using directivities of measured symphonic instruments (2012)

International audience
Devices, measurements, and properties (1995)

Fibre optics optical fibres and communications optical fibre communication technologies and systems fibre optic gratings optical fibre amplifiers non-linear effects in fibre optics solitons sources, modulators, and detectors for fibre optic communication systems fibre based couplers, isolators, MUX and deMUX micro-optics based components for networks semiconductor optical amplifier and wavelength conversions fibre optic communications links (telecommunications, data communications, and analogue) time domain multiplexed (TDM) networks wavelength domain multiplexed (WDM) networks optical fibre sections infrared fibres.
Capillary liquid chromatography fraction collection and postcolumn reaction using segmented flow microfluidics (2013)

A challenge for capillary LC (cLC) is fraction collection and the manipulation of fractions from microscale columns. An emerging approach is the use of segmented flow or droplet technology to perform such tasks. In this work, a fraction collection and postcolumn reaction system based on segmented flow was developed for the gradient cLC of proteins. In the system, column effluent and immiscible oil are pumped into separate arms of a tee resulting in regular fractions of effluent segmented by oil. Fractions were generated at 1 Hz corresponding to 5 nL volumes. The fraction collection rate was high enough to generate over 30 fractions per peak and preserve chromatographic resolution achieved for a five-protein test mixture. The resulting fractions could be stored and subsequently derivatized for fluorescence detection by pumping them into a second tee where naphthalene dicarboxyaldehyde, a fluorogenic reagent, was pumped into a second arm and added to each fraction. Proteins were derivatized within the droplets enabling postcolumn fluorescence detection of the proteins. The experiments demonstrate that fraction collection from cLC by segmented flow can be extended to proteins. Further, they illustrate a potential workflow for protein analysis based on postcolumn derivatization for fluorescence detection.
The activating NKG2D receptor assembles in the membrane with two signaling dimers into a hexameric structure (2005)

The activating NKG2D receptor plays a critical role in innate and adaptive immune responses by natural killer cells and subpopulations of T cells. The human receptor assembles with the DAP10 signaling dimer, and it is thought that one NKG2D homodimer pairs with a single DAP10 dimer by formation of two salt bridges between charged transmembrane (TM) residues. However, direct stoichiometry measurements demonstrated that one NKG2D homodimer assembles with four DAP10 chains. Selective mutation of one of the basic TM residues of NKG2D resulted in loss of two DAP10 chains, indicating that each TM arginine serves as an interaction site for a DAP10 dimer. Assembly of the hexameric structure was cooperative because this mutation also significantly reduced NKG2D dimerization. A monomeric NKG2D TM peptide was sufficient for assembly with a DAP10 dimer, indicating that the interaction between these proteins occurs in the membrane environment. Formation of a three-helix interface among the TM domains involved ionizable residues from all three chains, the TM arginine of NKG2D and both TM aspartic acids of the DAP10 dimer. The organization of the TM domains thus shows similarities to the T cell antigen receptor-CD3 complex, in particular to the six-chain assembly intermediate between T cell antigen receptor and the CD3delta epsilon and CD3gamma epsilon dimers. Binding of a single ligand can thus result in phosphorylation of four DAP10 chains, which may be relevant for the sensitivity of NKG2D receptor signaling, in particular in situations of low ligand density.
L-O-(2-Malonyl)tyrosine: A New Phosphotyrosyl Mimetic for the Preparation of Src Homology 2 Domain Inhibitory Peptides (1995)

