gebhart/patrepeval huggingface dataset:
Mechanistic Studies of Palladium(II)-Catalyzed Hydrosilation and Dehydrogenative Silation Reactions (1997)

The cationic Pd(II) complexes, [(phen)Pd(CH3)(L)]+[BAr‘4]- phen = 1,10−phenanthroline; L = Et2O, Me3SiC⋮CSiMe3; Ar‘ = 3,5-(CF3)2C6H3) catalyze the hydrosilation and dehydrogenative silation of olefins. Hydrosilation of ethylene, tert-butylethylene, 1-hexene, and cyclohexene by HSiR3 (R = CH2CH3, C6H5) occurs in the presence of 1 mol % [(phen)Pd(CH3)(L)]+[BAr‘4]-. The reaction of tert-butylethylene with HSi(i-Pr)3 in the presence of [(phen)Pd(CH3)(L)]+[BAr‘4]- yields neohexane and t-BuCHCHSi(i-Pr)3. Low-temperature NMR experiments revealed that the catalyst resting state for the silations of ethylene and alkyl-substituted olefins is [(phen)Pd(SiR3)(η2-H2CCHR‘)]+[BAr‘4]-. Evidence for rapid, reversible silyl migration at −70 °C was observed by 1H NMR spectroscopy. Deuterium labeling studies show that the intermediate Pd(II) alkyl complexes can isomerize via a series of β-hydride eliminations followed by reinsertions of olefin prior to reaction with DSiEt3. Styrene undergoes both hydrosilation and dehydrogenative silation in the presence of [(phen)Pd(CH3)(L)]+[BAr‘4]- or [(phen)Pd(η3-CH(CH3)C6H5)]+[BAr‘4]- yielding ethylbenzene, R3SiCH2CH2C6H5 and trans-R3SiCHCHPh (R = CH2CH3, CH(CH3)2). 1H NMR spectroscopy revealed that the π-benzyl complexes [(phen)Pd(η3-CH(CH2SiR3)C6H5)]+[BAr‘4]- and [(phen)Pd(η3-CH(CH3)C6H5)]+[BAr‘4]- are the catalyst resting states for the silation reactions of styrene.
Regulatory RNAs derived from transfer RNA? (2010)

Four recent studies suggest that cleavages of transfer RNAs generate products with microRNA-like features, with some evidence of function. If their regulatory functions were to be confirmed, these newly revealed RNAs would add to the expanding repertoire of small noncoding RNAs and would also provide new perspectives on the coevolution of transfer RNA and messenger RNA.
3-D reconstruction of coronary arteries (2002)

Coronary arteriography is a technique used for evaluating the state of the coronary arteries. Matching of coronary arteries from multiple views is necessary for obtaining a 3-D (three dimensional) description of the arterial tree. Overlapping vessels and artifacts due to digital subtraction of the angiogram background make the matching process quite difficult. Simplex method based linear programming and relaxation based consistent labeling are applied to skeletons from three views in order to obtain a matching of branches between views. Results show low error for 3-D reconstruction, by overlapping its forward projection with the skeleton extracted from one view.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bandwidth as currency (2003)

Provisioning bandwidth in an actuarially consistent manner has many far-reaching implications reminiscent of the commercial rationalization of railways in the 1870s - in that period's path to profitability. Mapping packet flow to willingness to pay, as rail cargo content was matched to the cost of carry, will better utilize bandwidth, enhancing network value consistent with the information being exchanged. The author discusses the notion of a packet watermark which can enable bandwidth as currency. Payment facilities are generally treated as separate, independent data flows from the actual data being transacted. Packet watermarks map payment facilities to the fidelity, discreteness, or functionality of the data demanded, representing a consistent means of determining a willingness to pay. This mapping acts as a receipt for data commerce.
Mapping the Interacting Domains of STIM1 and Orai1 in Ca2+ Release-activated Ca2+ Channel Activation (2007)

