gebhart/patrepeval huggingface dataset:
Activation of Epidermal Growth Factor Receptor by Epidermal Growth Factor (1996)

The binding of epidermal growth factor (EGF) to epidermal growth factor receptor (EGF receptor) induces dimerization of the receptor and activation of its protein tyrosine kinase. Each of these three steps was followed as a function of the concentrations of EGF and of EGF receptor. Binding of EGF was followed by sedimentation of the complex between [3H]EGF and EGF receptor, dimerization was measured by quantitative cross-linking with glutaraldehyde, and the activation of the protein tyrosine kinase was monitored under the same conditions by following the initial velocity of the phosphorylation of peptides containing tyrosine. The binding of epidermal growth factor to its receptor was measured as a function of the concentration of epidermal growth factor, and the relationship was sigmoid with an average value of 1.7 for the Hill coefficient. Both dimerization and the activation of the tyrosine kinase displayed saturation as a function of the concentration of EGF. The ranges of the concentrations of EGF where dimerization and activation of the tyrosine kinase activity were half-maximal were 15-30 and 50-200 nM, respectively, but the value for the concentration of EGF at the half-maximum for the activation of the tyrosine kinase was a complex function of the concentration of EGF receptor. The observed behavior of the binding of EGF, the dimerization of EGF receptor, and the activation of the tyrosine kinase were used as criteria against which to test mechanisms for the process of activation. Equations were derived for various reversible and irreversible mechanisms and used to calculate the theoretical behaviors of the three properties. In direct comparisons of the experimental and the theoretical data, several of the previously proposed reversible and irreversible mechanisms for the activation of EGF receptor were found to be inadequate, but a reasonable mechanism was formulated that was compatible with the experimental data. In this mechanism, dimeric EGF receptor must be occupied by two molecules of EGF for enzymatic activity to be expressed.
Gene Expression Profile Correlates with T-Cell Infiltration and Relative Survival in Glioblastoma Patients Vaccinated with Dendritic Cell Immunotherapy (2010)

Autologous tumor lysate-pulsed DC vaccination in conjunction with TLR agonists is safe as adjuvant therapy in newly diagnosed and recurrent glioblastoma patients. Our results suggest that the mesenchymal gene expression profile may identify an immunogenic subgroup of glioblastoma that may be more responsive to immune-based therapies.
Rescue of synthetic minireplicons establishes the absence of the NS1 and NS2 genes from avian pneumovirus (1997)

We have determined the nucleotide sequences of the regions 3' and 5' proximal to the avian pneumovirus (APV) N and L genes, respectively. These sequences were used in the construction of a synthetic minireplicon construct in which the chloramphenicol acetyltransferase (CAT) reporter gene was flanked at its 3' end with the APV leader together with the APV N gene start signal and at its 5' end with the APV L gene end signal and the genome trailer region. The ability of T7 RNA polymerase runoff transcripts to direct the replication and expression of the CAT reporter gene in APV-infected cells demonstrated the ability of the putative leader and trailer regions to direct genome replication and gene expression. Furthermore, this confirms the absence of the NS1 and NS2 gene analogs within the APV genome. We were able to detect the expression of CAT protein from cells that had been infected with supernatants from the initially infected and transfected cells. These results have identified the cis-acting sequences of APV responsible for viral replication, gene expression, and packaging into virus-like particles.
Motor cortex stimulation for central and neuropathic pain: current status (2003)

aDepartment of Neurosurgery, Wayne State University, School of Medicine, 4160 John R #930, Detroit, MI 48201, USA bDepartment of Neurosurgery, University of San Francisco, School of Medicine, San Francisco, CA, USA *Corresponding author. Tel.: +1-313-966-5007; fax: +1-313-966-0368 E-mail address:[email protected] (J.A. Brown). Accepted May 14, 2003.
MORPHOLOGIC ALTERATION OF HEPATOCYTES AND SINUSOIDAL ENDOTHELIAL CELLS IN RAT FATTY LIVER DURING COLD PRESERVATION AND THE PROTECTIVE EFFECT OF HEPATOCYTE GROWTH FACTOR (1999)

The hepatic injury in both hepatocytes and SECs in cold-preserved fatty liver graft developed more rapidly and severely than in the corresponding controls and demonstrated a protective effect of hrHGF.
Carboxylate-derived calixarenes with high selectivity for actinium-225 (1998)