Inhibition of Src homology 2 (SH2) domain-binding interactions affords one potential means of modulating protein-tyrosine kinase-dependent signaling. Small phosphotyrosyl (pTyr)-containing peptides are able to bind to SH2 domains and compete with larger pTyr peptides or native pTyr-containing protein ligands. Such pTyr-containing peptides are limited in their utility as SH2 domain inhibitors in vivo due to their hydrolytic lability to protein-tyrosine phosphatases (PTPs) and the poor cellular penetration of the ionized phosphate moiety. An important aspect of SH2 domain inhibitor design is the creation of pTyr mimetics which are stable to PTPs and have reasonable bioavailability. To date, most PTP-resistant pTyr mimetics which bind to SH2 domains are phosphonates such as (phosphonomethyl)phenylalanine (Pmp, 2), [(monofluorophosphono)methyl]phenylalanine (FPmp, 3) or [(difluorophosphono)methyl]-phenylalanine (F2Pmp, 4). Herein we report the incorporation of a new non-phosphorus-containing pTyr mimetic, L-O-(2-malonyl)tyrosine (L-OMT, 5), into SH2 domain inhibitory peptides using the protected analogue L-N alpha-Fmoc-O'-(O",O"-di-tert-butyl-2-malonyl)tyrosine (6) and solid-phase peptide synthesis techniques. Five OMT-containing peptides were prepared against the following SH2 domains: the PI-3 kinase C-terminal p85 SH2 domain (Ac-D-(L-OMT)-V-P-M-L-amide, 10, IC50 = 14.2 microM), the Src SH2 domain (Ac-Q-(L-OMT)-E-E-I-P-amide, 11, IC50 = 25 microM, and Ac-Q-(L-OMT)-(L-OMT)-E-I-P-amide, 14, IC50 = 23 microM), the Grb2 SH2 domain (Ac-N-(L-OMT)-V-N-I-E-amide, 12, IC50 = 120 microM), and the N-terminal SH-PTP2 SH2 domain (Ac-L-N-(L-OMT)-I-D-L-D-L-V-amide, 13, IC50 = 22.0 microM). These results show that peptides 10, 11, 13, and 14 have reasonable affinity for their respective SH2 domains, with the IC50 value for the SH-PTP2 SH2 domain-directed peptide 13 being equivalent to that previously observed for the corresponding F2Pmp-containing peptide. OMT may afford a new structural starting point for the development of novel and useful SH2 domain inhibitors.
Estrogen receptor-alpha in the inhibition of cancer growth and angiogenesis. (2000)

A high level of estrogen receptor-alpha (ER-alpha) is believed to be favorable in the prognosis and treatment of certain female cancers. ER-alpha expression in the ER-negative breast cancer cell lines inhibits their proliferation and invasive, metastatic potential in vitro. We stably overexpressed the ER-alpha in the human endometrial cancer cell line Ishikawa and showed that, unlike estradiol, high levels of ER-alpha significantly inhibit the growth of tumors xenografted from the Ishikawa cells. Subsequent to ER-alpha overexpression, in vivo down-regulation of vascular endothelial growth factor was observed in tumor xenografts. In addition, these tumors showed an inhibition of vascularization and of the angiogenic agent, integrin alphavbeta3. Involvement of a switch in the angiogenic pathways during tumorigenesis has been a recent focus of interest. Our results indicate that a high level of ER-alpha may be beneficial in the control of female cancers because of its inhibitory effect on such angiogenic pathways.
Two Different Cell Types have Different Major Receptors for Human Tumor Necrosis Factor (TNFα) (1989)

The receptors for tumor necrosis factor alpha (TNF alpha) were analyzed on myeloid cells (HL60, U937, K562, and freshly isolated blood monocytes) and on cells of epithelial origin (MCF7, HEp2 and HeLa cells), by use of radiolabeled TNF alpha and cross-linking experiments. Both cell types had high but slightly different affinities for TNF alpha. The myeloid cells had major cross-linked products of 98-100 kDa, which were similar in their N-linked glycosylation, whereas the cells of epithelial origin contained a major cross-linked product of 75 kDa, a second product of 95 kDa. The major receptors of both cell types (studied mostly with HL60 and HEp2 cells) are different proteins because (a) their apparent molecular masses were different and no evidence was obtained for cell-specific proteases, which could generate the differently sized receptors from one common receptor molecule; (b) anti-receptor antibodies, which precipitated the 95- and 75-kDa products, did not precipitate the 100-kDa cross-linked complex; (c) the native TNF alpha-receptor complexes had different proteolytic fingerprints; (d) the tryptic fragments differed in their association with the cell membrane vesicles; (e) the receptors differed in their degree of N-linked glycosylation; and (f) O-linked glycosylation was found on the major receptor of HL60 but not of HEp2 cells. In addition, myeloid cells may also contain a small amount of the HEp2-type of TNF alpha receptor. We suggest that at least two different receptors for TNF alpha exist.
OVERVIEW AND EVALUATION OF FUEL ETHANOL FROM CELLULOSIC BIOMASS: Technology, Economics, the Environment, and Policy (1996)