STIM1 and Orai1 are essential components of Ca(2+) release-activated Ca(2+) channels (CRACs). After endoplasmic reticulum Ca(2+) store depletion, STIM1 in the endoplasmic reticulum aggregates and migrates toward the cell periphery to co-localize with Orai1 on the opposing plasma membrane. Little is known about the roles of different domains of STIM1 and Orai1 in protein clustering, migration, interaction, and, ultimately, opening CRAC channels. Here we demonstrate that the coiled-coil domain in the C terminus of STIM1 is crucial for its aggregation. Amino acids 425-671 of STIM1, which contain a serine-proline-rich region, are important for the correct targeting of the STIM1 cluster to the cell periphery after calcium store depletion. The polycationic region in the C-terminal tail of STIM1 also helps STIM1 targeting but is not essential for CRAC channel activation. The cytoplasmic C terminus but not the N terminus of Orai1 is required for its interaction with STIM1. We further identify a highly conserved region in the N terminus of Orai1 (amino acids 74-90) that is necessary for CRAC channel opening. Finally, we show that the transmembrane domain of Orai1 participates in Orai1-Orai1 interactions.
Extraction of β-lactamase from Moraxella catarrhalis (1994)

Journal Article Extraction of β-lactamase from Moraxella catarrhalis Get access CHANG-PHONE FUNG, CHANG-PHONE FUNG aSection of Infectious Diseases, Department of Medicine, Veterans General Hospital-TaipeiTaipei, Taiwan, 11217, ROCbDepartment of Medical Microbiology, The London Hospital Medical CollegeTurner Street, London, E1 2AD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar SIEW-FAH YEO, SIEW-FAH YEO bDepartment of Medical Microbiology, The London Hospital Medical CollegeTurner Street, London, E1 2AD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar DAVID M. LIVERMORE DAVID M. LIVERMORE bDepartment of Medical Microbiology, The London Hospital Medical CollegeTurner Street, London, E1 2AD, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Antimicrobial Chemotherapy, Volume 34, Issue 1, July 1994, Pages 183–184, https://doi.org/10.1093/jac/34.1.183 Published: 01 July 1994
Nr-CAM is a target gene of the β-catenin/LEF-1 pathway in melanoma and colon cancer and its expression enhances motility and confers tumorigenesis (2002)

beta-catenin and plakoglobin (gamma-catenin) are homologous molecules involved in cell adhesion, linking cadherin receptors to the cytoskeleton. beta-catenin is also a key component of the Wnt pathway by being a coactivator of LEF/TCF transcription factors. To identify novel target genes induced by beta-catenin and/or plakoglobin, DNA microarray analysis was carried out with RNA from cells overexpressing either protein. This analysis revealed that Nr-CAM is the gene most extensively induced by both catenins. Overexpression of either beta-catenin or plakoglobin induced Nr-CAM in a variety of cell types and the LEF/TCF binding sites in the Nr-CAM promoter were required for its activation by catenins. Retroviral transduction of Nr-CAM into NIH3T3 cells stimulated cell growth, enhanced motility, induced transformation, and produced rapidly growing tumors in nude mice. Nr-CAM and LEF-1 expression was elevated in human colon cancer tissue and cell lines and in human malignant melanoma cell lines but not in melanocytes or normal colon tissue. Dominant negative LEF-1 decreased Nr-CAM expression and antibodies to Nr-CAM inhibited the motility of B16 melanoma cells. The results indicate that induction of Nr-CAM transcription by beta-catenin or plakoglobin plays a role in melanoma and colon cancer tumorigenesis, probably by promoting cell growth and motility.
Cigarette smoking reduces histone deacetylase 2 expression, enhances cytokine expression, and inhibits glucocorticoid actions in alveolar macrophages (2001)

SPECIFIC AIMSGlucocorticoidsact, at least in part, through recruitment of histone deacetylases (HDACs) to sites of inflammatory gene transcription. In this study we show that cigarette smoke, an oxidative stress, decreased HDAC activity in human biopsies and macrophages in vivo. This reduced activity correlated with enhanced induction of inflammatory cytokines and a reduction in glucocorticoid responsiveness in vitro.PRINCIPAL FINDINGS1. HAT and HDAC expression in bronchial biopsies and alveolar macrophages.The histone acetyltransferases (HATs) CBP and HDAC1 and HDAC2 are localized within the airway to all cells with the most intense staining within the epithelium and inflammatory cells. Smoking did not affect the site of the expression of any of these proteins. Western blot analysis detected no difference in the expression of CBP or PCAF between the two groups. In contrast, there was a decrease in HDAC2 expression (0.63±0.02 vs. 0.37±0.06 OD units, P<0.01), but not HDAC1 (0.55±0.07 versus 0.55±0.10 OD un...
Abstract P169: A Novel Mitochondrial Permeability Transition Pore Inhibitor, Bendavia, Reduces Microvascular Obstruction (No-Reflow) due to Myocardial Ischemia/Reperfusion Injury in the Rabbit (2011)