The binding properties of two ligands, 5,11,17,23-tetra-tert-butyl-25,26,27,28-tetrakis(carboxymethoxy)calix[4]arene 1 and 5,11,17,23,29,35-hexa-tert-butyl-37,38,39,40,41,42- hexakiscarboxymethoxy)calix[6]arene 2, which show high selectivity for 225Ac3+ (an α-emitter with t1/2 = 10 days) over Na+, K+, Mg2+, Ca2+ and Zn2+ are described.
Respective roles of factors II, VII, IX, and X in the procoagulant activity of FEIBA (2002)

Activated prothrombin complex concentrates (APCCs) are effective in the therapy of bleeding episodes in hemophilic patients with inhibitors. We investigated the respective roles of factor II, factor VII, factor IX, and factor X in the procoagulant activity of the APCC FEIBA. Factor II, factor VII, factor IX, and factor X were reduced in platelet-poor plasma, and the thrombin potential (TP) was determined using a chromogenic substrate in the absence or presence of FEIBA. Reduction of factor II resulted in a significant decrease of the TP without influencing the lag phase until the onset of thrombin generation. The reduction of factor VII showed no effect on the TP, but resulted in a prolongation of the lag phase. Changes of factor IX or factor X concentrations showed neither an effect on the TP nor on lag phases. Our study demonstrates that thrombin generation in the presence of FEIBA mainly depends on prothrombin.
Circulating MicroRNAs in Patients With Coronary Artery Disease (2010)

Circulating levels of vascular and inflammation-associated microRNAs are significantly downregulated in patients with coronary artery disease.
Role of Oxygen Vacancies on the Performance of Li[Ni0.5–xMn1.5+x]O4 (x = 0, 0.05, and 0.08) Spinel Cathodes for Lithium-Ion Batteries (2012)

Investigation of the high-voltage Li[Ni0.5–xMn1.5+x]O4 (x = 0, 0.05, 0.08) spinels prepared at temperatures of T ≤ 900 °C and given different thermal treatments has shown that the solubility limit for oxygen vacancies in the disordered spinel phase is small at 600 °C. With x = 0, long-range ordering of Ni2+ and Mn4+ and elimination of all oxygen vacancies occurs after an anneal at 700 °C. Above 700 °C, a reversible transition from spinel to rock-salt is initiated, to accommodate oxygen loss. A sample quenched from 900 °C into liquid nitrogen traps some rock-salt second phase; the volume fraction of rock-salt phase decreases with oxygen uptake to 600 °C. However, upon slow cooling (1 °C min–1) from 900 °C, the particles have time to eliminate most of the rock-salt phase by 700 °C; upon further cooling below 700 °C, the spinel phase and the oxygen gain are retained. However, the spinel phase retains oxygen vacancies and attendant Mn3+ with only short-range order of Ni and Mn. The rock-salt phase lowers sharply the electrochemical capacity of the quenched sample; but retention of Mn3+ in the slow-cooled sample improves the electrochemical performance relative to that of an oxygen-stoichiometric spinel formed by annealing at 700 °C. The Mn-rich Li[Ni0.45Mn1.55]O4 sample annealed at 700 °C exhibits a segregation of a long-range-ordered spinel phase and a Ni-deficient spinel phase having a larger fraction near the particle surface. Removal of the Ni4+/Ni2+ redox reactions from the surface stabilizes the electrochemical performance at 55 °C, but the problem of Mn2+ dissolution resulting from surface disproportionation of Mn3+ to Mn2+ and Mn4+ remains.
The use of microgravity technique in archaeology: A case study from the St. Nicolas Church in Pukanec, Slovakia (2009)

The use of microgravity technique in archaeology: A case study from the St. Nicolas Church in Pukanec, Slovakia The detection of subsurface cavities, such as crypts, cellars and tunnels, in churches and castles belongs to successful applications of the employment of surface gravity measurement techniques in archaeo-prospecting. The old historic building exploration requires using of non-invasive methods, and hence the microgravity technique is a proper candidate for this task. On a case study from the Roman-Catholic Church of St. Nicolas in the town Pukanec the results of using microgravity for detection and delineation of local density variations caused by a near-surface void are shown. The acquired negative anomaly in the residual Bouguer anomalies field suggested the presence of a possible void feature. Euler deconvolution and 3D modelling were used to estimate the depth and shape of the anomalous source. Additionally, measurements of the vertical gravity gradient on several stations were performed. We tested how the use of a downward continuation of gravity, utilizing the real vertical gravity gradient, influences the shape and amplitude of the final Bouguer anomaly map.
Methionine adenosyltransferase α2 sumoylation positively regulate Bcl-2 expression in human colon and liver cancer cells (2015)