▪ Abstract Ethanol is a high performance fuel in internal combustion engines. It is a liquid, which is advantageous in terms of storage, delivery, and infrastructural compatability. Ethanol burns relatively cleanly, especially as the amount of gasoline with which it is blended decreases. Evaporative and toxicity-weighted air toxics emissions are consistently lower for ethanol than for gasoline. It is likely that vehicles can be configured so that exhaust emissions of priority pollutants are very low for ethanol-burning engines, although the same can probably be said for most other fuels under consideration. Recent work suggests that ethanol may be more compatible with fuel cell—powered vehicles than has generally been assumed. Research and development—driven advances have clear potential to lower the price of cellulosic ethanol to a level competitive with bulk fuels. Process areas with particular potential for large cost reductions include biological processing (with consolidated bioprocessing particularly notable in this context), pretreatment, and incorporation of an advanced power cycle for cogeneration of electricity from process residues. The cellulosic ethanol fuel cycle has a high thermodynamic efficiency (useful energy/high heating value = from 50% to over 65% on a first law basis, depending on the configuration), and a decidedly positive net energy balance (ratio of useful energy output to energy input). Cellulosic ethanol is one of the most promising technogical options available to reduce transportation sector greenhouse gas emissions. It may well be possible to develop biomass-based energy on a very large scale in the United States with acceptable and in some cases positive environmental impacts. To do so will however require responsible management and increased understanding of relevant technological and natural systems. The potential biomass resource is large, but so is demand for transportation fuels as well as other uses. The following hypotheses are offered as tentative hypotheses pertaining to biomass supply and demand in the United States: There will probably not be enough suitable land available to meet transportation demand if total vehicle miles traveled increase relative to current levels, and vehicle efficiency and animal protein utilization are unchanged. There probably is enough suitable land to meet transportation demand, even given some increase in vehicle miles traveled, given large but probably possible increases in vehicle efficiency, or large but probably possible decreases in reliance on animal protein, or a combination of less aggressive changes in both of these factors. The policy debate concerning fuel ethanol has tended to ignore cellulosic ethanol. It is suggested that an appropriate policy objective is to foster a transition to cellulosic feedstocks at a pace such that opportunities for ethanol producers and the farmers that supply them are expanded rather than contracted.
Identification of the First Bacterial Monoterpene Cyclase, a 1,8‐Cineole Synthase, that Catalyzes the Direct Conversion of Geranyl Diphosphate (2011)

Cycling gear: A sesquiterpene cyclase (SC) homologue, CnsA, from Streptomyces clavuligerus has been identified as a monoterpene cyclase that catalyzes the conversion of GPP into 1,8-cineole (see scheme). This suggests that bacterial SC homologues could include monoterpene cyclases, similar to plant SC homologues. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Production of Chitooligosaccharides and Their Potential Applications in Medicine (2010)

Chitooligosaccharides (CHOS) are homo- or heterooligomers of N-acetylglucosamine and D-glucosamine. CHOS can be produced using chitin or chitosan as a starting material, using enzymatic conversions, chemical methods or combinations thereof. Production of well-defined CHOS-mixtures, or even pure CHOS, is of great interest since these oligosaccharides are thought to have several interesting bioactivities. Understanding the mechanisms underlying these bioactivities is of major importance. However, so far in-depth knowledge on the mode-of-action of CHOS is scarce, one major reason being that most published studies are done with badly characterized heterogeneous mixtures of CHOS. Production of CHOS that are well-defined in terms of length, degree of N-acetylation, and sequence is not straightforward. Here we provide an overview of techniques that may be used to produce and characterize reasonably well-defined CHOS fractions. We also present possible medical applications of CHOS, including tumor growth inhibition and inhibition of T(H)2-induced inflammation in asthma, as well as use as a bone-strengthener in osteoporosis, a vector for gene delivery, an antibacterial agent, an antifungal agent, an anti-malaria agent, or a hemostatic agent in wound-dressings. By using well-defined CHOS-mixtures it will become possible to obtain a better understanding of the mechanisms underlying these bioactivities.
European elk papillomavirus: characterization of the genome, induction of tumors in animals, and transformation in vitro (1983)

The European elk papillomavirus (EEPV) genome was cloned in the BamHI cleavage site of the pBR322 vector. The cloned genome was used for construction of a physical map, employing restriction endonucleases BamHI, BglII, HindIII, PvuII, SacI, and XhoI. The sequence homology between the EEPV and bovine papillomavirus type 1 genomes was elucidated by performing hybridizations in different concentrations of formamide. Sequence homology could only be revealed under less stringent conditions, i.e., Tm - 43 degrees C. Nucleotide sequence information was also collected from the regions which lie adjacent to the three HindIII sites that are present in the EEPV genome. The results made it possible to align the EEPV and bovine papillomavirus type 1 genomes. Transformation by EEPV was demonstrated with the C127 mouse cell line, and fibrosarcomas were induced in young hamsters after subcutaneous injection. The transformed cells and the tumors contain multiple, nonintegrated copies of the EEPV genome. Virus particles could not be detected either in tumors or in transformed cells.
Targeted Single-Base Correction by RNA–DNA Oligonucleotides (2000)