Background: The no-reflow phenomenon is an important detrimental component of reperfusion injury with clinical implications, as it is an independent predictor of outcome after myocardial infarction. Whether the mitochondrial permeability transition pore (MPTP) is involved in vascular integrity and no-reflow post reperfusion is unknown. Therefore, we tested Bendavia, a compound that is known to inhibit the MPTP, for its effects on no-reflow. Methods: Anesthetized rabbits were subjected to 30 min coronary artery occlusion and 3 hrs reperfusion. Treated animals (n=49) received Bendavia (0.05 mg/kg/hr) after the onset of ischemia, 1, 10 or 20 min before reperfusion. Control animals (n=15) received saline. Risk zone was measured by Unisperse blue staining, anatomic no-reflow area using thioflavin S and necrosis by triphenyltetrazolium chloride. Results: The ischemic insult was similar in both groups (31% of left ventricle (LV) in Bendavia and 30% in control). Bendavia treatment resulted in a non-significant 11% reduction in necrosis, expressed as a percentage of the risk zone. However for any given risk zone size, no-reflow was significantly reduced by Bendavia, as there was a significant group effect on the relationship between the extent of the no-reflow zone and that of the risk zone (ANCOVA, p = 0.0085). Overall, the no-reflow zone, expressed as a % of the risk zone was 22 ± 2% in treated hearts vs. 28 ± 3% in controls (p=0.07). In hearts with less severe risk zones (below the mean value of 31% of LV), Bendavia treatment significantly reduced the no-reflow zone by 35% (17±2 vs. 26±4% of risk zone, p &lt;0.05); in hearts with large risk zone, Bendavia non-significantly reduced no-reflow by 17%. Bendavia treatment had no effect on hemodynamic parameters or regional myocardial blood flow during the ischemic period. Conclusion: These data suggest that the MPTP may play a role in the pathophysiology of no-reflow after myocardial ischemia/reperfusion. Bendavia reduced the extent of the no-reflow zone for any given risk zone size, suggesting that it helped prevent microvascular obstruction.
Bone marrow transplantation corrects the enzyme defect in neurons of the central nervous system in a lysosomal storage disease. (1994)

Neuronal storage disorders are fatal neurodegenerative diseases of humans and animals that are caused by inherited deficiencies of lysosomal hydrolase activity. Affected individuals often appear normal at birth but eventually develop progressive neurologic symptoms including sensory and motor deficits, mental retardation, and seizures. We have examined efficacy of bone marrow transplantation as a means of enzyme replacement, using cats with the lysosomal storage disease alpha-mannosidosis. Treated animals showed little or no progression of neurologic signs 1-2 years after transplant, whereas untreated cats became severely impaired and reached endstage disease by 6 months of age. Increased lysosomal alpha-mannosidase activity was found in brain tissue of the treated animals, and electron microscopy revealed no evidence of lysosomal storage within most neurons. Histochemical localization of acidic alpha-D-mannoside mannohydrolase (EC 3.2. 1.24), using 5-bromo-4-chloro-3-indolyl alpha-D-mannopyranoside, showed that functional enzyme was present in neurons, glial cells, and cells associated with blood vessels. This study provides direct evidence that bone marrow transplantation as treatment for a neuronal storage disease can lead to significant levels of a missing lysosomal hydrolase within neurons of the central nervous system and to compensation for the genetic metabolic defect.
Understanding Sources of Electrical Disorder in Graphene Grown by Chemical Vapor Deposition for Wafer-Scale Device Applications (2019)

