gebhart/patrepeval huggingface dataset:
Insect cell-expressed p180erbB3 possesses an impaired tyrosine kinase activity. (1994)

Protein kinases share a number of highly conserved or invariant amino acid residues in their catalytic domains, suggesting that these residues are necessary for kinase activity. In p180erbB3, a receptor tyrosine kinase belonging to the epidermal growth factor (EGF) receptor subfamily, three of these residues are altered, suggesting that this protein might have an impaired protein tyrosine kinase activity. To test this hypothesis, we have expressed human EGF receptor and bovine p180erbB3 in insect cells via baculovirus infection and have compared their autophosphorylation and substrate phosphorylation activities. We have found that, while the EGF receptor readily undergoes EGF-stimulated autophosphorylation and catalyzes the incorporation of phosphate into the model substrates (E4Y1)n (random 4:1 copolymer of glutamic acid and tyrosine) and GST-p85 (glutathione S-transferase fusion protein with the 85-kDa subunit of phosphatidylinositol 3-kinase), p180erbB3 autophosphorylation and substrate phosphorylation are at least 2 orders of magnitude less efficient. However, p180erbB3 is capable of binding the ATP analog 5'-p-fluorosulfonylbenzoyladenosine, indicating that the lack of observed kinase activity is probably not due to nonfunctional or denatured receptors expressed by the insect cells. On the basis of these results, we propose that p180erbB3 possesses an impaired intrinsic tyrosine kinase activity.
Molecular And Genetic Insights Into T Cell Antigen Receptor Structure And Function (1991)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
ROLE OF BUTYRYL PHOSPHATE IN THE ENERGY METABOLISM OF CLOSTRIDIUM TETANOMORPHUM (1963)

Twarog, R. (University of Illinois, Urbana) and R. S. Wolfe. Role of butyryl phosphate in the energy metabolism of Clostridium tetanomorphum. J. Bacteriol. 86:112-117. 1963.-A partially purified butyrokinase from Clostridium tetanomorphum has been found to phosphorylate valerate, butyrate, isobutyrate, and propionate. The divalent cation requirement is satisfied with magnesium. The pH optimum lies between 7.4 and 8.3. Growth of the organism was followed using glutamate or histidine as substrate, butyrokinase being formed in each instance. The average dry weight of cells formed per mmole of substrate utilized was 6.8 mg for glutamate and 11.1 mg for histidine. Since both phosphotransbutyrylase and butyrokinase are present in the cells, it is proposed that a significant portion of energy derived from glutamate oxidation by this organism is obtained from butyryl phosphate.
Perfluoroalkyl Acids: A Review of Monitoring and Toxicological Findings (2007)

In recent years, human and wildlife monitoring studies have identified perfluoroalkyl acids (PFAA) worldwide. This has led to efforts to better understand the hazards that may be inherent in these compounds, as well as the global distribution of the PFAAs. Much attention has focused on understanding the toxicology of the two most widely known PFAAs, perfluorooctanoic acid, and perfluorooctane sulfate. More recently, research was extended to other PFAAs. There has been substantial progress in understanding additional aspects of the toxicology of these compounds, particularly related to the developmental toxicity, immunotoxicity, hepatotoxicity, and the potential modes of action. This review provides an overview of the recent advances in the toxicology and mode of action for PFAAs, and of the monitoring data now available for the environment, wildlife, and humans. Several avenues of research are proposed that would further our understanding of this class of compounds.
Lipoproteins Containing Apo B Extracted from Human Aortas Structure and Functiona (1985)