Ubiquitin-conjugating enzyme 9 (Ubc9) is required for sumoylation and inhibits apoptosis via Bcl-2 by unknown mechanism. Methionine adenosyltransferase 2A (MAT2A) encodes for MATα2, the catalytic subunit of the MATII isoenzyme that synthesizes S-adenosylmethionine (SAMe). Ubc9, Bcl-2 and MAT2A expression are up-regulated in several malignancies. Exogenous SAMe decreases Ubc9 and MAT2A expression and is pro-apoptotic in liver and colon cancer cells. Here we investigated whether there is interplay between Ubc9, MAT2A and Bcl-2. We used human colon and liver cancer cell lines RKO and HepG2, respectively, and confirmed key finding in colon cancer specimens. We found MATα2 can regulate Bcl-2 expression at multiple levels. MATα2 binds to Bcl-2 promoter to activate its transcription. This effect is independent of SAMe as MATα2 catalytic mutant was also effective. MATα2 also directly interacts with Bcl-2 to enhance its protein stability. MATα2's effect on Bcl-2 requires Ubc9 as MATα2's stability is influenced by sumoylation at K340, K372 and K394. Overexpressing wild type (but not less stable MATα2 sumoylation mutants) protected from 5-fluorouracil-induced apoptosis in both colon and liver cancer cells. Colon cancer have higher levels of sumoylated MATα2, total MATα2, Ubc9 and Bcl-2 and higher MATα2 binding to the Bcl-2 P2 promoter. Taken together, Ubc9's protective effect on apoptosis may be mediated at least in part by sumoylating and stabilizing MATα2 protein, which in turn positively maintains Bcl-2 expression. These interactions feed forward to further enhance growth and survival of the cancer cell.
A Multistep Chemical Modification Procedure To Create DNA Arrays on Gold Surfaces for the Study of Protein−DNA Interactions with Surface Plasmon Resonance Imaging (1999)

A multistep surface modification procedure for the creation of DNA arrays on chemically modified gold surfaces that can be used in surface plasmon resonance (SPR) imaging studies of protein−DNA interactions is demonstrated. The multistep procedure is required to create an array of spots that are surrounded first by a hydrophobic background which allows for the pinning of aqueous DNA solutions onto individual array elements and then to replace that hydrophobic background with one that resists the nonspecific adsorption of proteins during in situ SPR imaging measurements. An amine-terminated alkanethiol monolayer is employed as the base layer, and Fmoc and PEG modifiers are used to create the sequentially hydrophobic and protein adsorption-resistant surfaces, respectively. Specifically, the chemical modification steps are the following: (1) the adsorption and self-assembly of an 11-mercaptoundecylamine (MUAM) monolayer on an evaporated gold thin film, (2) the reaction of the MUAM monolayer with an Fmoc protecting group to create a hydrophobic surface, (3) the photopatterned removal of the alkanethiol followed by (4) the readsorption of MUAM to create an array of MUAM squares (750 × 750 μm) surrounded by a hydrophobic MUAM-Fmoc background that can pin drops of aqueous solution, (5) the attachment of oligonucleotide sequences onto the MUAM squares by the reaction of the amine-terminated surface with the heterobifunctional cross linker SSMCC followed by a coupling reaction to a small volume (0.1 μL) of thiol-modified DNA, and (6) the removal of the Fmoc protecting group followed by (7) a pegylation reaction of the MUAM with PEG-NHS to create a protein adsorption-resistant background. A combination of polarization-modulation FTIR spectroscopy, contact angle, and scanning angle SPR measurements is used to characterize the surface modification procedure. An SPR imaging measurement of the adsorption of single-stranded DNA binding protein (SSB) onto an oligonucleotide array created by this procedure is used to demonstrate the utility of these surfaces.
Virus therapy of human cancers (2003)