We present a comprehensive explanation of the sources of electrical disorder in graphene grown by chemical vapor deposition (CVD) and transferred onto SiO2 substrates. By correlating carrier concentration distribution to the topographical mapping, we show that, due to the embedded ripple array created by the thermal expansion mismatch during growth, graphene forms uneven charge interaction with the SiO2 substrate, causing the areas in proximity of SiO2 to have higher hole concentration while the raised regions have lower hole doping. The net disorder of graphene is, therefore, a function of the density and scale of the thermal expansion ripples. We further show that, while the ripple-induced topographical nonuniformity can be alleviated by thermal annealing, the reduced topography actually has competing effects on overall disorder. On one hand, the reduced topography decreases the concentration nonuniformity between the raised and lowered regions, but on the other hand, annealing more closely couples the entire graphene layer to impurities in the SiO2 substrate. The results show that the ripple structure is not a disorder source by itself, but only contributes to disorder via the substrate interaction. This study suggests that minimizing substrate-induced disorder is of fundamental importance to reducing electrical disorder in transferred CVD graphene, which is significant for enabling wafer-scale integration of graphene devices for electronic, photonic, and sensing applications.
Purification and characterization of oxalyl-coenzyme A decarboxylase from Oxalobacter formigenes (1989)

Oxalyl-coenzyme A (oxalyl-CoA) decarboxylase was purified from Oxalobacter formigenes by high-pressure liquid chromatography with hydrophobic interaction chromatography, DEAE anion-exchange chromatography, and gel permeation chromatography. The enzyme is made up of four identical subunits (Mr, 65,000) to give the active enzyme (Mr, 260,000). The enzyme catalyzed the thiamine PPi-dependent decarboxylation of oxalyl-CoA to formate and carbon dioxide. Apparent Km and Vmax values, respectively, were 0.24 mM and 0.25 mumol/min for oxalyl-CoA and 1.1 pM and 0.14 mumol/min for thiamine pyrophosphate. The maximum specific activity was 13.5 microM oxalyl-CoA decarboxylated per min per mg of protein.
Low-resolution refinement tools in REFMAC5 (2012)

Two aspects of low-resolution macromolecular crystal structure analysis are considered: (i) the use of reference structures and structural units for provision of structural prior information and (ii) map sharpening in the presence of noise and the effects of Fourier series termination. The generation of interatomic distance restraints by ProSMART and their subsequent application in REFMAC5 is described. It is shown that the use of such external structural information can enhance the reliability of derived atomic models and stabilize refinement. The problem of map sharpening is considered as an inverse deblurring problem and is solved using Tikhonov regularizers. It is demonstrated that this type of map sharpening can automatically produce a map with more structural features whilst maintaining connectivity. Tests show that both of these directions are promising, although more work needs to be performed in order to further exploit structural information and to address the problem of reliable electron-density calculation.
CORDIC-based VLSI architectures for digital signal processing (1992)

The evolution of CORDIC, an iterative arithmetic computing algorithm capable of evaluating various elementary functions using a unified shift-and-add approach, and of CORDIC processors is reviewed. A method to utilize a CORDIC processor array to implement digital signal processing algorithms is presented. The approach is to reformulate existing DSP algorithms so that they are suitable for implementation with an array performing circular or hyperbolic rotation operations. Three categories of algorithm are surveyed: linear transformations, digital filters, and matrix-based DSP algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Steady-State Voltammetric Response of the Nanopore Electrode (2005)

The steady-state voltammetric response of the truncated conical-shaped glass nanopore electrode is presented. Analytical theory, finite-element simulations, and experimental measurement of the diffusive flux of a redox molecule through the pore orifice demonstrate that the steady-state current decreases rapidly as the pore depth increases and then asymptotically approaches a constant value when the pore depth is approximately 50x larger than the pore orifice. The asymptotic limit of the steady-state current is only a function of the pore orifice radius and the cone angle of the pore and has a finite value for all cone angles greater than zero. Experimental confirmation of the predicted dependence on pore depth is obtained using nanopore electrodes with 100-1000 nm orifice radii, by measuring the steady-state voltammetric current corresponding to the oxidation of ferrocene in acetonitrile solutions containing an excess of supporting electrolyte.
Diverse signaling pathways modulate nuclear receptor recruitment of N-CoR and SMRT complexes (1998)

