gebhart/patrepeval huggingface dataset:
The gene for a novel transmembrane protein containing epidermal growth factor and follistatin domains is frequently hypermethylated in human tumor cells. (2000)

A DNA fragment frequently hypermethylated in tumor cells was isolated using a novel screening strategy termed methylation-sensitive arbitrarily primed PCR. The isolated sequence corresponded to a CpG island at the 5' end of a previously unknown gene, TPEF (transmembrane protein containing epidermal growth factor and follistatin domains). Expression of TPEF was observed using Northern master blot analysis of a variety of normal tissues including colon, bladder, and prostate tissue. TPEF maps to human chromosome 2q33, where frequent loss of heterozygosity is seen in various human tumors, and TPEF was not expressed in most human colon and various other tumor cell lines examined by reverse transcription-PCR. Nine of 11 tumor cell lines were highly methylated in the 5' region and the first exon of the gene that demonstrated features characteristic of a CpG island. However the other two cell lines, which expressed TPEF, were hypomethylated in the 5' end of the gene. The region was also hypermethylated in 11 of 16 primary bladder tumors and in 3 of 4 primary colon tumors when compared with adjacent normal tissue. Our results suggest that potential tumor suppressor genes can be isolated from human tumors by virtue of their altered methylation patterns.
Profiling under UNIX by patching (1987)

Abstract Profiling under UNIX is done by inserting counters into programs either before compiling, during compiling or during assembly. A fourth type of profiling involves monitoring the execution of a program, and gathering relevant statistics during the run. This paper looks at this method and an implementation of it, and discusses its advantages and disadvantages.
A Novel Method for Analysis of Nuclear Receptor Function at Natural Promoters: Peroxisome Proliferator-Activated Receptor γ Agonist Actions on aP2 Gene Expression Detected Using Branched DNA Messenger RNA Quantitation (1999)

Peroxisome proliferator-activated receptor-gamma (PPARgamma), a member of the nuclear hormone receptor superfamily, plays an essential role in the mediation of the actions of antidiabetic drugs known as thiazolidinediones (TZDs). PPARgamma activates many target genes involved in lipid anabolism including the adipocyte fatty acid binding protein (aP2). In this study, induction of aP2 gene expression by PPARgamma agonists was examined in both cultured cells and diabetic mice using branched DNA (bDNA)-mediated mRNA quantitation. bDNA technology allows for the direct measurement of a particular mRNA directly within cellular lysate using a 96-well plate format in a time frame comparable to a reporter gene assay. In cultured human subcutaneous preadipocytes, the TZDs, troglitazone and BRL-49653, both rapidly induced aP2 mRNA as detected with the bDNA method. In these cells, the effect of BRL-49653 on aP2 mRNA levels was detectable as early as 30 min after treatment (47% increase) and was maximal after 24 h of treatment (12-fold increase). The effects of troglitazone on aP2 mRNA induction were similar to those of BRL-49653 except that the maximal level of induction was consistently lower (e.g. 24 h treatment = 4-fold increase). Dose-response relationships for both of the TZDs were also determined using the 24-h treatment time point. EC50s for both BRL-49653 and troglitazone were estimated to be 80 nM and 690 nM, respectively. A natural PPARgamma ligand, 15-deoxy-delta12,14-PGJ2, was also active in this assay with a maximal induction of aP2 mRNA of approximately 5-fold when tested at 1 microM. Since the PPARgamma:retinoid X receptor (RXR) heterodimer has been characterized as a permissive heterodimer with respect to RXR ligands, the ability of 9-cis-retinoic acid (9-cis-RA) to induce aP2 mRNA was examined. Although 9-cis-RA had very low efficacy (2-fold induction), the maximal effect was reached at 100 nM. No synergism or additivity in aP2 mRNA induction was detected when 9-cis-RA was included with either of the TZDs used in this study. Significant induction of aP2 mRNA in bone marrow of db/db mice treated with either troglitazone or BRL-49653 was also detected, indicating that the bDNA assay may be a simple method to monitor nuclear receptor target gene induction in vivo.
Bandwidth and power efficiency analysis of fading communication link (2016)

