gebhart/patrepeval huggingface dataset:
Purification and characterization of single-chain urokinase-type plasminogen activator from human cell cultures. (1986)

A urokinase-type plasminogen activator was purified from conditioned media of several human cell cultures, but preferably from the human lung adenocarcinoma line CALU-3 (ATCC, HTB-55), using a combination of chromatography on zinc chelate-Sepharose, SP-Sephadex C-50, and Sephadex G-100. Final yields of 65-100 micrograms/liter of starting material were obtained with a 290-fold purification factor and a recovery of 30%. The purified plasminogen activator consists of a single polypeptide chain with Mr 54,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and is very similar or identical to single-chain urokinase-type plasminogen activator on the basis of immunodiffusion, amino acid composition, and the lack of specific binding to fibrin. It has very low amidolytic activity on Pyroglu-Gly-Arg-rho-nitroanilide and is converted to two-chain urokinase by limited exposure to plasmin. It has a specific activity of 60,000 IU/mg on fibrin plates and directly activates plasminogen following Michaelis-Menten kinetics with Km = 1.1 microM and kappa cat = 0.0026 S-1. It is concluded that the plasminogen activator purified from CALU-3-conditioned media is physically and kinetically identical to single-chain urokinase-type plasminogen activator. With the present straightforward purification method and a readily available source, sufficient amounts of single-chain urokinase-type plasminogen activator can be obtained for more detailed investigations of its biochemical, biological, and thrombolytic properties.
Hybrid automata models in continuous-linear hybrid systems analysis (1999)

We introduce some analysis tools for a class of continuous-linear hybrid systems. The continuous-linear term is used in the sense of system theory and it is in this sense that continuous-linear hybrid automata are defined. Using the defined automaton representation, we provide an analytical formulation of the system dynamic behavior. With the analysis results, dynamic properties for reachability and limit cycle analysis purposes are established. Finally, a coupled hybrid case is conducted.
Tyrosine 192 in Apolipoprotein A-I Is the Major Site of Nitration and Chlorination by Myeloperoxidase, but Only Chlorination Markedly Impairs ABCA1-dependent Cholesterol Transport (2004)

High density lipoprotein (HDL) isolated from human atherosclerotic lesions and the blood of patients with established coronary artery disease contains elevated levels of 3-nitrotyrosine and 3-chlorotyrosine. Myeloperoxidase (MPO) is the only known source of 3-chlorotyrosine in humans, indicating that MPO oxidizes HDL in vivo. In the current studies, we used tandem mass spectrometry to identify the major sites of tyrosine oxidation when lipid-free apolipoprotein A-I (apoA-I), the major protein of HDL, was exposed to MPO or peroxynitrite (ONOO(-)). Tyrosine 192 was the predominant site of both nitration and chlorination by MPO and was also the major site of nitration by ONOO(-). Electron paramagnetic spin resonance studies of spin-labeled apoA-I revealed that residue 192 was located in an unusually hydrophilic environment. Moreover, the environment of residue 192 became much more hydrophobic when apoA-I was incorporated into discoidal HDL, and Tyr(192) of HDL-associated apoA-I was a poor substrate for nitration by both myeloperoxidase and ONOO(-), suggesting that solvent accessibility accounted in part for the reactivity of Tyr(192). The ability of lipid-free apoA-I to facilitate ATP-binding cassette transporter A1 cholesterol transport was greatly reduced after chlorination by MPO. Loss of activity occurred in concert with chlorination of Tyr(192). Both ONOO(-) and MPO nitrated Tyr(192) in high yield, but unlike chlorination, nitration minimally affected the ability of apoA-I to promote cholesterol efflux from cells. Our results indicate that Tyr(192) is the predominant site of nitration and chlorination when MPO or ONOO(-) oxidizes lipid-free apoA-I but that only chlorination markedly reduces the cholesterol efflux activity of apoA-I. This impaired biological activity of chlorinated apoA-I suggests that MPO-mediated oxidation of HDL might contribute to the link between inflammation and cardiovascular disease.
Duality, achievable rates, and sum-rate capacity of gaussian mimo broadcast channels (2003)