Several lines of evidence indicate that the nuclear receptor corepressor (N-CoR) complex imposes ligand dependence on transcriptional activation by the retinoic acid receptor and mediates the inhibitory effects of estrogen receptor antagonists, such as tamoxifen, suppressing a constitutive N-terminal, Creb-binding protein/coactivator complex-dependent activation domain. Functional interactions between specific receptors and N-CoR or SMRT corepressor complexes are regulated, positively or negatively, by diverse signal transduction pathways. Decreased levels of N-CoR correlate with the acquisition of tamoxifen resistance in a mouse model system for human breast cancer. Our data suggest that N-CoR- and SMRT-containing complexes act as rate-limiting components in the actions of specific nuclear receptors, and that their actions are regulated by multiple signal transduction pathways.
Stable RNA interference: comparison of U6 and H1 promoters in endothelial cells and in mouse brain (2006)

These results show that LV-mediated RNAi is a powerful gene-silencing method for the long-term inhibition of gene expression in vitro and in vivo.
A Preclinical System Prototype for Focused Microwave Thermal Therapy of the Breast (2012)

A preclinical prototype of a transcutaneous thermal therapy system has been developed for the targeted treatment of breast cancer cells using focused microwaves as an adjuvant to radiation, chemotherapy, and high-intensity-focused ultrasound. The prototype system employs a 2-D array of tapered microstrip patch antennas operating at 915 MHz to focus continuous-wave microwave energy transcutaneously into the pendent breast suspended in a coupling medium. Prior imaging studies are used to ascertain the material properties of the breast tissue, and these data are incorporated into a multiphysics model. Time-reversal techniques are employed to find a solution (relative amplitudes and phase) for focusing at a given location. Modeling tests of this time-reversal focusing method have been performed, which demonstrate good targeting accuracy within heterogeneous breast tissue. Experimental results using the laboratory prototype to perform focused heating in tissue-mimicking gelatin phantoms have demonstrated 1.5-cm-diameter focal spot sizes and differential heating at the desired focus sufficient to achieve an antitumor effect confined to the target region.
Vascular endothelial growth factor (VEGF) stimulates neurogenesis in vitro and in vivo (2002)

Vascular endothelial growth factor (VEGF) is an angiogenic protein with neurotrophic and neuroprotective effects. Because VEGF promotes the proliferation of vascular endothelial cells, we examined the possibility that it also stimulates the proliferation of neuronal precursors in murine cerebral cortical cultures and in adult rat brain in vivo. VEGF (>10 ng/ml) stimulated 5-bromo-2'-deoxyuridine (BrdUrd) incorporation into cells that expressed immature neuronal marker proteins and increased cell number in cultures by 20-30%. Cultured cells labeled by BrdUrd expressed VEGFR2/Flk-1, but not VEGFR1/Flt-1 receptors, and the effect of VEGF was blocked by the VEGFR2/Flk-1 receptor tyrosine kinase inhibitor SU1498. Intracerebroventricular administration of VEGF into rat brain increased BrdUrd labeling of cells in the subventricular zone (SVZ) and the subgranular zone (SGZ) of the hippocampal dentate gyrus (DG), where VEGFR2/Flk-1 was colocalized with the immature neuronal marker, doublecortin (Dcx). The increase in BrdUrd labeling after the administration of VEGF was caused by an increase in cell proliferation, rather than a decrease in cell death, because VEGF did not reduce caspase-3 cleavage in SVZ or SGZ. Cells labeled with BrdUrd after VEGF treatment in vivo include immature and mature neurons, astroglia, and endothelial cells. These findings implicate the angiogenesis factor VEGF in neurogenesis as well.
Corneal epithelial wound healing. (1994)

The corneal surface is, without question, the most specialised 123 mm2* of the body's surface. It forms an integral part of the ocular surface with which it shares several anatomical and physiological attributes. Like the rest ofthe body surface, it is in a state of constant 'healing'. Squamous epithelial cells are continually shed into the tear pool and simultaneously replenished by cells moving centrally from the limbus and anteriorly from the basal layers of the epithelium. This concept was propounded by Thoft' in his X, Y, Z hypothesis and is substantiated by several observations and experiments. X represents the proliferation of basal epithelial cells, Y is the proliferation and centripetal migration ofthe limbal cells, and Z the epithelial cell loss from the surface. For a state of equilibrium to be maintained X+Y must equal Z. It is estimated that the corneal epithelium is constantly renewed every 7 to 10 days.2