Bandwidth and power are the major radio resources of a wireless communication system. Designing an efficient wireless communication system requires trade-off between these resources. In this context, definitions of radio resource efficiencies are given in terms of bandwidth efficiency, bit/s/Hz, and power efficiency, bit/Thermal Noise Energy Unit, for an arbitrary communication system. These efficiencies are analyzed and discussed over Rayleigh and Nakagami fading channels for M-QAM. Investigation shows that the efficiency metrics are degraded by the channel effects. Also, it is evident that each M-QAM level attains highest power efficiency in a specific range of signal to noise ratio (SNR). Thus, an adaptive transmission technique is proposed and analyzed for enhancing resource efficiencies based on number of levels in M-QAM to achieve maximum power efficiency in specific SNR regions. It is shown that efficiency metrics can be significantly improved by using the proposed technique for a broad range of signal to noise ratio, even when fading is severe.
Chitosan/gelatin–based films crosslinked by proanthocyanidin (2005)

Abstract Novel polymer networks consisting of crosslinked gelatin/chitosan were prepared by a solution casting technique. Methods for bulk crosslinking were developed to modify the gelatin/chitosan blends with the use of a nontoxic crosslinking reagent, proanthocyanidin (PA). FTIR spectral analyses of the preparations showed network formations of crosslinked gelatin, chitosan, and PA by amide and ester linkages. The crosslinked networks were stable in the aqueous state, and had improved mechanical properties and thermal stability when compared with nonlinked gelatin (G) and chitosan/gelatin (C/G) films. In vitro protease digestion and cell‐culture studies showed that the PA‐crosslinked C/G films are nontoxic and exhibited decreased biodegradation rate and a better ability to support cell adhesion and proliferation than noncrosslinked gelatin or chitosan alone. These results suggest that such a nontoxic crosslinked gelatin/chitosan scaffold can become a promising matrix for tissue‐engineering applications. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2005
The role of ribavirin in direct acting antiviral drug regimens for chronic hepatitis C (2011)

Despite years of clinical use and extensive research efforts, the mechanism of action of ribavirin (RBV) is not well understood. Although it has only a mild, transient antiviral effect on HCV replication when administered as monotherapy, when combined with interferon, RBV improves sustained virological response (SVR) rates by approximately 25-30%. Proposed mechanisms of action for RBV against HCV include (1) a direct effect against the HCV RNA dependent RNA polymerase; (2) induction of misincorporation of nucleotides leading to lethal mutagenesis; (3) depletion of intracellular pools via inhibition of inosine monophosphate dehydrogenase; (4) alteration in the cytokine balance between a Th2 profile (anti-inflammatory) to a Th1 profile (pro-inflammatory); and (5) potentiating the effect of interferon via up-regulation of genes involved in interferon signalling. Given the lack of a clear understanding of RBV mechanism of action, it has been challenging to confidently position this drug with new direct antiviral agents (DAA). However, early clinical studies provide strong evidence for a benefit of RBV in combination with DAAs for both IFN containing and sparing regimens. The addition of RBV reduces viral breakthroughs and/or relapses, at least when drugs with low to moderate genetic barriers to resistance are paired together. This is particularly true in patients harbouring HCV subtype 1a. Ongoing studies are now addressing the utility of RBV in nucleoside containing DAA regimens, which offer both potent antiviral activity as well as a high genetic barrier to resistance. It is remarkable that the age-old question of the role of RBV in the future of HCV therapy remains as real today as it was two decades ago.
Enabling instantaneous feedback with full-duplex backscatter (2014)

This paper introduces the first design that enables full-duplex communication on battery-free backscatter devices. Specifically, it gives receivers a way to provide low-rate feedback to the transmitter on the same frequency as that of the backscatter transmissions, using neither multiple antennas nor power-consuming cancellation hardware. Our design achieves this goal using only fully-passive analog components that consume near-zero power. We integrate our design with the backscatter network stack and demonstrate that it can minimize energy wastes that occur due to collisions and also correct for errors and changes in channel conditions at a granularity smaller than that of a packet. To show the feasibility of our design, we build a hardware prototype using off-the-shelf analog components. Our evaluation shows that our design cancels the self-interference down to the noise floor, while consuming only 0.25 μW and 0.54 μW of transmit and receive power, respectively.
Induction of the Epstein-Barr Virus Latent Membrane Protein 2 Antigen-specific Cytotoxic T Lymphocytes Using Human Leukocyte Antigen Tetramer-based Artificial Antigen-presenting Cells (2006)