We consider a multiuser multiple-input multiple- output (MIMO) Gaussian broadcast channel (BC), where the transmitter and receivers have multiple antennas. Since the MIMO BC is in general a nondegraded BC, its capacity region remains an unsolved problem. We establish a duality between what is termed the "dirty paper" achievable region (the Caire-Shamai (see Proc. IEEE Int. Symp. Information Theory, Washington, DC, June 2001, p.322) achievable region) for the MIMO BC and the capacity region of the MIMO multiple-access channel (MAC), which is easy to compute. Using this duality, we greatly reduce the computational complexity required for obtaining the dirty paper achievable region for the MIMO BC. We also show that the dirty paper achievable region achieves the sum-rate capacity of the MIMO BC by establishing that the maximum sum rate of this region equals an upper bound on the sum rate of the MIMO BC.
Mechanism of the Reaction Catalyzed by Acetoacetate Decarboxylase. Importance of Lysine 116 in Determining the pKa of Active-Site Lysine 115 (1996)

Acetoacetate decarboxylase from Clostridium acetobutylicum (AAD) catalyzes the decarboxylation of acetoacetate via a Schiff base intermediate [Hamilton, G. A., & Westheimer, F. H. (1959) J. Am. Chem. Soc. 81, 6332; Fridovich, I., & Westheimer F. H. (1962) J. Am. Chem. Soc. 84, 3208]. The pKa of the active-site lysine (Lys 115) is 6.0, 4.5 pKa units less than the pKa of lysine in solution [Kokesh, F. C., & Westheimer, F. H. (1971) J. Am. Chem. Soc. 93, 7270; Frey, P. A., Kokesh, F. C., & Westheimer, F. H. (1971) J. Am. Chem. Soc. 93, 7266; Schmidt, D. E., Jr., & Westheimer, F. H. (1971) Biochemistry 10, 1249]. Westheimer and co-workers hypothesized that the pKa of Lys 115 is decreased by its spatial proximity to the epsilon-ammonium group of Lys 116. We have investigated this proposal by studying site-directed mutants of Lys 115 and Lys 116. Two substitutions for Lys 115 (K115C and K115Q) were both catalytically inactive at pH 5.95, the pH optimum of wild type AAD, demonstrating the importance of this residue in catalysis. Activity could be restored to K115C by aminoethylation with 2-bromoethyl-ammonium bromide (2-BEAB). Substitutions for Lys 116 (K116C, K116N, and K116R) had reduced but significant activities at pH 5.95. The effects of Lys 116 on the pKa of Lys 115 in the mutant AADs were evaluated following imine formation with 5-nitrosalicylaldehyde and reduction with NaBH4. Whereas the pKa of Lys 115 in K116R is similar to that observed for wild type AAD, the pKaS of Lys 115 in K116C and K116N were elevated to > 9.2. Alkylation of Cys 116 in K116C with 2-BEAB resulted in both significant activation and restoration of the pKa of Lys 115 to 5.9. These data support Westheimer's hypothesis that the pKa of the Schiff base-forming Lys 115 is decreased by its spatial proximity to the epsilon-ammonium group of Lys 116.
A phase II trial of nilotinib in the treatment of patients with KIT mutated advanced acral and mucosal melanoma (NICAM). (2011)

TPS229 Background: Recent studies have indicated that KIT mutations occur in approximately 20% of acral and mucosal melanomas (Curtin, al. 2006; Beadling, et al. 2008). Several case reports have shown that KIT mutated melanomas can respond to treatment with KIT inhibitors (Hodi et al. 2008; Lutzky et al. 2008; Quintas-Cardama et al. 2008; Handolias et al. 2010; Itoh, et al. 2010; Satzger et al. 2010; Terheyden et al. 2010; Woodman and Davies 2010) suggesting that such tumours critically depend on upregulated KIT signalling. Nilotinib, which potently inhibits the tyrosine kinase activity of BCR-ABL and KIT, has been evaluated in patients with advanced KIT mutated GIST and has shown clinical efficacy at well tolerated doses (Demetri et al. 2009; Montemurro et al. 2009; Schlemmer et al. 2010). Methods: NICAM is a single arm 2-stage open label phase II study of nilotinib in KIT mutated advanced mucosal or acral melanoma. Patients with KIT mutations known to confer resistance to nilotinib are excluded. The primary objective in this feasibility study is to evaluate the efficacy of nilotinib in KIT mutated advanced mucosal and acral melanoma with a primary endpoint of progression free survival at 6 months. Secondary endpoints include response rate at 12 weeks; overall survival; toxicity of treatment; correlation between the response to nilotinib and KIT genotype, KIT gene copy number and KIT expression. In addition, the following will be explored: 1. Suppression of phosphorylation of KIT and downstream pathways on day 15 tumour biopsies; 2. Possible mechanisms of resistance by analysis of biopsies obtained at disease progression; 3. The use of circulating tumour DNA for non–invasive KIT mutational testing; 4. Genetic lesions that potentially cooperate with oncogenic KIT in melanoma (using Next Generation Sequencing). All patients are treated until disease progression or unacceptable toxicity. If 2 or more of the first 9 patients are progression free at 6 months, patient entry will continue into the second stage until a total of 24 patients have been recruited. To date, 45 patients have been registered and screened for KIT mutation and 5 patients have entered the study.
Development of XUV projection lithography at 60-80 nm (Poster Paper) (1992)