We have isolated, by anti-LDL affinity chromatography, apo B-containing lipoproteins from homogenates of atherosclerotic plaques excised from the human aorta. This fraction, called A-LP, has similarities with plasma LDL, such as having similar size and relative lipid composition, along with containing apo B. However, the fraction also contains some particles larger than LDL, it is more electronegative than LDL, the relative protein content is less than in LDL, and its apo B is highly degraded. A-LP is recognized by a high affinity binding site on mouse peritoneal macrophages (MPM), as suggested by dose-response curves of stimulation of cholesterol esterification. The interaction is inhibited by negatively-charged carbohydrates such as fucoidin, but excess A-LP did not inhibit the degradation of labeled acetyl-LDL by MPM, suggesting that the binding site recognizing A-LP may not be the scavenger receptor. Finally, stimulation of cholesterol esterification by A-LP in MPM is unregulated over a 48 hr time interval, leading to massive accumulations of cholesteryl esters and a transition of these MPM to a morphology characteristic of foam cells. It is possible that when monocytes enter the arterial intima at specific sites and become tissue macrophages, they internalize A-LP in an unregulated fashion. This, in turn, would make the monocyte-macrophage lipid-laden, and could explain the etiology of foam cells in fatty streak lesions. The modification in A-LP relative to P-LDL responsible for the enhanced recognition still needs to be elucidated.
Mode matching technique for highly efficient coupling between dielectric waveguides and planar photonic crystal circuits (2002)

In this paper, a mode matching technique for highly efficient coupling between dielectric silica waveguides (SWG) and planar photonic crystal (PPC) waveguides based on setting localized defects in a PPC tapered waveguide is reported. The introduction of multiple defects is designed properly depending on mode mismatching arising from the different widths of the SWG and the PPC waveguide. The procedure to obtain the optimum defects configuration is described. Transmission efficiencies above 80% at a wavelength of 1.55m are reported improving significantly the transmission efficiencies achieved with conventional PPC tapered structures without defects. Furthermore, the feasibility of the coupling technique for both input/output coupling over a large frequency band is shown.
Streaming potential from multiphase flow (1994)

Abstract In trying to understand the affect of electrokinetics on the spontaneous potential (SP) log, the focus has generally been on the solid-brine streaming potential. Within the accuracy of the measurements, the streaming-potential coupling coefficient is shown to be independent of the permeability of the rock. The solid-brine streaming potential is of much smaller magnitude than the electrostatic potentials from gas-liquid and liquid-liquid flow. Air bubbles were found to increase the streaming potential coupling coefficient by more than two orders of magnitude over the value for single-phase brine flow. Thus, two-phase gas-liquid flow is more likely to have a significant impact on the SP log than is single phase liquid flow.Two-phase oil-brine flow may also produce a larger electrokinetic potential than single-phase flow. The magnitude of the electrokinetic potential caused by oil-brine flow will depend on the composition of the oil and the brine. Trace materials can have a major impact on the electrokinetic potential of hydrocarbons. In a system with multiphase flow, the solid-liquid interaction is probably the smallest component of the electrokinetic potential.
A B lymphocyte mitogen is aBrucella abortusvirulence factor required for persistent infection (2006)

Microbial pathogens with the ability to establish chronic infections have evolved strategies to actively modulate the host immune response. Brucellosis is a disease caused by a Gram-negative intracellular pathogen that if not treated during the initial phase of the infection becomes chronic as the bacteria persist for the lifespan of the host. How this pathogen and others achieve this action is a largely unanswered question. We report here the identification of a Brucella abortus gene (prpA) directly involved in the immune modulation of the host. PrpA belongs to the proline-racemase family and elicits a B lymphocyte polyclonal activation that depends on the integrity of its proline-racemase catalytic site. Stimulation of splenocytes with PrpA also results in IL-10 secretion. Construction of a B. abortus-prpA mutant allowed us to assess the contribution of PrpA to the infection process. Mice infected with B. abortus induced an early and transient nonresponsive status of splenocytes to both Escherichia coli LPS and ConA. This phenomenon was not observed when mice were infected with a B. abortus-prpA mutant. Moreover, the B. abortus-prpA mutant had a reduced capacity to establish a chronic infection in mice. We propose that an early and transient nonresponsive immune condition of the host mediated by this B cell polyclonal activator is required for establishing a successful chronic infection by Brucella.
Deadlock-Free Message Routing in Multiprocessor Interconnection Networks (1987)

A deadlock-free routing algorithm can be generated for arbitrary interconnection networks using the concept of virtual channels. A necessary and sufficient condition for deadlock-free routing is the absence of cycles in a channel dependency graph. Given an arbitrary network and a routing function, the cycles of the channel dependency graph can be removed by splitting physical channels into groups of virtual channels. This method is used to develop deadlock-free routing algorithms for k-ary n-cubes, for cube-connected cycles, and for shuffle-exchange networks.
A Practical Procedure for the Synthesis of Alkyl Azides at Ambient Temperature in Dimethyl Sulfoxide in High Purity and Yield (1997)