Cytotoxic T lymphocytes (CTLs) specific for the Epstein-Barr virus (EBV) latent membrane protein 2 (LMP2) antigen are important reagents for the treatment of some EBV-associated malignancies, such as EBV-positive Hodgkin's disease and nasopharyngeal carcinoma. However, the therapeutic amount of CTLs is often hampered by the limited supply of antigen-presenting cells. To address this issue, an artificial antigen-presenting cell (aAPC) was made by coating a human leukocyte antigen (HLA)-pLMP2 tetrameric complex, anti-CD28 antibody and CD54 molecule to a cell-sized latex bead, which provided the dual signals required for T cell activation. By co-culture of the HLA-A2-LMP2 bearing aAPC and peripheral blood mononuclear cells from HLA-A2 positive healthy donors, LMP2 antigen-specific CTLs were induced and expanded in vitro. The specificity of the aAPC-induced CTLs was demonstrated by both HLA-A2-LMP2 tetramer staining and cytotoxicity against HLA-A2-LMP2 bearing T2 cell, the cytotoxicity was inhibited by the anti-HLA class I antibody (W6/32). These results showed that LMP2 antigen-specific CTLs could be induced and expanded in vitro by the HLA-A2-LMP2-bearing aAPC. Thus, aAPCs coated with an HLA-pLMP2 complex, anti-CD28 and CD54 might be promising tools for the enrichment of LMP2-specific CTLs for adoptive immunotherapy.
Study of Energy Storage Capacitor Reduction for Single Phase PWM Rectifier (2009)

It is well known that there exist second-order harmonic current and corresponding ripple voltage on dc bus for single phase PWM rectifiers. The low frequency harmonic current is normally filtered using a bulk capacitor in the bus which results in low power density. This paper studies the energy storage capacitor reduction methods for single phase rectifiers. The minimum ripple energy storage requirement is derived independent of a specific topology. Based on the minimum ripple energy requirement, the feasibility of the active capacitor's reduction schemes is verified. Then, we propose a bidirectional buck-boost converter as our ripple energy storage circuit that can effectively reduce the energy storage capacitance. Simulation and experimental results are provided for verification purposes.
Radiation‐induced crosslinking of polyethylene in the presence of acetylene: A gel fraction, UV‐visible, and ESR spectroscopy study (1993)

Abstract Electron‐spin resonance (ESR) and altraviolet (UV) visible spectroscopic evidence has been found for the formation of diene, triene and tetraene, following the irradiation of polyethylene in the presence of acetylene. The polyenes are formed by a mechanism which is different from that observed under vacuum or with inert gas saturation. The sum of the G (polyene) values obtained by UV spectroscopy is almost half that of initial radical formation. It is concluded that polyene bridges, predominantly diene, form crosslinks between radical pairs. G (X) values determined from gel fraction data, using Saito‐Kang‐Dole theory, are found to be greatly in error and misrepresentative of crosslink changes. © 1993 John Wiley &amp; Sons, Inc.
Phosphorylation of the hepatitis C virus NS5A protein in vitro and in vivo: properties of the NS5A-associated kinase (1997)

NS5A derived from a hepatitis C virus (HCV) genotype 1b isolate has previously been shown to undergo phosphorylation on serine residues (T. Kaneko, Y. Tanji, S. Satoh, M. Hijikata, S. Asabe, K. Kimura, and K. Shimotohno, Biochem. Biophys. Res. Commun. 205:320-326, 1994). In this report, phosphorylation of NS5A derived from HCV isolates of the 1a and distantly related 2a genotypes is demonstrated. Phosphoamino acid analysis of NS5A from the 1a isolate indicated that phosphorylation occurs predominantly on serine, with a minor fraction of threonine residues also being phosphorylated. NS5A phosphorylation was observed in diverse cell types, including COS-1, BHK-21, HeLa, and the hepatoma cell line HuH-7. Phosphorylation of a glutathione S-transferase (GST)/HCV-H NS5A fusion protein was also demonstrated in an in vitro kinase assay. This activity seemed to be highest when the pH of the reaction was neutral or slightly alkaline and displayed a preference for Mn2+ over Mg2+, with an optimum concentration of approximately 10 mM Mn2+. Somewhat surprisingly, in vitro phosphorylation of NS5A was inhibited by the addition of > or = 0.25 mM Ca2+ to reaction buffer containing Mn2+ and/or Mg2+. Comparison of phosphopeptide maps of NS5A phosphorylated in vitro and in cultured cells showed that most of the phosphopeptides comigrated, suggesting that one or more kinases involved in NS5A phosphorylation in vivo and in vitro are the same. The effects of various kinase inhibitors on NS5A phosphorylation were consistent with a kinase activity belonging to the CMGC group of serine-threonine kinases. The development of an in vitro kinase assay for NS5A phosphorylation should facilitate identification of kinase(s) responsible for its phosphorylation and of phosphorylation sites which may influence the function of NS5A in HCV propagation.
Frustum Casting for Progressive, Interactive Rendering (1998)