The rationale, design, component properties, and potential capabilities of extreme-ultraviolet (XUV) projection lithography systems using 60 - 80 nm illumination and single-surface reflectors are described. These systems are evaluated for potential application to high-volume production of future generations of gigabit chips.
Triheptanoin Supplementation to Ketogenic Diet Curbs Cognitive Impairment in APP/PS1 Mice Used as a Model of Familial Alzheimer’s Disease (2013)

Diets containing a high proportion of fat with respect to protein plus carbohydrates are capable of inducing ketone body production in the liver, which provides an energetic alternative to glucose. Some ketogenic diets have been tested as therapeutic strategies for treating metabolic disorders related to a deficiency in glucose-driven ATP generation. However, ketone bodies are not capable of providing extra tricarboxylic acid cycle intermediates, limiting the anabolic capacity of the cell. Therefore, it is reasonable to hypothesize that supplementing a ketogenic diet with anaplerotic compounds such as triheptanoin may improve ketogenic diet effectiveness. The present study tests this hypothesis in APP/PS1 (APPswe/PS1dE9) transgenic mice, used as a model of familial Alzheimer's disease because impaired energy supply to neurons has been linked to this neurodegenerative process. Triheptanoin supplementation to a ketogenic diet for three months and starting at the age of three months reduces the memory impairment of APP/PS1 mice at the age of 6 months. The Aβ production and deposition were not significantly altered by the ketogenic diet, supplemented or not by triheptanoin. However, mice fed with triheptanoin-rich ketogenic diet have shown decreased astroglial response in the vicinity of Aβ plaques and decreased expression of the pro-inflammatory cytokine interferon-γ in astrocytes. These findings correlate with transcriptional up-regulation of the ROS detoxifying mechanisms Sirt1 and Pparg, thus linking triheptanoin with improved mitochondrial status. Present findings support the concept that ketogenic diets supplemented with anaplerotic compounds can be considered potential therapeutic strategies at early stages of Alzheimer's disease.
TAT-BH4 and TAT-Bcl-xL Peptides Protect against Sepsis-Induced Lymphocyte Apoptosis In Vivo (2006)

Apoptosis is a key pathogenic mechanism in sepsis that induces extensive death of lymphocytes and dendritic cells, thereby contributing to the immunosuppression that characterizes the septic disorder. Numerous animal studies indicate that prevention of apoptosis in sepsis improves survival and may represent a potential therapy for this highly lethal disorder. Recently, novel cell-penetrating peptide constructs such as HIV-1 TAT basic domain and related peptides have been developed to deliver bioactive cargoes and peptides into cells. In the present study, we investigated the effects of sepsis-induced apoptosis in Bcl-x(L) transgenic mice and in wild-type mice treated with an antiapoptotic TAT-Bcl-x(L) fusion protein and TAT-BH4 peptide. Lymphocytes from Bcl-x(L) transgenic mice were resistant to sepsis-induced apoptosis, and these mice had a approximately 3-fold improvement in survival. TAT-Bcl-x(L) and TAT-BH4 prevented Escherichia coli-induced human lymphocyte apoptosis ex vivo and markedly decreased lymphocyte apoptosis in an in vivo mouse model of sepsis. In conclusion, TAT-conjugated antiapoptotic Bcl-2-like peptides may offer a novel therapy to prevent apoptosis in sepsis and improve survival.
When Can I Get My AMOLED TV? (2010)