An oligonucleotide composed of a contiguous stretch of RNA and DNA residues has been developed to facilitate correction of single-base mutations of episomal and chromosomal targets in mammalian cells. We demonstrated that an RNA-DNA oligonucleotide (RDO) induced heritable correction of a point mutation in the tyrosinase gene at the level of genomic sequence, protein, and phenotype of albino mouse melanocytes and albino mouse skin. Such RDOs might hold promise as a therapeutic method for the treatment of skin diseases. However, the general application of RDO technology has been hampered by the absence of a standardized system to measure the gene conversion in a particular cell type in a rapid and reproducible manner. For this purpose, we established an in vitro system in which nuclear extracts from mammalian cells showed RDO-mediated gene correction of a shuttle vector containing a point mutation in the E. coli β-galactosidase gene. This sensitive and convenient assay has been utilized to optimize the design of RDOs and to compare frequencies of gene conversion among different cell types. The general application of the RDO for site-specific gene correction or mutation would benefit from such mechanistic studies.
ANTIBODIES AGAINST THE HUMAN HEAT SHOCK PROTEIN hsp70 IN PATIENTS WITH SEVERE CORONARY ARTERY DISEASE (2002)

Heat shock proteins (hsps) play complex role in the function of the immune system, they can activate both humoral and cellular immune response, as well the complement system. Although autoimmunity to hsp70 was implicated in certain autoimmune diseases and other conditions, the exact role of anti-hsp70 antibodies is not known. It was demonstrated by our previous work and other's findings that antibodies against the 60 kDa hsps are strongly associated with coronary atherosclerosis and carotis disease. It is also known that there is increased hsp70 expression at different sites of atherosclerosis. Therefore our aim was to study whether level of anti-hsp70 antibodies correlate with the presence of severe coronary artery disease (CAD). We measured and compared anti-hsp70 IgG antibody levels in CAD patients (n = 99) and healthy subjects (n = 99) with ELISA. The frequency of these antibodies was high in both groups and there was no significant difference in the median level of anti-hsp70 antibodies between patients with severe CAD and controls (653 (400-1141) vs. 630 (326-1152) AU/mL, P = 0.337). Adjustment for age, sex, BMI and lipid parameters did not change this result. Furthermore we did not find a correlation between anti-hsp70 antibody levels and certain risk factors of CAD (age, lipid parameters, body mass index, C-reactive protein, gender, smoking, diabetes and anti-hsp60 antibodies). By contrast, in accordance with our previous findings, anti-hsp60 and anti-hsp65 antibody levels were significantly higher in CAD patients, compared to this control group (p < 0.0001 for both variables). We did not find any correlation between the levels of anti-hsp70 and anti-hsp60 or anti-hsp65 antibodies either in the patients or the controls. The exact role of hsp70 in atherosclerosis is controversial, but we suggest that humoral immunity against human hsp70 does not contribute to coronary atherosclerosis in contrast to antibodies against 60kDa hsps.
A novel matrix metalloproteinase inhibitor, FYK-1388 suppresses tumor growth, metastasis and angiogenesis by human fibrosarcoma cell line (2003)

The matrix metalloproteinases (MMPs) are likely to contribute to tumor cell invasion, metastasis and angiogenesis. Several MMP inhibitors have been developed, recently and their anti-tumor efficacy is being evaluated in clinical trials. FYK-1388 is a novel broad MMP inhibitor which blocks the activity of MMP-1, -2, -3, -7, -9, -13 and -14 (MT-MMP-1). It is especially effective against MMP-2 and -9 more so than other MMP inhibitors such as Marimastat, Ro 32-3555 and D-2163. Here, we investigated the anti-tumor efficacy of FYK-1388 using the human fibrosarcoma cell line HT-1080. These cells produced MMP-2 and -9, which FYK-1388 inhibited at a dose of 10(-8) M. FYK-1388 at 0.2 mg/mouse/day significantly suppressed tumor growth when given by s.c. injection for 22 days, experimental lung metastasis after 5 days s.c. injection and also suppressed tumor-induced angiogenesis in the dorsal air sac assay after 7 days s.c. injection. In the MTT assay, FYK-1388 had no effect on the in vitro growth of HT-1080 cells. These results suggest that FYK-1388 possesses anti-tumor efficacy as a result of inhibiting angiogenesis through the suppression of MMP-2 and -9 activity.