Efficient visible surface determination algorithms have long been a fundamental goal of computer graphics. We discuss the well-known ray casting problem: given a geometric scene description, a synthetic camera, and a viewport which discretizes the camera film plane into pixels, ray casting identifies the visible surface at each pixel, i.e., that scene primitive which is first encountered by an eye ray directed through the pixel center. Interactive rendering systems have not ordinarily been based on ray casting, due to its computational cost. Instead, the dominant method for achieving interactive rendering is hardware-assisted rasterization and depth buffering of polygons, often produced by static or dynamic tesselation of higher-level objects. Modern polygon rasterization architectures are extremely powerful, having undergone an extensive development path. Several trends indicate, however, that alternatives to polygon rasterization and depth buffering deserve examination in the design ...
Kinetics of the dehydration of methylene glycol in aqueous solution (1966)

Abstract Methods are described for measuring the velocity of the reaction CH2(OH)2 → CH2O+H2O in aqueous solution by making use of the rapid reaction of unhydrated formaldehyde with the scavenging reagents semicarbazide, hydroxylamine, phenylhydrazine, hydrazine and sulphite. The reaction exhibits general acid-base catalysis, and catalytic constants are given for 14 acids and 30 bases. Relations between acid-base strength and catalytic power extend over an unusually wide range of velocities and types of catalyst, and this behaviour is discussed in terms of reaction mechanisms. The catalytic behaviour observed shows unexpected contrasts with that reported for the hydration of carbon dioxide. It is shown that, contrary to previous reports, the rate of removal of formaldehyde from aqueous solution by a gas stream is not appreciably affected by the rate of dehydration of methylene glycol. A few experiments are reported on the application of the chemical scavenger method to measure the rate of the reaction CH3CH(OH)2 → CH3CHO+H2O, and the results compared with those obtained by other methods.
Mapping of neutralizing epitopes and the receptor binding site of human interleukin 1 beta (1993)

Antibodies to synthetic peptides of human interleukin 1 beta (IL-1 beta) and to recombinant human IL-1 beta were used to identify epitopes of IL-1 beta associated with the neutralization of its biological activity. Analysis of antisera raised to 17 synthetic peptides derived from the mature IL-1 beta sequence showed that five regions (residues 6-15, 49-80, 58-80, 92-101, and 120-133) were both immunoprecipitating and neutralizing. Using a hexamer epitope mapping method, comparison of the regions recognized by four neutralizing rabbit antisera with those recognized by a rabbit antiserum raised to denatured IL-1 beta suggested two further neutralizing epitopes, residues 39-48 and 83-95. Finally, a neutralizing monoclonal antibody was shown to bind to the peptides 6-11 and 87-95 by peptide binding and mutagenesis. All of these regions appear predominantly on one face of IL-1 beta. The effect of mutations in residues 4-11 and 88-97, which lie within this face, on receptor binding and biological activity was determined. Most of the mutations tested affected both receptor binding and activity, whereas mutations in another face of IL-1 beta (residues 74-80) had no effect. Purification of two of the mutants with reduced bioactivity and receptor binding and analysis by two-dimensional NMR indicated no gross changes in tertiary structure. A third mutant had reduced bioactivity in two different bioassays but no change in receptor binding. Although two-dimensional NMR revealed no gross changes in conformation, small changes did occur at a site distal from that mutated. The data are consistent with other epitope mapping and receptor binding mutagenesis data and suggest that the neutralizing antibodies and receptor recognize different but overlapping regions of IL-1 beta.
A novel blood-based biomarker for detection of autism spectrum disorders (2012)