Described is the often neglected, but very efficient, procedure for the preparation of primary and secondary alkyl and cycloalkyl azides in excellent purity and high yields. At ambient temperature conditions, the alkyl azides were readily obtained from alkyl bromides by the nucleophilic substitution of bromide with 1.2 equivalents of sodium azide in dimethyl sulfoxide (DMSO). This facile and practical procedure provides highly pure products and eliminates the hazards associated with distillation of alkyl azides.
Room temperature excitonic nonlinear absorption and refraction in GaAs/AlGaAs multiple quantum well structures (1984)

We present detailed experimental studies and modeling of the nonlinear absorption and refraction of GaAs/AlGaAs multiple quantum well structures (MQWS) in the small signal regime. Nonlinear absorption and degenerate four-wave mixing in the vicinity of the room temperature exciton resonances are observed and analyzed. Spectra of the real and imaginary parts of the nonlinear cross section as a function of wavelength are obtained, and these are in excellent agreement with experimental data. A simple model for excitonic absorption saturation is proposed; it accounts qualitatively for the very low saturation intensities of room temperature excitons in MQWS.
为恩科马蒂·梅恩(Nkomati Main)选厂推荐的磨矿回路的确定 (1999)

位于南非穆普马兰加(Mpumalanga)省的恩科马蒂矿(Nkomati)是一个很大的镍/铜矿石资源基地。目前正对该砂体的梅恩(Main)矿化区进行矿石选别方法的研究。本文论述了该矿选厂磨矿回路选择的程序。磨矿回路选择中的主要问题与地质、矿物组成、采矿及冶金等密切相关。广泛的磨矿回路选择程序是以月处理能力为300000t为基础的,包括整个半工业试验和小型试验结果、设计标准、矿物工艺因素、恩科马蒂工程法规以及磨矿回路结构与磨机尽寸定型的最终决策。为该选厂推荐的磨矿回路是世界上最大的磨矿回路之一。该回路中装有最大型的一段全自磨机以及最大型的二段砾磨机。在磨矿回路选择中关键的问题是通过用各种方法减少与这种规格磨机操作有关的风险。
Measuring Security Risk of Networks Using Attack Graphs (2010)

Today’s computer systems face sophisticated attackers who combine multiple vulnerabilities to penetrate networks with devastating impact. The overall security of a network cannot be determined by simply counting the number of vulnerabilities. To accurately assess the security of networked systems, one must understand how vulnerabilities can be combined to stage an attack. We model such composition of vulnerabilities through attack graphs. By simulating incremental network penetration, and propagating attack likelihoods, we measure the overall security of a networked system. From this, we score risk mitigation options in terms of maximizing security and minimizing cost. We populate our attack graph models from live network scans and databases that have knowledge about properties such as vulnerability likelihood, impact, severity, and ease of exploitation. Our exible model can be used to quantify overall security of networked systems, and to study cost/benet tradeos for analyzing return on security investment.
Artificial Neural Networks for Control of a Grid-Connected Rectifier/Inverter Under Disturbance, Dynamic and Power Converter Switching Conditions (2013)

Three-phase grid-connected converters are widely used in renewable and electric power system applications. Traditionally, grid-connected converters are controlled with standard decoupled d-q vector control mechanisms. However, recent studies indicate that such mechanisms show limitations in their applicability to dynamic systems. This paper investigates how to mitigate such restrictions using a neural network to control a grid-connected rectifier/inverter. The neural network implements a dynamic programming algorithm and is trained by using back-propagation through time. To enhance performance and stability under disturbance, additional strategies are adopted, including the use of integrals of error signals to the network inputs and the introduction of grid disturbance voltage to the outputs of a well-trained network. The performance of the neural-network controller is studied under typical vector control conditions and compared against conventional vector control methods, which demonstrates that the neural vector control strategy proposed in this paper is effective. Even in dynamic and power converter switching environments, the neural vector controller shows strong ability to trace rapidly changing reference commands, tolerate system disturbances, and satisfy control requirements for a faulted power system.
Osteopontin (2007)