Prototypes have whetted consumers' appetites for AMOLED TVs. Meanwhile, companies are working to overcome production challenges in order to produce the TVs in volume.
Current Trends in Broker/Dealer Litigation (2002)

This article is an up‐to‐date review of the trends that are developing in both the capital markets and private client litigation. This includes, of course, the trends in arbitration and clearing firm cases as well.
Rapid, Automated Nucleic Acid Probe Assays Using Silicon Microstructures for Nucleic Acid Concentration (1999)

A system for rapid point-of-use nucleic acid (NA) analysis based on PCR techniques is described. The extraction and concentration of DNA from test samples has been accomplished utilizing silicon fluidic microchips with high surface-area-to-volume ratios. Short (500 bp) and medium size (48,000 bp) DNA have been captured, washed, and eluted using the silicon dioxide surfaces of these chips. Chaotropic (GuHCl) salt solutions were used as binding agents. Wash and elution agents consisted of ethanol-based solutions and water, respectively. DNA quantities approaching 40 ng/cm2 of binding area were captured from input solutions in the 100-1000 ng/mL concentration range. For dilute samples of interest for pathogen detection, PCR and gel electrophoresis were used to demonstrate extraction efficiencies of about 50 percent, and concentration factors of about 10x using bacteriophage lambda DNA as the target. Rapid, multichannel PCR thermal cycling modules with integrated solid-state detection components have also been demonstrated. These results confirm the viability of utilizing these components as elements of a compact, disposable cartridge system for the detection of NA in applications such as clinical diagnostics, biowarfare agent detection, food quality control, and environmental monitoring.
VH gene usage in immunoglobulin E responses of seasonal rhinitis patients allergic to grass pollen is oligoclonal and antigen driven (2004)

In contrast to previous studies we observed no preferred VH gene common to IgE transcripts of the three subjects allergic to grass pollen. Moreover, most of the VH gene characteristics of the IgE transcripts were consistent with oligoclonal antigen-driven IgE responses.
Use of diodes to enable &#x03BC;Loop<sup>&#x00AE;</sup> test structures for buried defects and voltage to grayscale calibration (2014)

Two test structures that address key problems for voltage contrast inspection are introduced. These structures both utilize diodes to provide unique capability. The first structure illustrates how a two-pass area accelerated inspection can be used for detection of buried defects such as gate shorts or via opens. Like standard μLoop <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> test structures, the first inspection pass is able to detect the existence of all the defects affecting the structure while only scanning a small fraction of the structure. The purpose of the second inspection pass is to look for physical signs of the defect, but none are generally visible for buried defects. The key to this structure is that diodes are used to indicate the location of the buried defect. The second structure is used to map voltage to grayscale. This structure takes advantage of the well-known fact that there is a 0.6V drop across a forward biased diode.
Branching of Colloidal Chains in Capillary-Confined Nematics (2006)

We report on the observation of colloidal chain assembly and branching inside capillaries filled with a nematic liquid crystal. Because of the homeotropic anchoring of liquid crystalline molecules on the capillary and colloidal droplet surfaces, the assembly of droplets along the capillary axis is expected, producing a transformation of the nematic director field from an escape-radial to quasiradial configuration. However, the subsequent over time branching of the straight colloidal chains is counterintuitive. By numerical simulations, we demonstrate that chain branching can occur by overcoming an energy barrier and can at least dwell as a metastable configuration. Moreover, manipulation of colloidal chains by electric fields and their gradients demonstrates various regimes of chain behavior in electric fields.
Tauroursodeoxycholic acid protects rat hepatocytes from bile acid-induced apoptosis via activation of survival pathways† (2004)