Autism spectrum disorders (ASD) are classified as neurological developmental disorders. Several studies have been carried out to find a candidate biomarker linked to the development of these disorders, but up to date no reliable biomarker is available. Mass spectrometry techniques have been used for protein profiling of blood plasma of children with such disorders in order to identify proteins/peptides that may be used as biomarkers for detection of the disorders. Three differentially expressed peptides with mass-charge (m/z) values of 2020 ± 1, 1864 ± 1 and 1978 ± 1 Da in the heparin plasma of children with ASD that were significantly changed as compared with the peptide pattern of the non-ASD control group are reported here. This novel set of biomarkers allows for a reliable blood-based diagnostic tool that may be used in diagnosis and potentially, in prognosis of ASD.
A more potent bystander cytocidal effect elicited by tumor cells expressing the herpes simplex virus—thymidine kinase gene than by fibroblast virus—producer cells in vitro (1995)

Retrovirus-mediated herpes simplex virus-thymidine kinase (HSV-tk) gene therapy is a promising approach in the treatment of brain tumors. Previous in vitro and in vivo studies have demonstrated a bystander effect in which nonmodified tumor cells in proximity to HSV-tk-modified tumor cells are killed with the modified cells in the presence of ganciclovir. In the present study the authors assessed the contribution of infectious HSV-tk retrovirus made by producer cells to the bystander cytocidal effect in tissue culture using Walker 256 rat breast carcinosarcoma cells, which represent an established model for carcinomatous meningitis. The authors observed ganciclovir-dependent growth inhibition even when only one HSV-tk-positive Walker cell was mixed with 1000 HSV-tk-negative Walker cells and showed that the bystander cytocidal effect is not mediated by toxic cell lysis products. Walker cells engineered to produce HSV-tk retrovirus with titers ranging from 10(3) to 10(5) colony-forming units/ml exert no greater cytocidal effect than nonviral producer HSV-tk-positive Walker cells in vitro. Murine fibroblast-producer cells with viral titers ranging from 10(6) to 10(7) colony-forming units/ml exerted a stronger cytocidal effect than nonviral producer HSV-tk-positive murine fibroblasts. Despite the high viral titers of fibroblast producer cells, HSV-tk-modified Walker cells performed better than fibroblast producer cells in their cytotoxic effect on wild-type Walker tumor cells. Given that HSV-tk-modified tumor cells can become ganciclovir resistant, we tested gamma-irradiation as a means to overcome resistance. Lethal gamma-irradiation of the HSV-tk-positive Walker cells did not abolish their bystander effect on Walker HSV-tk-negative cells. One can infer from these results that HSV-tk-modified tumor cells, irradiated or not, may be a better alternative to murine fibroblast producer cells in the treatment of central nervous system neoplasia.
Glucose transporter glut-1 expression correlates with tumor hypoxia and predicts metastasis-free survival in advanced carcinoma of the cervix. (2001)

Hypoxic tumors are known to be more malignant, to be more likely to metastasize, and to have a poor prognosis. They are also radio- and chemoresistant. For this reason, it is desirable that a clinically useful marker of hypoxia is found, so that treatment with radiotherapy and bioreductive chemotherapy can be rationally applied to individual patients. Glut-1 is a facilitative glucose transporter that is ubiquitously expressed in normal tissue and expressed at higher levels in a number of tumors. Its potential as an intrinsic hypoxia marker arises from its dual control in hypoxic conditions by reduced oxidative phosphorylation and the hypoxia-inducible factor (HIF-1) oxygen-sensing pathway. Eppendorf histography, by virtue of its proven predictive qualities, is a suitable gold standard used in our laboratory to validate new hypoxia markers. Using this technique, pretreatment pO(2) measurements were performed on 54 patients with locally advanced cervical carcinoma. Then, immunohistochemical staining was used to detect Glut-1 protein in individual tumor biopsy sections. Both measurements were made before initiation of treatment. By using a low-tech scoring system, pO(2) was found to correlate weakly with Glut-1 score (r = 0.28; P = 0.04). To extrapolate this correlation to the known adverse effects of tumor hypoxia on outcome, we examined the prognostic significance of Glut-1 staining in a retrospective series of 121 patients. An absence of Glut-1 significantly increased the likelihood of metastasis-free survival (P = 0.022) but did not significantly effect disease-free or recurrence-free survival. These findings suggest that Glut-1 be an intrinsic marker of hypoxia that can easily be applied in a clinical setting.