Cancer Institute St Joseph's Hospital, Department of Medical Microbiology and Immunology, University of South Florida College of Medicine, Tampa, FL, USA. Correspondence to J. G. Sinkovics, Cancer Institute St Joseph's Hospital, Department of Medical Microbiology and Immunology, University of South Florida College of Medicine, Tampa, FL, USA. Tel: 813-870-4255, 813-870-4977; fax: 813-870-4825, 813-870-4002; e-mail: [email protected], [email protected]
Analyzing biodiesel: standards and other methods (2006)

Abstract Biodiesel occupies a prominent position among the alternatives to conventional petrodiesel fuel owing to various technical and economic factors. It is obtained by reacting the parent vegetable oil or fat with an alcohol)transesterification) in the presence of a catalyst to give the corresponding monoalkyl esters, which are defined as biodiesel. Because of the nature of the starting material, the production process, and subsequent handling, various factors can influence biodiesel fuel quality. Fuel quality issues are commonly reflected in the contaminants or other minor components of biodiesel. This work categorizes both the restricted species in biodiesel and the physical properties prescribed by the standards, and details the standard reference methods to determine them as well as other procedures. Other aspects of biodiesel analysis, including production monitoring and assessing biodiesel/petrodiesel blends, are also addressed. The types of analyses include chromatographic, spectroscopic, physical properties‐based, and wet chemical methods. The justifications for specifications in standards are also addressed.
Investigation of driver circuits for GaN HEMTs in leaded packages (2014)

GaN devices have superior performance over Si-based devices, but even a very small parasitic inductance makes GaN HEMT hard to drive. Many advanced leadless packages are proposed for lower parasitic inductance to fully realize advantages of GaN devices. However, leaded packages are still dominant in industrial applications because of their simplicity for PCB assembly and capability for a wide variety of heat-sinking techniques. In this paper, the performance of a basic half bridge power circuit based on GaN HEMTs with TO package (TO-220) is analyzed, and GaN device driver design is also discussed. Simulation and experimental results are provided for validation.
Affinity for α‐tocopherol transfer protein as a determinant of the biological activities of vitamin E analogs (1997)

alpha-Tocopherol transfer protein (alphaTTP), a product of the gene which causes familial isolated vitamin E deficiency, plays an important role in determining the plasma vitamin E level. We examined the structural characteristics of vitamin E analogs required for recognition by alphaTTP. Ligand specificity was assessed by evaluating the competition of non-labeled vitamin E analogs and alpha-[3H]tocopherol for transfer between membranes in vitro. Relative affinities (RRR-alpha-tocopherol = 100%) calculated from the degree of competition were as follows: beta-tocopherol, 38%; gamma-tocopherol, 9%; delta-tocopherol, 2%; alpha-tocopherol acetate, 2%; alpha-tocopherol quinone, 2%; SRR-alpha-tocopherol, 11%; alpha-tocotrienol, 12%; trolox, 9%. Interestingly, there was a linear relationship between the relative affinity and the known biological activity obtained from the rat resorption-gestation assay. From these observations, we conclude that the affinity of vitamin E analogs for alphaTTP is one of the critical determinants of their biological activity.
A light, nontoxic interleukin 12 protocol inhibits HER-2/neu mammary carcinogenesis in BALB/c transgenic mice with established hyperplasia. (2001)

With a slight asynchronous but consistent progression, all of the mammary glands of female BALB/c mice transgenic for the transforming rat HER-2/neu oncogene progress to atypical hyperplasia and to invasive carcinoma. Previous studies have shown that chronic administration of interleukin (IL) 12 started at the 2nd week of age hampers this progression because of its ability to inhibit tumor angiogenesis and activate a nonspecific immune response. Here we show that a similar inhibition is achieved when 7-week-old mice with fully blown atypical hyperplasia receive a weekly injection of 100 ng IL-12 for 16 times. This lower-dose and later IL-12 administration induces high and sustained levels of serum IFN-gamma equivalent to those elicited by more frequent administrations. A lower-dose and less toxic treatment may thus be envisaged as a possible option in the management of preneoplastic mammary lesions.
Lead halide perovskites: Crystal-liquid duality, phonon glass electron crystals, and large polaron formation (2017)