Ursodeoxycholic acid (UDCA) is used in the treatment of cholestatic liver diseases, but its mechanism of action is not yet well defined. The aim of this study was to explore the protective mechanisms of the taurine-conjugate of UDCA (tauroursodeoxycholic acid [TUDCA]) against glycochenodeoxycholic acid (GCDCA)-induced apoptosis in primary cultures of rat hepatocytes. Hepatocytes were exposed to GCDCA, TUDCA, the glyco-conjugate of UDCA (GUDCA), and TCDCA. The phosphatidylinositol-3 kinase pathway (PI3K) and nuclear factor-kappaB were inhibited using LY 294002 and adenoviral overexpression of dominant-negative IkappaB, respectively. The role of p38 and extracellular signal-regulated protein kinase mitogen-activated protein kinase (MAPK) pathways were investigated using the inhibitors SB 203580 and U0 126 and Western blot analysis. Transcription was blocked by actinomycin-D. Apoptosis was determined by measuring caspase-3, -9, and -8 activity using fluorimetric enzyme detection, Western blot analysis, immunocytochemistry, and nuclear morphological analysis. Our results demonstrated that uptake of GCDCA is needed for apoptosis induction. TUDCA, but not TCDCA and GUDCA, rapidly inhibited, but did not delay, apoptosis at all time points tested. However, the protective effect of TUDCA was independent of its inhibition of caspase-8. Up to 6 hours of preincubation with TUDCA before addition of GCDCA clearly decreased GCDCA-induced apoptosis. At up to 1.5 hours after exposure with GCDCA, the addition of TUDCA was still protective. This protection was dependent on activation of p38, ERK MAPK, and PI3K pathways, but independent of competition on the cell membrane, NF-kappaB activation, and transcription. In conclusion, TUDCA contributes to the protection against GCDCA-induced mitochondria-controlled apoptosis by activating survival pathways.
Yeast Sugar Transporters (1993)

Transport of sugars is a fundamental property of all eukaryotic cells. Of particular importance is the uptake of glucose, a preferred carbon and energy source. The rate of glucose utilization in yeast is often dictated by the activity and concentration of glucose transporters in the plasma membrane. Given the importance of transport as a site of control of glycolytic flux, the regulation of glucose transporters is necessarily complex. The molecular analysis of these transporters in Saccharomyces has revealed the existence of a multigene family of sugar carriers. Recent data have raised the question of the actual role of all of these proteins in sugar catabolism, as some appear to be lowly expressed, and point mutations of these genes may confer pleiotropic phenotypes, inconsistent with a simple role as catabolic transporters. The transporters themselves appear to be intimately involved in the process of sensing glucose, a model for which there is growing support.
[Atelocollagen/hydroxylapatite composite material as bone defect filler in an experiment on rats]. (1995)

Many types of biomaterials are used as skeletal bone fillers in reconstructive surgery. An attention is paid to hydroxyapatite due to its high biocompatibility with the surrounding tissue. The paper deals with the testing of new collagen/hydroxyapatite composite material applied to the bone defect on os parietale of rats. The composite material was prepared from the bovine atelocollagen dispersion and the dispersion of hydroxyapatite. Collagen serves as a matrix in which the particles of hydroxyapatite are anchored. The composite presents the advantage that after the saturation with physiological solution it is compact and can be shaped. The composite material was implanted in the form of plate into six male Wistar rats to the ground bed on the surface of os parietale. The implants were taken out after four moths. The macroscopic finding of soft tissue, bones and implants gave evidence about good healing without any undesirable reaction. This was also confirmed by the histological observations. Collagen was resorbed and the rest of the material strongly adhered to the bone. The marked osteocytes were present in the zone of the newly formed bone and the dividing line between new and old bone was clear. The experimental results give preconditions to the clinical use of this new composite implant material the structural improvement of which is in progress. (Fig. 2, Ref. 12.)
Thermal decomposition of the amino acids glycine, cysteine, aspartic acid, asparagine, glutamic acid, glutamine, arginine and histidine (2018)

Eight of the 20 standard amino acids decompose at well-defined, characteristic temperatures, in contrast to commonly accepted knowledge. Products of decomposition are simple. The novel quantitative results emphasize the impact of water and cyclic condensates with peptide bonds and put constraints on hypotheses of the origin, state and stability of amino acids in the range between 200 °C and 300 °C.
Silk Microspheres Prepared by Spray-drying of an Aqueous System (2000)

Scoured silk fibre was dissolved in a solution of calcium chloride in water and ethanol. After dialysis against purified water, theophylline as model drug was added to the solution. Silk microspheres prepared after spray-drying were round but somewhat wrinkled; their diameter was 5 μm (approx.). According to powder X-ray diffractometry, and FTIR and Raman spectroscopy, fibroin and theophylline were amorphous in the microsphere. The microspheres formed gels immediately after soaking in purified water and in Japanese Pharmacopoeia XIII solutions 1 (pH 1.2) and 2 (pH 6.8); the gels dissolved slightly in these aqueous media. In this way we have developed a new drug carrier for sustained release without the use of poisonous organic solvents or glutaraldehyde.