Osteopontin (OPN) is a multifunctional molecule highly expressed in chronic inflammatory and autoimmune diseases, and it is specifically localized in and around inflammatory cells. OPN is a secreted adhesive molecule, and it is thought to aid in the recruitment of monocytes-macrophages and to regulate cytokine production in macrophages, dendritic cells, and T-cells. OPN has been classified as T-helper 1 cytokine and thus believed to exacerbate inflammation in several chronic inflammatory diseases, including atherosclerosis. Besides proinflammatory functions, physiologically OPN is a potent inhibitor of mineralization, it prevents ectopic calcium deposits and is a potent inducible inhibitor of vascular calcification. Clinically, OPN plasma levels have been found associated with various inflammatory diseases, including cardiovascular burden. It is thus imperative to dissect the OPN proinflammatory and anticalcific functions. OPN recruitment functions of inflammatory cells are thought to be mediated through its adhesive domains, especially the arginine-glycine-aspartate (RGD) sequence that interacts with several integrin heterodimers. However, the integrin receptors and intracellular pathways mediating OPN effects on immune cells are not well established. Furthermore, several studies show that OPN is cleaved by at least 2 classes of proteases: thrombin and matrix-metalloproteases (MMPs). Most importantly, at least in vitro, fragments generated by cleavage not only maintain OPN adhesive functions but also expose new active domains that may impart new activities. The role for OPN proteolytic fragments in vivo is almost completely unexplored. We believe that further knowledge of the effects of OPN fragments on cell responses might help in designing therapeutics targeting inflammatory and cardiovascular diseases.
An in vitro selection strategy for conferring protease resistance to ligand binding peptides (2009)

One drawback to the use of peptides as therapeutics has been their susceptibility to proteolysis. Here, we have used an in vitro display technology, CIS display, to enhance the proteolytic resistance of ligand-binding peptides by selection of protecting motifs from a large peptide library. The premise to this selection was that certain linear peptides within a library could form structures capable of preventing the access of proteases to defined cleavage sites without affecting ligand binding. A diverse 12-mer peptide library was inserted between a FLAG epitope motif and a thrombin cleavage site and this construct was fused to the bacterial initiator protein RepA for CIS display selection. After five rounds of selection, protection motifs were isolated that were capable of preventing proteolytic cleavage of the adjacent thrombin site. Some of the selected peptides were also resistant to more promiscuous proteases, such as chymotrypsin and trypsin, which were not used in the selection. The observed resistance to thrombin, trypsin and chymotrypsin translated into increased resistance to plasma proteases in vitro and to an increase in circulating half-lives in rats. This method can be applied to enhancing the in vivo stability of therapeutic peptides.
Regulation of B cell survival in xid mice by the proto-oncogene bcl-2 (1996)

CBA/N mice carry an X-linked immunodeficiency (xid) due to a point mutation in the Bruton's tyrosine kinase (btk) gene. xid mice have a smaller peripheral B cell pool than normal animals, lack CD5+ B cells (B1), and are hyporesponsive to mitogenic anti-Igs and thymus-independent type 2 Ags. The proto-oncogene bcl-2 affects B cell homeostasis by suppressing programmed cell death. We hypothesized that reduced bcl-2 expression could enhance programmed cell death in xid B cells, directly causing poor peripheral B cell survival and indirectly affecting Ag responsiveness. We measured and compared levels of endogenous Bcl-2 protein and spontaneous apoptosis in xid and normal B cells, and determined the effect of a human bcl-2/Ig minigene on B cell survival and Ag responsiveness in bcl-2 transgenics. The amount of endogenous Bcl-2 was reduced fivefold in freshly isolated xid B cells compared with that in normal cells, but was equal in xid and normal T cells. Attrition by spontaneous apoptosis was significantly higher in cultured xid B cells. Expression of the bcl-2 transgene suppressed apoptosis equally in normal and xid B cells, prolonged in vitro survival, and markedly expanded in vivo the follicular B cell population normally reduced in xid mice. However, most xid defects persisted; xid/bcl-2 mice remained deficient in B1 cells and hyporesponsive to anti-Igs, thymus-independent type 1 Ags, and thymus-independent type 2 Ags. The data suggest that signal transduction pathways using Btk independently regulate B cell survival and Ag responsiveness.
Unsupervised Classification of High-Frequency Oscillations in Human Neocortical Epilepsy and Control Patients (2010)