Lead halide perovskites have been demonstrated as high performance materials in solar cells and light-emitting devices. These materials are characterized by coherent band transport expected from crystalline semiconductors, but dielectric responses and phonon dynamics typical of liquids. This "crystal-liquid" duality implies that lead halide perovskites belong to phonon glass electron crystals, a class of materials believed to make the most efficient thermoelectrics. We show that the crystal-liquid duality and the resulting dielectric response are responsible for large polaron formation and screening of charge carriers, leading to defect tolerance, moderate charge carrier mobility, and radiative recombination properties. Large polaron formation, along with the phonon glass character, may also explain the marked reduction in hot carrier cooling rates in these materials.
Amplification of the Driving Oncogene, KRAS or BRAF , Underpins Acquired Resistance to MEK1/2 Inhibitors in Colorectal Cancer Cells (2011)

The acquisition of resistance to protein kinase inhibitors is a growing problem in cancer treatment. We modeled acquired resistance to the MEK1/2 (mitogen-activated or extracellular signal-regulated protein kinase kinases 1 and 2) inhibitor selumetinib (AZD6244) in colorectal cancer cell lines harboring mutations in BRAF (COLO205 and HT29 lines) or KRAS (HCT116 and LoVo lines). AZD6244-resistant derivatives were refractory to AZD6244-induced cell cycle arrest and death and exhibited a marked increase in ERK1/2 (extracellular signal-regulated kinases 1 and 2) pathway signaling and cyclin D1 abundance when assessed in the absence of inhibitor. Genomic sequencing revealed no acquired mutations in MEK1 or MEK2, the primary target of AZD6244. Rather, resistant lines showed a marked up-regulation of their respective driving oncogenes, BRAF(600E) or KRAS(13D), due to intrachromosomal amplification. Inhibition of BRAF reversed resistance to AZD6244 in COLO205 cells, which suggested that combined inhibition of MEK1/2 and BRAF may reduce the likelihood of acquired resistance in tumors with BRAF(600E). Knockdown of KRAS reversed AZD6244 resistance in HCT116 cells as well as reduced the activation of ERK1/2 and protein kinase B; however, the combined inhibition of ERK1/2 and phosphatidylinositol 3-kinase signaling had little effect on AZD6244 resistance, suggesting that additional KRAS effector pathways contribute to this process. Microarray analysis identified increased expression of an 18-gene signature previously identified as reflecting MEK1/2 pathway output in resistant cells. Thus, amplification of the driving oncogene (BRAF(600E) or KRAS(13D)) can drive acquired resistance to MEK1/2 inhibitors by increasing signaling through the ERK1/2 pathway. However, up-regulation of KRAS(13D) leads to activation of multiple KRAS effector pathways, underlining the therapeutic challenge posed by KRAS mutations. These results may have implications for the use of combination therapies.
Uric Acid – A Uremic Toxin? (2005)

Uric acid might often be regarded as a simple marker of renal disease. Although it is well known that hyperuricemia causes gout which is associated with renal insufficiency and cardiovascular disease, one might think that it could attribute to the intrarenal urate crystal, but not to uric acid per se. In order to clarify the role of uric acid in the kidney, we hypothesized that uric acid causes renal disease. To generate mild hyperuricemia without intrarenal crystal in rats, we used low doses of an uricase inhibitor (2% oxonic acid). Hyperuricemia induced systemic hypertension, glomerular hypertrophy/hypertension, afferent arteriolar sclerosis, and macrophage infiltration in normal rat kidney. In progressive renal disease, such as cyclosporine nephropathy and remnant kidney in rat, uric acid accelerated the progression of renal disease. Thus, we concluded that uric acid is not a simple marker, but a cause of renal disease.
Novel acyclic adenosine analogs inhibit Epstein-Barr virus replication (1987)

The effect of three new acyclic adenosine analogs, (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)adenine [(S)-HPMPA], 9-(2-phosphonylmethoxyethyl)adenine (PMEA), and (S)-9-(2,3-dihydroxypropyl)adenine [(S)-DHPA], on Epstein-Barr virus (EBV) replication was studied. Both (S)-HPMPA and PMEA but not (S)-DHPA effectively inhibited EBV DNA replication in virus-producer P3HR-1 cells and in latently infected Raji cells superinfected with P3HR-1 virus, as determined by cRNA-DNA hybridization and density gradient centrifugation. The 50% effective doses for inhibiting virus replication were 0.08 and 1.1 microM for (S)-HPMPA and PMEA, respectively. Both drugs were cytostatic but not cytotoxic to the cells at a concentration as high as 100 microM. These results indicate that (S)-HPMPA and PMEA are potent and selective anti-EBV agents in vitro.