High-frequency oscillations (HFOs) have been observed in animal and human intracranial recordings during both normal and aberrant brain states. It has been proposed that the relationship between subclasses of these oscillations can be used to identify epileptic brain. Studies of HFOs in epilepsy have been hampered by selection bias arising primarily out of the need to reduce the volume of data so that clinicians can manually review it. In this study, we introduce an algorithm for detecting and classifying these signals automatically and demonstrate the tractability of analyzing a data set of unprecedented size, over 31,000 channel-hours of intracranial electroencephalographic (iEEG) recordings from micro- and macroelectrodes in humans. Using an unsupervised approach that does not presuppose a specific number of clusters in the data, we show direct evidence for the existence of distinct classes of transient oscillations within the 100- to 500-Hz frequency range in a population of nine neocortical epilepsy patients and two controls. The number of classes we find, four (three plus one putative artifact class), is consistent with prior studies that identify "ripple" and "fast ripple" oscillations using human-intensive methods and, additionally, identifies a less examined class of mixed-frequency events.
Selective Dual Path Execution (1996)

Selective Dual Path Execution (SDPE) reduces branch misprediction penalties by selectively forking a second path and executing instructions from both paths following a conditional branch instruction. SDPE restricts the number of simultaneously executed paths to two, and uses a branch prediction confidence mechanism to fork selectively only for branches that are more likely to be mispredicted. A branch forking policy defines the behavior of SDPE when a low confidence branch prediction is encountered while two paths are already being executed. Trace driven simulation is used to evaluate the effectiveness of SDPE with three different forking policies. SDPE can reduce the cycles lost to branch mispredictions by 34 to 50%, resulting in an approximate 10% reduction in overall execution time. However, it is shown that both branch mispredictions and low confidence predictions tend to occur in clusters, limiting the effectiveness of SDPE. A number of design parameters are studied via simulation. These include prediction and confidence table sizes. Finally, a number of implementation issues are discussed, with emphasis on instruction fetching mechanisms and register renaming. 1.0
Familial concordance for age at natural menopause (2011)

We confirm that early menopause aggregates within families and show, for the first time, that there is also strong familial concordance for late menopause. Both genes and shared environment were the source of variation in menopause age. Past heritability estimates have not accounted for shared environment, and thus, the effect of genetic variants on menopause age may previously have been overestimated.
Gene Therapy for the Treatment of Malignant Brain Tumors with In Vivo Tumor Transduction with the Herpes Simplex Thymidine Kinase Gene/Ganciclovir System. Iowa Methodist Medical Center, Des Moines, Iowa (1994)

Murine retroviral vectors can infect a wide variety of proliferating mammalian cell types (e.g. lymphocytes). Non-proliferating tissues (e.g. neurons) are not transduced by murine retroviral vectors. These findings suggest that this type of vector may be useful for the selective introduction of genes into growing tumors in the brain, since the tumor is essentially the only tissue that will integrate and express the vector genes.
Alternative donor sources in HLA-mismatched marrow transplantation: T cell depletion of surgically resected cadaveric marrow. (1988)

Allogeneic bone marrow transplantation has been largely confined in its application to patients with an HLA-matched marrow donor, thereby limiting potential therapeutic benefits for patients with diseases amenable to treatment by marrow transplantation who lack effective alternative therapies and an identified matched marrow donor. T cells in the donor marrow generate graft-versus-host disease which is a major consideration in attempts to widen the application of allogeneic marrow transplantation to the minimally HLA-matched or mismatched setting. The method of marrow harvest influences both the number of such T cells in the donor marrow inoculum and the functional capacity of T cells in murine marrow. We have therefore evaluated surgically resected cadaveric marrow for T cell content and for T cell depletion. Surgically resected marrow is more easily depleted of T cells than aspirated marrow and clinically useful quantities of marrow have been obtained and cryopreserved in a bank of characterized donor marrow for future use in HLA minimally matched or unmatched marrow transplantation.